RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux fisher04 3.13.0-8-generic #28-Ubuntu SMP Tue Feb 11 17:58:07 UTC 2014 ppc64le Buildd toolchain package versions: launchpad-buildd_121~0.IS.08.04.0 python-lpbuildd_121~0.IS.08.04.0 dpkg-dev_1.17.5ubuntu4. Syncing the system clock with the buildd NTP service... 17 Feb 07:03:30 ntpdate[24720]: adjust time server 10.211.37.1 offset -0.000096 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-5607500', '/home/buildd/filecache-default/1418c9e5f0eb143d9f77e4665c5b7c89c42011cc'] Unpacking chroot for build PACKAGEBUILD-5607500 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-5607500'] Mounting chroot for build PACKAGEBUILD-5607500 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-5607500', 'deb http://ftpmaster.internal/ubuntu trusty main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-updates main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu trusty-proposed main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-5607500 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-5607500', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-5607500 Ign http://ftpmaster.internal trusty InRelease Ign http://archive-team.internal trusty InRelease Ign http://ftpmaster.internal trusty InRelease Ign http://archive-team.internal trusty Release.gpg Ign http://ftpmaster.internal trusty-security InRelease Hit http://archive-team.internal trusty Release Ign http://ftpmaster.internal trusty-security InRelease Ign http://archive-team.internal trusty/main ppc64el Packages/DiffIndex Ign http://ftpmaster.internal trusty-updates InRelease Ign http://ftpmaster.internal trusty-updates InRelease Ign http://ftpmaster.internal trusty-proposed InRelease Ign http://ftpmaster.internal trusty-proposed InRelease Get:1 http://ftpmaster.internal trusty Release.gpg [933 B] Get:2 http://ftpmaster.internal trusty Release.gpg [933 B] Get:3 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:4 http://ftpmaster.internal trusty-security Release.gpg [933 B] Get:5 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Ign http://archive-team.internal trusty/main Translation-en Get:6 http://ftpmaster.internal trusty-updates Release.gpg [933 B] Hit http://archive-team.internal trusty/main ppc64el Packages Get:7 http://ftpmaster.internal trusty-proposed Release.gpg [933 B] Get:8 http://ftpmaster.internal trusty-proposed Release.gpg [933 B] Get:9 http://ftpmaster.internal trusty Release [58.5 kB] Get:10 http://ftpmaster.internal trusty Release [58.5 kB] Get:11 http://ftpmaster.internal trusty-security Release [58.5 kB] Get:12 http://ftpmaster.internal trusty-security Release [58.5 kB] Get:13 http://ftpmaster.internal trusty-updates Release [58.5 kB] Get:14 http://ftpmaster.internal trusty-updates Release [58.5 kB] Get:15 http://ftpmaster.internal trusty-proposed Release [58.5 kB] Get:16 http://ftpmaster.internal trusty-proposed Release [58.5 kB] Get:17 http://ftpmaster.internal trusty/main ppc64el Packages [588 kB] Get:18 http://ftpmaster.internal trusty/restricted ppc64el Packages [14 B] Get:19 http://ftpmaster.internal trusty/universe ppc64el Packages [2567 kB] Get:20 http://ftpmaster.internal trusty/multiverse ppc64el Packages [71.0 kB] Hit http://ftpmaster.internal trusty/main Translation-en Get:21 http://ftpmaster.internal trusty/multiverse Translation-en [102 kB] Get:22 http://ftpmaster.internal trusty/restricted Translation-en [3457 B] Get:23 http://ftpmaster.internal trusty/universe Translation-en [4058 kB] Get:24 http://ftpmaster.internal trusty/main ppc64el Packages [1226 kB] Get:25 http://ftpmaster.internal trusty/restricted ppc64el Packages [14 B] Get:26 http://ftpmaster.internal trusty/universe ppc64el Packages [5005 kB] Get:27 http://ftpmaster.internal trusty/multiverse ppc64el Packages [107 kB] Get:28 http://ftpmaster.internal trusty/main Translation-en [760 kB] Get:29 http://ftpmaster.internal trusty/multiverse Translation-en [102 kB] Get:30 http://ftpmaster.internal trusty/restricted Translation-en [3457 B] Get:31 http://ftpmaster.internal trusty/universe Translation-en [4056 kB] Get:32 http://ftpmaster.internal trusty-security/main ppc64el Packages [14 B] Get:33 http://ftpmaster.internal trusty-security/restricted ppc64el Packages [14 B] Get:34 http://ftpmaster.internal trusty-security/universe ppc64el Packages [14 B] Get:35 http://ftpmaster.internal trusty-security/multiverse ppc64el Packages [14 B] Get:36 http://ftpmaster.internal trusty-security/main Translation-en [14 B] Get:37 http://ftpmaster.internal trusty-security/multiverse Translation-en [14 B] Get:38 http://ftpmaster.internal trusty-security/restricted Translation-en [14 B] Get:39 http://ftpmaster.internal trusty-security/universe Translation-en [14 B] Get:40 http://ftpmaster.internal trusty-security/main ppc64el Packages [14 B] Get:41 http://ftpmaster.internal trusty-security/restricted ppc64el Packages [14 B] Get:42 http://ftpmaster.internal trusty-security/universe ppc64el Packages [14 B] Get:43 http://ftpmaster.internal trusty-security/multiverse ppc64el Packages [14 B] Get:44 http://ftpmaster.internal trusty-security/main Translation-en [14 B] Get:45 http://ftpmaster.internal trusty-security/multiverse Translation-en [14 B] Get:46 http://ftpmaster.internal trusty-security/restricted Translation-en [14 B] Get:47 http://ftpmaster.internal trusty-security/universe Translation-en [14 B] Get:48 http://ftpmaster.internal trusty-updates/main ppc64el Packages [14 B] Get:49 http://ftpmaster.internal trusty-updates/restricted ppc64el Packages [14 B] Get:50 http://ftpmaster.internal trusty-updates/universe ppc64el Packages [14 B] Get:51 http://ftpmaster.internal trusty-updates/multiverse ppc64el Packages [14 B] Get:52 http://ftpmaster.internal trusty-updates/main Translation-en [14 B] Get:53 http://ftpmaster.internal trusty-updates/multiverse Translation-en [14 B] Get:54 http://ftpmaster.internal trusty-updates/restricted Translation-en [14 B] Get:55 http://ftpmaster.internal trusty-updates/universe Translation-en [14 B] Get:56 http://ftpmaster.internal trusty-updates/main ppc64el Packages [14 B] Get:57 http://ftpmaster.internal trusty-updates/restricted ppc64el Packages [14 B] Get:58 http://ftpmaster.internal trusty-updates/universe ppc64el Packages [14 B] Get:59 http://ftpmaster.internal trusty-updates/multiverse ppc64el Packages [14 B] Get:60 http://ftpmaster.internal trusty-updates/main Translation-en [14 B] Get:61 http://ftpmaster.internal trusty-updates/multiverse Translation-en [14 B] Get:62 http://ftpmaster.internal trusty-updates/restricted Translation-en [14 B] Get:63 http://ftpmaster.internal trusty-updates/universe Translation-en [14 B] Get:64 http://ftpmaster.internal trusty-proposed/main ppc64el Packages [20.2 kB] Get:65 http://ftpmaster.internal trusty-proposed/restricted ppc64el Packages [14 B] Get:66 http://ftpmaster.internal trusty-proposed/universe ppc64el Packages [42.5 kB] Get:67 http://ftpmaster.internal trusty-proposed/multiverse ppc64el Packages [611 B] Get:68 http://ftpmaster.internal trusty-proposed/main Translation-en [17.5 kB] Get:69 http://ftpmaster.internal trusty-proposed/multiverse Translation-en [2995 B] Get:70 http://ftpmaster.internal trusty-proposed/restricted Translation-en [14 B] Get:71 http://ftpmaster.internal trusty-proposed/universe Translation-en [53.5 kB] Get:72 http://ftpmaster.internal trusty-proposed/main ppc64el Packages [12.6 kB] Get:73 http://ftpmaster.internal trusty-proposed/restricted ppc64el Packages [14 B] Get:74 http://ftpmaster.internal trusty-proposed/universe ppc64el Packages [45.9 kB] Get:75 http://ftpmaster.internal trusty-proposed/multiverse ppc64el Packages [3313 B] Get:76 http://ftpmaster.internal trusty-proposed/main Translation-en [14.0 kB] Get:77 http://ftpmaster.internal trusty-proposed/multiverse Translation-en [2995 B] Get:78 http://ftpmaster.internal trusty-proposed/restricted Translation-en [14 B] Get:79 http://ftpmaster.internal trusty-proposed/universe Translation-en [56.7 kB] Fetched 19.4 MB in 21s (888 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt apt-transport-https libapt-pkg4.12 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1604 kB of archives. After this operation, 13.3 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu/ trusty-proposed/main libapt-pkg4.12 ppc64el 0.9.15.2ubuntu1 [623 kB] Get:2 http://ftpmaster.internal/ubuntu/ trusty-proposed/main apt ppc64el 0.9.15.2ubuntu1 [957 kB] Get:3 http://ftpmaster.internal/ubuntu/ trusty-proposed/main apt-transport-https ppc64el 0.9.15.2ubuntu1 [24.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1604 kB in 6s (261 kB/s) (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libapt-pkg4.12_0.9.15.2ubuntu1_ppc64el.deb ... Unpacking libapt-pkg4.12:ppc64el (0.9.15.2ubuntu1) over (0.9.15.1ubuntu1) ... Setting up libapt-pkg4.12:ppc64el (0.9.15.2ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../apt_0.9.15.2ubuntu1_ppc64el.deb ... Unpacking apt (0.9.15.2ubuntu1) over (0.9.15.1ubuntu1) ... Setting up apt (0.9.15.2ubuntu1) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../apt-transport-https_0.9.15.2ubuntu1_ppc64el.deb ... Unpacking apt-transport-https (0.9.15.2ubuntu1) over (0.9.15.1ubuntu1) ... Setting up apt-transport-https (0.9.15.2ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-5607500', 'ppc64el', 'trusty-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=trusty-proposed', '--purpose=PRIMARY', '--architecture=ppc64el', '--comp=multiverse', 'gmap_2013-07-20-1.dsc'] Initiating build PACKAGEBUILD-5607500 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.13.0-8-generic #28-Ubuntu SMP Tue Feb 11 17:58:07 UTC 2014 ppc64le Automatic build of gmap_2013-07-20-1 on fisher04 by sbuild/ppc64el 1.170.5 Build started at 20140217-0704 ****************************************************************************** gmap_2013-07-20-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), autotools-dev Checking for already installed source dependencies... debhelper: missing autotools-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper autotools-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: apparmor-easyprof bsdmainutils dh-apparmor dh-python file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1 libglib2.0-0 libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl python3-doc python3-tk python3.3-doc binfmt-support Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: apparmor-easyprof autotools-dev bsdmainutils debhelper dh-apparmor dh-python file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libexpat1 libglib2.0-0 libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libssl1.0.0 libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3.3 python3.3-minimal 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 10.4 MB of archives. After this operation, 45.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ppc64el/ trusty/main libexpat1 ppc64el 2.1.0-4ubuntu1 [64.4 kB] Get:2 http://ftpmaster.internal/ppc64el/ trusty/main libmagic1 ppc64el 1:5.14-2ubuntu1 [181 kB] Get:3 http://ftpmaster.internal/ppc64el/ trusty/main libssl1.0.0 ppc64el 1.0.1f-1ubuntu1 [713 kB] Get:4 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.3-minimal ppc64el 3.3.4-1 [393 kB] Get:5 http://ftpmaster.internal/ubuntu/ trusty/main mime-support all 3.54ubuntu1 [31.7 kB] Get:6 http://ftpmaster.internal/ppc64el/ trusty/main libmpdec2 ppc64el 2.4.0-6 [79.8 kB] Get:7 http://ftpmaster.internal/ubuntu/ trusty/main libpython3.3-stdlib ppc64el 3.3.4-1 [1911 kB] Get:8 http://ftpmaster.internal/ubuntu/ trusty/main python3.3-minimal ppc64el 3.3.4-1 [1119 kB] Get:9 http://ftpmaster.internal/ppc64el/ trusty/main libasprintf0c2 ppc64el 0.18.3.1-1ubuntu2 [6734 B] Get:10 http://ftpmaster.internal/ppc64el/ trusty/main libglib2.0-0 ppc64el 2.39.4-0ubuntu1 [923 kB] Get:11 http://ftpmaster.internal/ppc64el/ trusty/main libpipeline1 ppc64el 1.2.6-2 [22.4 kB] Get:12 http://ftpmaster.internal/ppc64el/ trusty/main libxml2 ppc64el 2.9.1+dfsg1-3ubuntu3 [502 kB] Get:13 http://ftpmaster.internal/ppc64el/ trusty/main groff-base ppc64el 1.22.2-5 [1111 kB] Get:14 http://ftpmaster.internal/ppc64el/ trusty/main bsdmainutils ppc64el 9.0.5ubuntu1 [171 kB] Get:15 http://ftpmaster.internal/ppc64el/ trusty/main man-db ppc64el 2.6.6-1 [837 kB] Get:16 http://ftpmaster.internal/ppc64el/ trusty/main libcroco3 ppc64el 0.6.8-2ubuntu1 [72.2 kB] Get:17 http://ftpmaster.internal/ppc64el/ trusty/main libunistring0 ppc64el 0.9.3-5ubuntu3 [255 kB] Get:18 http://ftpmaster.internal/ubuntu/ trusty/main python3.3 ppc64el 3.3.4-1 [133 kB] Get:19 http://ftpmaster.internal/ppc64el/ trusty/main python3-minimal ppc64el 3.3.3-1 [23.4 kB] Get:20 http://ftpmaster.internal/ppc64el/ trusty/main libpython3-stdlib ppc64el 3.3.3-1 [7112 B] Get:21 http://ftpmaster.internal/ppc64el/ trusty/main python3 ppc64el 3.3.3-1 [8660 B] Get:22 http://ftpmaster.internal/ubuntu/ trusty/main dh-python all 1.20140128-1ubuntu2 [51.0 kB] Get:23 http://ftpmaster.internal/ppc64el/ trusty/main file ppc64el 1:5.14-2ubuntu1 [18.8 kB] Get:24 http://ftpmaster.internal/ppc64el/ trusty/main gettext-base ppc64el 0.18.3.1-1ubuntu2 [46.7 kB] Get:25 http://ftpmaster.internal/ubuntu/ trusty/main autotools-dev all 20130810.1 [44.3 kB] Get:26 http://ftpmaster.internal/ppc64el/ trusty/main gettext ppc64el 0.18.3.1-1ubuntu2 [794 kB] Get:27 http://ftpmaster.internal/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:28 http://ftpmaster.internal/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:29 http://ftpmaster.internal/ubuntu/ trusty/main apparmor-easyprof all 2.8.0-0ubuntu38 [20.1 kB] Get:30 http://ftpmaster.internal/ubuntu/ trusty/main dh-apparmor all 2.8.0-0ubuntu38 [7286 B] Get:31 http://ftpmaster.internal/ubuntu/ trusty/main debhelper all 9.20131127ubuntu2 [603 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.4 MB in 16s (624 kB/s) Selecting previously unselected package libexpat1:ppc64el. (Reading database ... 11450 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-4ubuntu1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.1.0-4ubuntu1) ... Selecting previously unselected package libmagic1:ppc64el. Preparing to unpack .../libmagic1_1%3a5.14-2ubuntu1_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.14-2ubuntu1) ... Selecting previously unselected package libssl1.0.0:ppc64el. Preparing to unpack .../libssl1.0.0_1.0.1f-1ubuntu1_ppc64el.deb ... Unpacking libssl1.0.0:ppc64el (1.0.1f-1ubuntu1) ... Selecting previously unselected package libpython3.3-minimal:ppc64el. Preparing to unpack .../libpython3.3-minimal_3.3.4-1_ppc64el.deb ... Unpacking libpython3.3-minimal:ppc64el (3.3.4-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.54ubuntu1_all.deb ... Unpacking mime-support (3.54ubuntu1) ... Selecting previously unselected package libmpdec2:ppc64el. Preparing to unpack .../libmpdec2_2.4.0-6_ppc64el.deb ... Unpacking libmpdec2:ppc64el (2.4.0-6) ... Selecting previously unselected package libpython3.3-stdlib:ppc64el. Preparing to unpack .../libpython3.3-stdlib_3.3.4-1_ppc64el.deb ... Unpacking libpython3.3-stdlib:ppc64el (3.3.4-1) ... Selecting previously unselected package python3.3-minimal. Preparing to unpack .../python3.3-minimal_3.3.4-1_ppc64el.deb ... Unpacking python3.3-minimal (3.3.4-1) ... Selecting previously unselected package libasprintf0c2:ppc64el. Preparing to unpack .../libasprintf0c2_0.18.3.1-1ubuntu2_ppc64el.deb ... Unpacking libasprintf0c2:ppc64el (0.18.3.1-1ubuntu2) ... Selecting previously unselected package libglib2.0-0:ppc64el. Preparing to unpack .../libglib2.0-0_2.39.4-0ubuntu1_ppc64el.deb ... Unpacking libglib2.0-0:ppc64el (2.39.4-0ubuntu1) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../libpipeline1_1.2.6-2_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.2.6-2) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../libxml2_2.9.1+dfsg1-3ubuntu3_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.1+dfsg1-3ubuntu3) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-5_ppc64el.deb ... Unpacking groff-base (1.22.2-5) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.5ubuntu1_ppc64el.deb ... Unpacking bsdmainutils (9.0.5ubuntu1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.6.6-1_ppc64el.deb ... Unpacking man-db (2.6.6-1) ... Selecting previously unselected package libcroco3:ppc64el. Preparing to unpack .../libcroco3_0.6.8-2ubuntu1_ppc64el.deb ... Unpacking libcroco3:ppc64el (0.6.8-2ubuntu1) ... Selecting previously unselected package libunistring0:ppc64el. Preparing to unpack .../libunistring0_0.9.3-5ubuntu3_ppc64el.deb ... Unpacking libunistring0:ppc64el (0.9.3-5ubuntu3) ... Selecting previously unselected package python3.3. Preparing to unpack .../python3.3_3.3.4-1_ppc64el.deb ... Unpacking python3.3 (3.3.4-1) ... Selecting previously unselected package python3-minimal. Preparing to unpack .../python3-minimal_3.3.3-1_ppc64el.deb ... Unpacking python3-minimal (3.3.3-1) ... Selecting previously unselected package libpython3-stdlib:ppc64el. Preparing to unpack .../libpython3-stdlib_3.3.3-1_ppc64el.deb ... Unpacking libpython3-stdlib:ppc64el (3.3.3-1) ... Selecting previously unselected package python3. Preparing to unpack .../python3_3.3.3-1_ppc64el.deb ... Unpacking python3 (3.3.3-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../dh-python_1.20140128-1ubuntu2_all.deb ... Unpacking dh-python (1.20140128-1ubuntu2) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.14-2ubuntu1_ppc64el.deb ... Unpacking file (1:5.14-2ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.18.3.1-1ubuntu2_ppc64el.deb ... Unpacking gettext-base (0.18.3.1-1ubuntu2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../autotools-dev_20130810.1_all.deb ... Unpacking autotools-dev (20130810.1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.18.3.1-1ubuntu2_ppc64el.deb ... Unpacking gettext (0.18.3.1-1ubuntu2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ... Unpacking intltool-debian (0.35.0+20060710.1) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.16+nmu2ubuntu1_all.deb ... Unpacking po-debconf (1.0.16+nmu2ubuntu1) ... Selecting previously unselected package apparmor-easyprof. Preparing to unpack .../apparmor-easyprof_2.8.0-0ubuntu38_all.deb ... Unpacking apparmor-easyprof (2.8.0-0ubuntu38) ... Selecting previously unselected package dh-apparmor. Preparing to unpack .../dh-apparmor_2.8.0-0ubuntu38_all.deb ... Unpacking dh-apparmor (2.8.0-0ubuntu38) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20131127ubuntu2_all.deb ... Unpacking debhelper (9.20131127ubuntu2) ... Setting up libexpat1:ppc64el (2.1.0-4ubuntu1) ... Setting up libmagic1:ppc64el (1:5.14-2ubuntu1) ... Setting up libssl1.0.0:ppc64el (1.0.1f-1ubuntu1) ... Setting up libpython3.3-minimal:ppc64el (3.3.4-1) ... Setting up mime-support (3.54ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libmpdec2:ppc64el (2.4.0-6) ... Setting up libpython3.3-stdlib:ppc64el (3.3.4-1) ... Setting up python3.3-minimal (3.3.4-1) ... Setting up libasprintf0c2:ppc64el (0.18.3.1-1ubuntu2) ... Setting up libglib2.0-0:ppc64el (2.39.4-0ubuntu1) ... No schema files found: doing nothing. Setting up libpipeline1:ppc64el (1.2.6-2) ... Setting up libxml2:ppc64el (2.9.1+dfsg1-3ubuntu3) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.6-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:ppc64el (0.6.8-2ubuntu1) ... Setting up libunistring0:ppc64el (0.9.3-5ubuntu3) ... Setting up python3.3 (3.3.4-1) ... Setting up python3-minimal (3.3.3-1) ... Setting up libpython3-stdlib:ppc64el (3.3.3-1) ... Setting up file (1:5.14-2ubuntu1) ... Setting up gettext-base (0.18.3.1-1ubuntu2) ... Setting up autotools-dev (20130810.1) ... Setting up gettext (0.18.3.1-1ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-python (1.20140128-1ubuntu2) ... Setting up python3 (3.3.3-1) ... running python rtupdate hooks for python3.3... running python post-rtupdate hooks for python3.3... Setting up apparmor-easyprof (2.8.0-0ubuntu38) ... Setting up dh-apparmor (2.8.0-0ubuntu38) ... Setting up debhelper (9.20131127ubuntu2) ... Processing triggers for libc-bin (2.18-0ubuntu7) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.18-0ubuntu7 make_3.81-8.2ubuntu3 dpkg-dev_1.17.5ubuntu4 gcc-4.8_4.8.2-15ubuntu3 g++-4.8_4.8.2-15ubuntu3 binutils_2.24-2ubuntu3.1 libstdc++-4.8-dev_4.8.2-15ubuntu3 libstdc++6_4.8.2-15ubuntu3 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Fri Aug 2 13:37:15 2013 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./gmap_2013-07-20-1.dsc dpkg-source: info: extracting gmap in gmap-2013-07-20 dpkg-source: info: unpacking gmap_2013-07-20.orig.tar.gz dpkg-source: info: unpacking gmap_2013-07-20-1.debian.tar.gz dpkg-source: info: applying install-data-local dpkg-buildpackage: source package gmap dpkg-buildpackage: source version 2013-07-20-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build gmap-2013-07-20 dpkg-buildpackage: host architecture ppc64el /usr/bin/fakeroot debian/rules clean dh clean --with autotools_dev dh_testdir dh_auto_clean dh_autotools-dev_restoreconfig dh_clean debian/rules build-arch dh build-arch --with autotools_dev dh_testdir -a dh_autotools-dev_updateconfig -a debian/rules override_dh_auto_configure make[1]: Entering directory `/build/buildd/gmap-2013-07-20' dh_auto_configure -- --with-gmapdb=/var/cache/gmap configure: WARNING: unrecognized options: --disable-maintainer-mode checking package version... 2013-07-20 checking CONFIG_SITE... ./config.site loading script ./config.site checking CFLAGS... -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security checking build system type... powerpc64le-unknown-linux-gnu checking host system type... powerpc64le-unknown-linux-gnu checking target system type... powerpc64le-unknown-linux-gnu checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking dependency style of gcc... none checking bindir... /usr/bin checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc and cc understand -c and -o together... yes checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3458764513820540925 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf64ppc) supports shared libraries... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... unsupported checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... no checking whether to build shared libraries... no checking whether to build static libraries... yes checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... yes checking for sigaction... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for __builtin_popcount... yes checking for __builtin_clz... yes checking for __builtin_ctz... yes checking for bsr instruction in assembly... yes checking for popcnt feature... not specified so enabled by default checking whether -mpopcnt compiler flag works... no checking whether sse2 is enabled... not specified so enabled by default checking whether sse4.1 is enabled... not specified so enabled by default checking whether simd is enabled... not specified so enabled by default checking whether altivec is enabled and supported... checking gmapdb... /var/cache/gmap checking MAX_READLENGTH... 250 checking for zlib support... enabled checking zlib.h usability... no checking zlib.h presence... no checking for zlib.h... no checking for gzopen in -lz... no checking for gzeof in -lz... no checking for gzgetc in -lz... no checking for gzgets in -lz... no checking for gzclose in -lz... no checking if zlib package is complete... no -- some components failed test checking for bzlib support... enabled checking bzlib.h usability... no checking bzlib.h presence... no checking for bzlib.h... no checking for BZ2_bzReadOpen in -lbz2... no checking for BZ2_bzRead in -lbz2... no checking for BZ2_bzReadClose in -lbz2... no checking if bzlib package is complete... no -- some components failed test checking for goby library... disabled configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_compress.pl config.status: creating util/gmap_uncompress.pl config.status: creating util/gmap_process.pl config.status: creating util/gmap_setup.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_reassemble.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory `/build/buildd/gmap-2013-07-20' dh_auto_build -a make[1]: Entering directory `/build/buildd/gmap-2013-07-20' Making all in src make[2]: Entering directory `/build/buildd/gmap-2013-07-20/src' make all-am make[3]: Entering directory `/build/buildd/gmap-2013-07-20/src' gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:9968:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:342:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10103:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10200:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10306:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:10484:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c: In function 'genome_write_file': genome-write.c:253:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:253:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:256:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:256:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'genome_writeraw_file': genome-write.c:430:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:430:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:433:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:433:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'fill_circular_chromosomes': genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ^ genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'Univcoord_T' [-Wformat=] genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'genome_write_memory': genome-write.c:643:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:643:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:646:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:646:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'Genome_write': genome-write.c:786:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function 'positions_read_multiple': indexdb_hr.c:592:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome-write.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-stage2.o gmap-smooth.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lm libtool: link: gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome-write.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-stage2.o gmap-smooth.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:9968:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:342:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10103:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10200:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10306:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:10484:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c genome_hr.c: In function 'Genome_print_blocks': genome_hr.c:66386:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",startblock/3*32U); ^ genome_hr.c:66401:5: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",ptr/3*32U); ^ genome_hr.c:66408:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",(endblock+3)/3*32U); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c: In function 'genome_write_file': genome-write.c:253:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:253:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:256:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:256:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'genome_writeraw_file': genome-write.c:430:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:430:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:433:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:433:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'fill_circular_chromosomes': genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ^ genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'Univcoord_T' [-Wformat=] genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'genome_write_memory': genome-write.c:643:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:643:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:646:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:646:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'Genome_write': genome-write.c:786:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function 'Compoundpos_dump': indexdb_hr.c:964:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); ^ indexdb_hr.c: In function 'heap_even_dump': indexdb_hr.c:1188:5: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ^ indexdb_hr.c: In function 'positions_read_multiple': indexdb_hr.c:592:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-block.o `test -f 'block.c' || echo './'`block.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c: In function 'Segmentpos_print': segmentpos.c:90:3: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-gregion.o `test -f 'gregion.c' || echo './'`gregion.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-match.o `test -f 'match.c' || echo './'`match.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-stage1.o `test -f 'stage1.c' || echo './'`stage1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function 'print_genomic_sequence': pair.c:513:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function 'print_genomicalt_sequence': pair.c:540:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function 'compute_margin': pair.c:567:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ^ pair.c:574:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ^ pair.c: In function 'Pair_print_coordinates': pair.c:1242:3: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] this->genome); ^ pair.c:1247:3: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] this->genome); ^ pair.c: In function 'Pair_print_exonsummary': pair.c:1725:6: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1725:6: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c:1734:6: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1734:6: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c:1848:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1848:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c:1857:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1857:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c: In function 'Pair_print_compressed': pair.c:6896:3: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ^ pair.c:6896:3: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c: In function 'Splicetrie_dump': splicetrie_build.c:134:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("%d %u",(int) leaf,position); ^ splicetrie_build.c:148:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("%d %u",(int) leaf,position); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-result.o `test -f 'result.c' || echo './'`result.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapl-gmap.o `test -f 'gmap.c' || echo './'`gmap.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome-write.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-stage2.o gmapl-smooth.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lm libtool: link: gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome-write.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-stage2.o gmapl-smooth.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:9968:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:342:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10103:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10200:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10306:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:10484:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c parserange.c: In function 'translate_chromosomepos_universal': parserange.c:187:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] Univinterval_low(interval),left,*genomicstart); ^ parserange.c:187:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] parserange.c:187:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c get-genome.c: In function 'print_two_coords': get-genome.c:194:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu%s%lu\t",left+1,SEPARATOR,left+length); ^ get-genome.c:194:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] get-genome.c: In function 'print_sequence': get-genome.c:410:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U); ^ get-genome.c:410:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] get-genome.c:428:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength); ^ get-genome.c:428:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:9968:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:342:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10103:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10200:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10306:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:10484:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c: In function 'genome_write_file': genome-write.c:253:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:253:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:256:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:256:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'genome_writeraw_file': genome-write.c:430:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:430:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:433:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:433:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'fill_circular_chromosomes': genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ^ genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'Univcoord_T' [-Wformat=] genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'genome_write_memory': genome-write.c:643:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:643:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:646:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:646:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'Genome_write': genome-write.c:786:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c genome_hr.c: In function 'Genome_print_blocks': genome_hr.c:66386:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",startblock/3*32U); ^ genome_hr.c:66401:5: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",ptr/3*32U); ^ genome_hr.c:66408:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",(endblock+3)/3*32U); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function 'check_offsets_from_gammas': indexdb-write.c:274:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsetscomp[gammaptrs[p-1]],cum); ^ indexdb-write.c:285:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] oligok-1UL,offsets[oligok-1],cum); ^ indexdb-write.c:308:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] oligok-1UL,offsets[oligok-1],cum); ^ indexdb-write.c:335:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsetscomp[gammaptrs[p-1]],cum); ^ indexdb-write.c:346:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsets[oligok],*ptr); ^ indexdb-write.c: In function 'Indexdb_write_offsets': indexdb-write.c:446:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); ^ indexdb-write.c:453:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); ^ indexdb-write.c:531:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ indexdb-write.c:646:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Writing %lu offsets compressed to file with total of %u positions...",oligospace+1UL,offsets[oligospace]); ^ indexdb-write.c: In function 'compute_positions_in_file': indexdb-write.c:844:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ indexdb-write.c: In function 'compute_positions_in_memory': indexdb-write.c:1074:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c: In function 'Segmentpos_print': segmentpos.c:90:3: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c gmapindex.c: In function 'process_sequence_aux': gmapindex.c:297:3: warning: format '%lu' expects argument of type 'long unsigned int *', but argument 5 has type 'Univcoord_T *' [-Wformat=] nitems = sscanf(Buffer,"%s %s %lu",accession_p,chrpos_string,&universal_coord); ^ gmapindex.c: In function 'write_chromosome_file': gmapindex.c:502:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] chr_string,chroffset+1,chroffset+1+chrlength-1); ^ gmapindex.c:502:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gmapindex.c:513:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] chr_string,chroffset+1,chroffset+chrlength,chrlength); ^ gmapindex.c:513:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gmapindex.c: In function 'write_contig_file': gmapindex.c:690:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Segmentpos_length(segmentpos)); ^ gmapindex.c:690:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gmapindex.c:695:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Segmentpos_length(segmentpos)); ^ gmapindex.c:695:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gmapindex.c: In function 'main': gmapindex.c:1023:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Total genomic length = %lu bp\n",totalnts); ^ /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress.o gmapindex-genome-write.o gmapindex-genome_hr.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-gmapindex.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress.o gmapindex-genome-write.o gmapindex-genome_hr.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-gmapindex.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c iit_store.c: In function 'scan_header_spaces': iit_store.c:371:3: warning: format '%lu' expects argument of type 'long unsigned int *', but argument 4 has type 'Univcoord_T *' [-Wformat=] nscanned = sscanf(header,">%s %lu %lu\n",Buffer,&(*start),&(*end)); ^ iit_store.c:371:3: warning: format '%lu' expects argument of type 'long unsigned int *', but argument 5 has type 'Univcoord_T *' [-Wformat=] iit_store.c: In function 'parse_fasta': iit_store.c:596:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Maximum coordinate: %lu\n",*max_coordinate); ^ iit_store.c:597:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Total label length: %lu + %d separators\n",*label_totallength,nentries); ^ iit_store.c:598:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Total annotation length: %lu + %d separators\n",*annot_totallength,nentries); ^ iit_store.c: In function 'parse_fieldlist': iit_store.c:447:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(&(Buffer[1]),LINELENGTH-1,fp); ^ iit_store.c: In function 'parse_fasta': iit_store.c:482:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(Buffer,LINELENGTH,fp); ^ iit_store.c:485:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(&(Buffer[1]),LINELENGTH-1,fp); ^ /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c parserange.c: In function 'translate_chromosomepos_universal': parserange.c:187:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] Univinterval_low(interval),left,*genomicstart); ^ parserange.c:187:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] parserange.c:187:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c iit_get.c: In function 'print_interval_univ': iit_get.c:619:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu",Univinterval_low(interval),Univinterval_high(interval)); ^ iit_get.c:619:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:9968:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:342:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10103:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10200:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10306:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:10484:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function 'positions_read_multiple': indexdb_hr.c:592:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-samprint.o `test -f 'samprint.c' || echo './'`samprint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-substring.o `test -f 'substring.c' || echo './'`substring.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-goby.o `test -f 'goby.c' || echo './'`goby.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c stage1hr.c: In function 'run_gmap': stage1hr.c:12510:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] mappingstart,mappingend); ^ stage1hr.c:12510:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex.o gsnap-oligoindex_hr.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lm libtool: link: gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex.o gsnap-oligoindex_hr.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c: In function 'Uint8list_to_string': uint8list.c:174:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'UINT8' [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:177:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'UINT8' [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ uint8list.c:183:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'UINT8' [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:186:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'UINT8' [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:9968:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:342:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10103:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10200:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10306:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:10484:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c genome_hr.c: In function 'Genome_print_blocks': genome_hr.c:66386:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",startblock/3*32U); ^ genome_hr.c:66401:5: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",ptr/3*32U); ^ genome_hr.c:66408:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",(endblock+3)/3*32U); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function 'Compoundpos_dump': indexdb_hr.c:964:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); ^ indexdb_hr.c: In function 'heap_even_dump': indexdb_hr.c:1188:5: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ^ indexdb_hr.c: In function 'positions_read_multiple': indexdb_hr.c:592:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c: In function 'Segmentpos_print': segmentpos.c:90:3: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-samprint.o `test -f 'samprint.c' || echo './'`samprint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-substring.o `test -f 'substring.c' || echo './'`substring.c substring.c: In function 'Substring_print_ends': substring.c:991:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); ^ substring.c:991:5: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring.c: In function 'print_coordinates': substring.c:3328:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring->alignend_trim - substring->chroffset); ^ substring.c:3328:7: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] substring.c:3331:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring->alignstart_trim - substring->chroffset + 1U); ^ substring.c:3331:7: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] substring.c:3336:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring->alignend_trim - substring->chroffset + 1U); ^ substring.c:3336:7: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] substring.c:3339:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring->alignstart_trim - substring->chroffset); ^ substring.c:3339:7: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-goby.o `test -f 'goby.c' || echo './'`goby.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function 'print_genomic_sequence': pair.c:513:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function 'print_genomicalt_sequence': pair.c:540:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function 'compute_margin': pair.c:567:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ^ pair.c:574:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ^ pair.c: In function 'Pair_print_coordinates': pair.c:1242:3: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] this->genome); ^ pair.c:1247:3: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] this->genome); ^ pair.c: In function 'Pair_print_exonsummary': pair.c:1725:6: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1725:6: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c:1734:6: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1734:6: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c:1848:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1848:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c:1857:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1857:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c: In function 'Pair_print_compressed': pair.c:6896:3: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ^ pair.c:6896:3: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c: In function 'Splicetrie_dump': splicetrie_build.c:134:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("%d %u",(int) leaf,position); ^ splicetrie_build.c:148:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("%d %u",(int) leaf,position); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c stage1hr.c: In function 'run_gmap': stage1hr.c:12510:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] mappingstart,mappingend); ^ stage1hr.c:12510:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsnapl-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex.o gsnapl-oligoindex_hr.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lm libtool: link: gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex.o gsnapl-oligoindex_hr.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:9968:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:342:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10103:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10200:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10306:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:10484:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function 'positions_read_multiple': indexdb_hr.c:592:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-substring.o `test -f 'substring.c' || echo './'`substring.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c stage1hr.c: In function 'run_gmap': stage1hr.c:12510:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] mappingstart,mappingend); ^ stage1hr.c:12510:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscan-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex.o uniqscan-oligoindex_hr.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lm libtool: link: gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex.o uniqscan-oligoindex_hr.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:9968:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:342:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10103:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10200:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10306:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:10484:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c genome_hr.c: In function 'Genome_print_blocks': genome_hr.c:66386:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",startblock/3*32U); ^ genome_hr.c:66401:5: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",ptr/3*32U); ^ genome_hr.c:66408:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",(endblock+3)/3*32U); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function 'Compoundpos_dump': indexdb_hr.c:964:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm); ^ indexdb_hr.c: In function 'heap_even_dump': indexdb_hr.c:1188:5: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ^ indexdb_hr.c: In function 'positions_read_multiple': indexdb_hr.c:592:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c segmentpos.c: In function 'Segmentpos_print': segmentpos.c:90:3: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-substring.o `test -f 'substring.c' || echo './'`substring.c substring.c: In function 'Substring_print_ends': substring.c:991:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend); ^ substring.c:991:5: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring.c: In function 'print_coordinates': substring.c:3328:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring->alignend_trim - substring->chroffset); ^ substring.c:3328:7: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] substring.c:3331:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring->alignstart_trim - substring->chroffset + 1U); ^ substring.c:3331:7: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] substring.c:3336:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring->alignend_trim - substring->chroffset + 1U); ^ substring.c:3336:7: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] substring.c:3339:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] substring->alignstart_trim - substring->chroffset); ^ substring.c:3339:7: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function 'print_genomic_sequence': pair.c:513:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function 'print_genomicalt_sequence': pair.c:540:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function 'compute_margin': pair.c:567:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ^ pair.c:574:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ^ pair.c: In function 'Pair_print_coordinates': pair.c:1242:3: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] this->genome); ^ pair.c:1247:3: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] this->genome); ^ pair.c: In function 'Pair_print_exonsummary': pair.c:1725:6: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1725:6: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c:1734:6: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1734:6: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c:1848:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1848:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c:1857:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend); ^ pair.c:1857:7: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] pair.c: In function 'Pair_print_compressed': pair.c:6896:3: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP); ^ pair.c:6896:3: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c: In function 'Splicetrie_dump': splicetrie_build.c:134:5: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("%d %u",(int) leaf,position); ^ splicetrie_build.c:148:7: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("%d %u",(int) leaf,position); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c stage1hr.c: In function 'run_gmap': stage1hr.c:12510:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] mappingstart,mappingend); ^ stage1hr.c:12510:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o uniqscanl-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex.o uniqscanl-oligoindex_hr.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lm libtool: link: gcc -pthread -DTARGET=\"powerpc64le-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex.o uniqscanl-oligoindex_hr.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c genome_hr.c: In function 'Genome_print_blocks': genome_hr.c:66386:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",startblock/3*32U); ^ genome_hr.c:66401:5: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",ptr/3*32U); ^ genome_hr.c:66408:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",(endblock+3)/3*32U); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function 'check_offsets_from_gammas': indexdb-write.c:274:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsetscomp[gammaptrs[p-1]],cum); ^ indexdb-write.c:285:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] oligok-1UL,offsets[oligok-1],cum); ^ indexdb-write.c:308:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] oligok-1UL,offsets[oligok-1],cum); ^ indexdb-write.c:335:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsetscomp[gammaptrs[p-1]],cum); ^ indexdb-write.c:346:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsets[oligok],*ptr); ^ indexdb-write.c: In function 'Indexdb_write_offsets': indexdb-write.c:446:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); ^ indexdb-write.c:453:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); ^ indexdb-write.c:531:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ indexdb-write.c:646:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Writing %lu offsets compressed to file with total of %u positions...",oligospace+1UL,offsets[oligospace]); ^ indexdb-write.c: In function 'compute_positions_in_file': indexdb-write.c:844:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ indexdb-write.c: In function 'compute_positions_in_memory': indexdb-write.c:1074:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10075:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10175:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:9968:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:342:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10103:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10200:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10306:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:10484:11: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c snpindex.c: In function 'merge_positions8': snpindex.c:888:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'UINT8' [-Wformat=] fprintf(stderr,"Problem: saw duplicate positions %lu in oligo %s\n",*ptr1,nt); ^ snpindex.c: In function 'main': snpindex.c:1143:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Allocating %lu*3*%lu bytes for compressed genome\n",nblocks,sizeof(Genomecomp_T)); ^ snpindex.c:1240:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] fprintf(stderr,"Writing %lu offsets with %u total positions\n",oligospace+1,offsets[oligospace]); ^ /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-genome_hr.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-genome_hr.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c genome_hr.c: In function 'Genome_print_blocks': genome_hr.c:66386:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",startblock/3*32U); ^ genome_hr.c:66401:5: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",ptr/3*32U); ^ genome_hr.c:66408:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",(endblock+3)/3*32U); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function 'check_offsets_from_gammas': indexdb-write.c:274:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsetscomp[gammaptrs[p-1]],cum); ^ indexdb-write.c:285:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] oligok-1UL,offsets[oligok-1],cum); ^ indexdb-write.c:308:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] oligok-1UL,offsets[oligok-1],cum); ^ indexdb-write.c:335:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsetscomp[gammaptrs[p-1]],cum); ^ indexdb-write.c:346:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsets[oligok],*ptr); ^ indexdb-write.c: In function 'Indexdb_write_offsets': indexdb-write.c:446:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); ^ indexdb-write.c:453:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); ^ indexdb-write.c:531:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ indexdb-write.c:646:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Writing %lu offsets compressed to file with total of %u positions...",oligospace+1UL,offsets[oligospace]); ^ indexdb-write.c: In function 'compute_positions_in_file': indexdb-write.c:844:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ indexdb-write.c: In function 'compute_positions_in_memory': indexdb-write.c:1074:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-genome_hr.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-genome_hr.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm -pthread gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_uint': littleendian.c:17:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:34:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:47:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:53:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c In file included from access.c:41:0: access.c: In function 'Access_allocated': littleendian.h:20:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ access.c:235:5: note: in expansion of macro 'FREAD_UINTS' FREAD_UINTS(memory,(*len)/eltsize,fp); ^ littleendian.h:23:35: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp) ^ access.c:237:5: note: in expansion of macro 'FREAD_UINT8S' FREAD_UINT8S(memory,(*len)/eltsize,fp); ^ access.c:254:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:259:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:63:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:507:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:544:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:694:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:700:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:703:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:873:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:875:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:876:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:877:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:878:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:920:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:921:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:922:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:927:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:929:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:931:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:991:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1213:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1217:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1221:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1225:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1229:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1073:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2237:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2495:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1604:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1605:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1606:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1607:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1608:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1689:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1690:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1692:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1696:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1785:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1791:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2141:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2147:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2152:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2163:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2169:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2174:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2185:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:17:30: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2898:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:22:32: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1913:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:18:31: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1918:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c compress.c: In function 'fill_buffer': compress.c:80:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress.c: In function 'Compress_compress': compress.c:176:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Non-standard nucleotide %c at position %lu. Using N instead\n",c,position); ^ compress.c:193:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Compressing position %lu\n",position); ^ compress.c: In function 'Compress_uncompress': compress.c:233:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c:244:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Uncompressing position %lu\n",position); ^ compress.c: In function 'write_compressed_one': compress.c:350:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress.c: In function 'put_compressed_one': compress.c:397:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c genome_hr.c: In function 'Genome_print_blocks': genome_hr.c:66386:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",startblock/3*32U); ^ genome_hr.c:66401:5: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",ptr/3*32U); ^ genome_hr.c:66408:3: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%u\t",(endblock+3)/3*32U); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_offsets_from_gammas': indexdb.c:1277:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1175:9: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function 'check_offsets_from_gammas': indexdb-write.c:274:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsetscomp[gammaptrs[p-1]],cum); ^ indexdb-write.c:285:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] oligok-1UL,offsets[oligok-1],cum); ^ indexdb-write.c:308:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] oligok-1UL,offsets[oligok-1],cum); ^ indexdb-write.c:335:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsetscomp[gammaptrs[p-1]],cum); ^ indexdb-write.c:346:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] oligok,offsets[oligok],*ptr); ^ indexdb-write.c: In function 'Indexdb_write_offsets': indexdb-write.c:446:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T)); ^ indexdb-write.c:453:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part); ^ indexdb-write.c:531:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ indexdb-write.c:646:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=] fprintf(stderr,"Writing %lu offsets compressed to file with total of %u positions...",oligospace+1UL,offsets[oligospace]); ^ indexdb-write.c: In function 'compute_positions_in_file': indexdb-write.c:844:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ indexdb-write.c: In function 'compute_positions_in_memory': indexdb-write.c:1074:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Bad character %c at position %lu\n",c,position); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-genome_hr.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O3 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-genome_hr.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm -pthread make[3]: Leaving directory `/build/buildd/gmap-2013-07-20/src' make[2]: Leaving directory `/build/buildd/gmap-2013-07-20/src' Making all in util make[2]: Entering directory `/build/buildd/gmap-2013-07-20/util' cp gmap_compress.pl gmap_compress chmod +x gmap_compress cp gmap_uncompress.pl gmap_uncompress chmod +x gmap_uncompress cp gmap_process.pl gmap_process chmod +x gmap_process cp gmap_setup.pl gmap_setup chmod +x gmap_setup cp gmap_build.pl gmap_build chmod +x gmap_build cp gmap_reassemble.pl gmap_reassemble chmod +x gmap_reassemble cp md_coords.pl md_coords chmod +x md_coords cp fa_coords.pl fa_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites cp psl_introns.pl psl_introns chmod +x psl_introns cp psl_genes.pl psl_genes chmod +x psl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x dbsnp_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[2]: Leaving directory `/build/buildd/gmap-2013-07-20/util' Making all in tests make[2]: Entering directory `/build/buildd/gmap-2013-07-20/tests' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/build/buildd/gmap-2013-07-20/tests' make[2]: Entering directory `/build/buildd/gmap-2013-07-20' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/build/buildd/gmap-2013-07-20' make[1]: Leaving directory `/build/buildd/gmap-2013-07-20' dh_auto_test -a make[1]: Entering directory `/build/buildd/gmap-2013-07-20' Making check in src make[2]: Entering directory `/build/buildd/gmap-2013-07-20/src' make[2]: Leaving directory `/build/buildd/gmap-2013-07-20/src' Making check in util make[2]: Entering directory `/build/buildd/gmap-2013-07-20/util' make[2]: Nothing to be done for `check'. make[2]: Leaving directory `/build/buildd/gmap-2013-07-20/util' Making check in tests make[2]: Entering directory `/build/buildd/gmap-2013-07-20/tests' make check-TESTS make[3]: Entering directory `/build/buildd/gmap-2013-07-20/tests' GMAP version 2013-07-20 called with args: /build/buildd/gmap-2013-07-20/src/gmap -A -g /build/buildd/gmap-2013-07-20/tests/ss.chr17test /build/buildd/gmap-2013-07-20/tests/ss.her2 Checking compiler assumptions for popcnt: 6B8B4567 clz=1 clz=0 popcount=17 Processed 1 queries in 0.05 seconds (20.00 queries/sec) PASS: align.test Opening file /build/buildd/gmap-2013-07-20/tests/ss.chr17test Processed short contigs (<1000000 nt): . ============================================================ Contig mapping information has been written to file coords.chr17test. You should look at this file, and edit it if necessary If everything is okay, you should proceed by running make -f Makefile.chr17test gmapdb ============================================================ PASS: coords1.test -k flag specified (not as 15), but not -b, so building with basesize == kmer size Sorting chromosomes in chrom order. To turn off or sort other ways, use the -s flag. Running /build/buildd/gmap-2013-07-20/src/fa_coords -o ./chr17test.coords "/build/buildd/gmap-2013-07-20/tests/ss.chr17test" Opening file /build/buildd/gmap-2013-07-20/tests/ss.chr17test Processed short contigs (<1000000 nt): . ============================================================ Contig mapping information has been written to file ./chr17test.coords. You should look at this file, and edit it if necessary If everything is okay, you should proceed by running make gmapdb ============================================================ Running /build/buildd/gmap-2013-07-20/src/gmap_process -c ./chr17test.coords "/build/buildd/gmap-2013-07-20/tests/ss.chr17test" | /build/buildd/gmap-2013-07-20/src/gmapindex -d chr17test -D . -A Reading coordinates from file ./chr17test.coords Logging contig chr17test at chr17test:1..200000 in genome chr17test Total genomic length = 200000 bp Chromosome chr17test has universal coordinates 1..200000 Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (1 intervals) Writing IIT file footer information...done Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (1 intervals) Writing IIT file footer information...done Running /build/buildd/gmap-2013-07-20/src/gmap_process -c ./chr17test.coords "/build/buildd/gmap-2013-07-20/tests/ss.chr17test" | /build/buildd/gmap-2013-07-20/src/gmapindex -d chr17test -F . -D . -G Genome length is 200000 nt Trying to allocate 18750*4 bytes of memory...succeeded. Building genome in memory. Reading coordinates from file ./chr17test.coords Writing contig chr17test to universal coordinates 1..200000 in genome chr17test A total of 0 non-ACGTNX characters were seen in the genome. Running cat ./chr17test.genomecomp | /build/buildd/gmap-2013-07-20/src/gmapindex -b 12 -k 12 -q 3 -d chr17test -F . -D . -O Allocating 16777217*4 bytes for offsets Indexing offsets of oligomers in genome chr17test (12 bp every 3 bp), position 0 Writing 16777217 offsets compressed to file with total of 66663 positions...done Running cat ./chr17test.genomecomp | /build/buildd/gmap-2013-07-20/src/gmapindex -b 12 -k 12 -q 3 -d chr17test -F . -D . -P Trying to allocate 66663*4 bytes of memory...succeeded. Building positions in memory. Indexing positions of oligomers in genome chr17test (12 bp every 3 bp), position 0 Writing 66663 genomic positions to file ./chr17test.ref123positions ... Copying files to directory ./chr17test GMAP version 2013-07-20 called with args: /build/buildd/gmap-2013-07-20/src/gmap -D . -d chr17test /build/buildd/gmap-2013-07-20/tests/ss.her2 Checking compiler assumptions for popcnt: 6B8B4567 clz=1 clz=0 popcount=17 Looking for index files in directory ./chr17test No gammaptrs file, because kmersize 12 == basesize 12 Offsetscomp file is chr17test.ref12123offsetscomp Positions file is chr17test.ref123positions Processed 1 queries in 0.04 seconds (25.00 queries/sec) PASS: setup1.test Finished reading FASTA file -- total entries: 3 Maximum coordinate: 40000 Total label length: 3 + 3 separators Total annotation length: 80 + 3 separators Saw 0 distinct divisions/chromosomes Saw 3 distinct tags/types No divs/chromosomes provided, so storing as IIT version 1 Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (3 intervals) Writing IIT file footer information...done PASS: iit.test ================== All 4 tests passed ================== make[3]: Leaving directory `/build/buildd/gmap-2013-07-20/tests' make[2]: Leaving directory `/build/buildd/gmap-2013-07-20/tests' make[2]: Entering directory `/build/buildd/gmap-2013-07-20' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/build/buildd/gmap-2013-07-20' make[1]: Leaving directory `/build/buildd/gmap-2013-07-20' /usr/bin/fakeroot debian/rules binary-arch dh binary-arch --with autotools_dev dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory `/build/buildd/gmap-2013-07-20' dh_auto_install --destdir=debian/tmp make[2]: Entering directory `/build/buildd/gmap-2013-07-20' Making install in src make[3]: Entering directory `/build/buildd/gmap-2013-07-20/src' make[4]: Entering directory `/build/buildd/gmap-2013-07-20/src' test -z "/usr/bin" || /bin/mkdir -p "/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin" /bin/bash ../libtool --mode=install /usr/bin/install -c 'gmap' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmap' libtool: install: /usr/bin/install -c gmap /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmap /bin/bash ../libtool --mode=install /usr/bin/install -c 'gmapl' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmapl' libtool: install: /usr/bin/install -c gmapl /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmapl /bin/bash ../libtool --mode=install /usr/bin/install -c 'get-genome' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/get-genome' libtool: install: /usr/bin/install -c get-genome /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/get-genome /bin/bash ../libtool --mode=install /usr/bin/install -c 'gmapindex' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmapindex' libtool: install: /usr/bin/install -c gmapindex /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmapindex /bin/bash ../libtool --mode=install /usr/bin/install -c 'iit_store' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/iit_store' libtool: install: /usr/bin/install -c iit_store /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/iit_store /bin/bash ../libtool --mode=install /usr/bin/install -c 'iit_get' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/iit_get' libtool: install: /usr/bin/install -c iit_get /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/iit_get /bin/bash ../libtool --mode=install /usr/bin/install -c 'iit_dump' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/iit_dump' libtool: install: /usr/bin/install -c iit_dump /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/iit_dump /bin/bash ../libtool --mode=install /usr/bin/install -c 'gsnap' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gsnap' libtool: install: /usr/bin/install -c gsnap /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gsnap /bin/bash ../libtool --mode=install /usr/bin/install -c 'gsnapl' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gsnapl' libtool: install: /usr/bin/install -c gsnapl /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gsnapl /bin/bash ../libtool --mode=install /usr/bin/install -c 'uniqscan' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/uniqscan' libtool: install: /usr/bin/install -c uniqscan /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/uniqscan /bin/bash ../libtool --mode=install /usr/bin/install -c 'uniqscanl' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/uniqscanl' libtool: install: /usr/bin/install -c uniqscanl /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/uniqscanl /bin/bash ../libtool --mode=install /usr/bin/install -c 'snpindex' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/snpindex' libtool: install: /usr/bin/install -c snpindex /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/snpindex /bin/bash ../libtool --mode=install /usr/bin/install -c 'cmetindex' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/cmetindex' libtool: install: /usr/bin/install -c cmetindex /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/cmetindex /bin/bash ../libtool --mode=install /usr/bin/install -c 'atoiindex' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/atoiindex' libtool: install: /usr/bin/install -c atoiindex /build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/atoiindex make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/gmap-2013-07-20/src' make[3]: Leaving directory `/build/buildd/gmap-2013-07-20/src' Making install in util make[3]: Entering directory `/build/buildd/gmap-2013-07-20/util' make[4]: Entering directory `/build/buildd/gmap-2013-07-20/util' test -z "/usr/bin" || /bin/mkdir -p "/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin" /usr/bin/install -c 'gmap_compress' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmap_compress' /usr/bin/install -c 'gmap_uncompress' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmap_uncompress' /usr/bin/install -c 'gmap_process' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmap_process' /usr/bin/install -c 'gmap_setup' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmap_setup' /usr/bin/install -c 'gmap_build' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmap_build' /usr/bin/install -c 'gmap_reassemble' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gmap_reassemble' /usr/bin/install -c 'md_coords' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/md_coords' /usr/bin/install -c 'fa_coords' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/fa_coords' /usr/bin/install -c 'psl_splicesites' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/psl_splicesites' /usr/bin/install -c 'psl_introns' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/psl_introns' /usr/bin/install -c 'psl_genes' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/psl_genes' /usr/bin/install -c 'gtf_splicesites' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gtf_splicesites' /usr/bin/install -c 'gtf_introns' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gtf_introns' /usr/bin/install -c 'gtf_genes' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gtf_genes' /usr/bin/install -c 'gff3_splicesites' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gff3_splicesites' /usr/bin/install -c 'gff3_introns' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gff3_introns' /usr/bin/install -c 'gff3_genes' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/gff3_genes' /usr/bin/install -c 'dbsnp_iit' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/dbsnp_iit' /usr/bin/install -c 'vcf_iit' '/build/buildd/gmap-2013-07-20/debian/tmp/usr/bin/vcf_iit' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/gmap-2013-07-20/util' make[3]: Leaving directory `/build/buildd/gmap-2013-07-20/util' Making install in tests make[3]: Entering directory `/build/buildd/gmap-2013-07-20/tests' make[4]: Entering directory `/build/buildd/gmap-2013-07-20/tests' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/build/buildd/gmap-2013-07-20/tests' make[3]: Leaving directory `/build/buildd/gmap-2013-07-20/tests' make[3]: Entering directory `/build/buildd/gmap-2013-07-20' make[4]: Entering directory `/build/buildd/gmap-2013-07-20' make[4]: Nothing to be done for `install-exec-am'. /bin/bash /build/buildd/gmap-2013-07-20/config/install-sh -d /build/buildd/gmap-2013-07-20/debian/tmp/var/cache/gmap make[4]: Leaving directory `/build/buildd/gmap-2013-07-20' make[3]: Leaving directory `/build/buildd/gmap-2013-07-20' make[2]: Leaving directory `/build/buildd/gmap-2013-07-20' make[1]: Leaving directory `/build/buildd/gmap-2013-07-20' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform ppc64el: gmap dh_strip debug symbol extraction: packages to act on: gmap dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: building ddeb package dpkg-deb: building package `gmap-dbgsym' in `../gmap-dbgsym_2013-07-20-1_ppc64el.ddeb'. dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 119 pkgstriptranslations: processing gmap (in debian/gmap); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/gmap/DEBIAN/control, package gmap, directory debian/gmap pkgstripfiles: Truncating usr/share/doc/gmap/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package gmap took 0 s dpkg-deb: warning: 'debian/gmap/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `gmap' in `../gmap_2013-07-20-1_ppc64el.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../gmap_2013-07-20-1_ppc64el.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build gmap-2013-07-20 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20140217-0712 Publishing debug debs. chroot-autobuild/build/buildd/gmap_2013-07-20-1_ppc64el.deb: new debian package, version 2.0. size 3301402 bytes: control archive=1610 bytes. 968 bytes, 21 lines control 1779 bytes, 30 lines md5sums Package: gmap Version: 2013-07-20-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 41017 Depends: libc6 (>= 2.17), perl Section: non-free/science Priority: optional Homepage: http://research-pub.gene.com/gmap/ Description: spliced and SNP-tolerant alignment for mRNA and short reads This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of * known splice sites and identify novel splice sites. * known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA. chroot-autobuild/build/buildd/gmap_2013-07-20-1_ppc64el.deb: drwxr-xr-x root/root 0 2014-02-17 07:12 ./ drwxr-xr-x root/root 0 2014-02-17 07:12 ./usr/ drwxr-xr-x root/root 0 2014-02-17 07:12 ./usr/bin/ -rwxr-xr-x root/root 9658232 2014-02-17 07:12 ./usr/bin/gmap -rwxr-xr-x root/root 17619 2014-02-17 07:12 ./usr/bin/gmap_setup -rwxr-xr-x root/root 11080000 2014-02-17 07:12 ./usr/bin/gsnap drwxr-xr-x root/root 0 2014-02-17 07:12 ./usr/lib/ drwxr-xr-x root/root 0 2014-02-17 07:12 ./usr/lib/gmap/ -rwxr-xr-x root/root 5286544 2014-02-17 07:12 ./usr/lib/gmap/snpindex -rwxr-xr-x root/root 12616 2014-02-17 07:12 ./usr/lib/gmap/gtf_splicesites -rwxr-xr-x root/root 5017 2014-02-17 07:12 ./usr/lib/gmap/gtf_genes -rwxr-xr-x root/root 1177 2014-02-17 07:12 ./usr/lib/gmap/psl_genes -rwxr-xr-x root/root 16514 2014-02-17 07:12 ./usr/lib/gmap/gmap_uncompress -rwxr-xr-x root/root 7863 2014-02-17 07:12 ./usr/lib/gmap/dbsnp_iit -rwxr-xr-x root/root 29421 2014-02-17 07:12 ./usr/lib/gmap/md_coords -rwxr-xr-x root/root 533 2014-02-17 07:12 ./usr/lib/gmap/gmap_reassemble -rwxr-xr-x root/root 137824 2014-02-17 07:12 ./usr/lib/gmap/iit_get -rwxr-xr-x root/root 10487 2014-02-17 07:12 ./usr/lib/gmap/gmap_compress -rwxr-xr-x root/root 8193 2014-02-17 07:12 ./usr/lib/gmap/gmap_build -rwxr-xr-x root/root 4142 2014-02-17 07:12 ./usr/lib/gmap/gmap_process -rwxr-xr-x root/root 4155816 2014-02-17 07:12 ./usr/lib/gmap/atoiindex -rwxr-xr-x root/root 121160 2014-02-17 07:12 ./usr/lib/gmap/iit_dump -rwxr-xr-x root/root 6985 2014-02-17 07:12 ./usr/lib/gmap/psl_splicesites -rwxr-xr-x root/root 92552 2014-02-17 07:12 ./usr/lib/gmap/iit_store -rwxr-xr-x root/root 1797216 2014-02-17 07:12 ./usr/lib/gmap/get-genome -rwxr-xr-x root/root 5302592 2014-02-17 07:12 ./usr/lib/gmap/gmapindex -rwxr-xr-x root/root 4155816 2014-02-17 07:12 ./usr/lib/gmap/cmetindex -rwxr-xr-x root/root 14210 2014-02-17 07:12 ./usr/lib/gmap/fa_coords drwxr-xr-x root/root 0 2014-02-17 07:12 ./usr/share/ drwxr-xr-x root/root 0 2014-02-17 07:12 ./usr/share/man/ drwxr-xr-x root/root 0 2014-02-17 07:12 ./usr/share/man/man1/ -rw-r--r-- root/root 1807 2014-02-17 07:12 ./usr/share/man/man1/gmap_setup.1.gz -rw-r--r-- root/root 4184 2014-02-17 07:12 ./usr/share/man/man1/gmap.1.gz -rw-r--r-- root/root 5625 2014-02-17 07:12 ./usr/share/man/man1/gsnap.1.gz drwxr-xr-x root/root 0 2014-02-17 07:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-02-17 07:12 ./usr/share/doc/gmap/ -rw-r--r-- root/root 2356 2013-08-02 09:30 ./usr/share/doc/gmap/copyright -rw-r--r-- root/root 18345 2013-07-10 23:01 ./usr/share/doc/gmap/README.gz -rw-r--r-- root/root 683 2014-02-17 07:12 ./usr/share/doc/gmap/changelog.Debian.gz -rw-r--r-- root/root 171 2013-08-02 09:30 ./usr/share/doc/gmap/README.Debian gmap_2013-07-20-1_ppc64el.changes: Format: 1.8 Date: Fri, 02 Aug 2013 15:09:36 +0200 Source: gmap Binary: gmap Architecture: ppc64el Version: 2013-07-20-1 Distribution: trusty-proposed Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Andreas Tille Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2013-07-20-1) unstable; urgency=low . * New upstream version * debian/control: - cme fix dpkg-control - debhelper 9 Checksums-Sha1: 7a5739087c95d0349526b8673a353169815e4758 3301402 gmap_2013-07-20-1_ppc64el.deb Checksums-Sha256: 144b5657e0d2a62916ef00a96dc86b92dd9ce1f0844b878240635c61237584c1 3301402 gmap_2013-07-20-1_ppc64el.deb Files: 1f8ae0287229b496371069156433871e 3301402 non-free/science optional gmap_2013-07-20-1_ppc64el.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20140217-0712 Build needed 00:08:15, 479492k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-5607500'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-5607500/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-5607500'] Unmounting chroot for build PACKAGEBUILD-5607500... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-5607500'] Removing build PACKAGEBUILD-5607500