I: pbuilder: network access will be disabled during build
I: Current time: Sun Apr 5 05:50:07 +14 2026
I: pbuilder-time-stamp: 1775317807
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [gmap_2024-11-20+ds-2.dsc]
I: copying [./gmap_2024-11-20+ds.orig.tar.xz]
I: copying [./gmap_2024-11-20+ds-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./gmap_2024-11-20+ds-2.dsc: unsupported subcommand
dpkg-source: info: extracting gmap in gmap-2024-11-20+ds
dpkg-source: info: unpacking gmap_2024-11-20+ds.orig.tar.xz
dpkg-source: info: unpacking gmap_2024-11-20+ds-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying install-data-local
dpkg-source: info: applying remove_getopt_code_copy.patch
dpkg-source: info: applying simd_fixes
dpkg-source: info: applying c23.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/11997/tmp/hooks/D01_modify_environment starting
debug: Running on ionos16-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Apr 4 15:50 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/11997/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/11997/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 '
DIRSTACK=()
DISTRIBUTION=trixie
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=a4172a17f6fc4d5bbb93ab729d6ef165
LANG=C
LANGUAGE=de_CH:de
LC_ALL=C
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
MACHTYPE=i686-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=11997
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dZZp8l9v/pbuilderrc_VYsE --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dZZp8l9v/b2 --logfile b2/build.log gmap_2024-11-20+ds-2.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://213.165.73.152:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/11997/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), architecture-is-little-endian, help2man, libbz2-dev, zlib1g-dev, debhelper, libsimde-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19789 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however:
Package architecture-is-little-endian is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
Package libbz2-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on debhelper; however:
Package debhelper is not installed.
pbuilder-satisfydepends-dummy depends on libsimde-dev; however:
Package libsimde-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bzip2-doc curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded.
Need to get 22.5 MB of archives. After unpacking 88.8 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 architecture-properties i386 0.2.6 [2340 B]
Get: 13 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 24 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 libsimde-dev all 0.8.2-2 [467 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Fetched 22.5 MB in 0s (134 MB/s)
Preconfiguring packages ...
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ...
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19789 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_i386.deb ...
Unpacking liblocale-gettext-perl (1.07-7+b1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:i386.
Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.45-3+b1_i386.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.23.1-1_i386.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../07-groff-base_1.23.0-7_i386.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../08-bsdextrautils_2.40.4-5_i386.deb ...
Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../09-libpipeline1_1.5.8-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../10-man-db_2.13.0-1_i386.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package architecture-properties:i386.
Preparing to unpack .../11-architecture-properties_0.2.6_i386.deb ...
Unpacking architecture-properties:i386 (0.2.6) ...
Selecting previously unselected package m4.
Preparing to unpack .../12-m4_1.4.19-5_i386.deb ...
Unpacking m4 (1.4.19-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../13-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../15-automake_1%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../16-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../17-libdebhelper-perl_13.24.1_all.deb ...
Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../18-libtool_2.5.4-3_all.deb ...
Unpacking libtool (2.5.4-3) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../19-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_1.14.1-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.1-2) ...
Selecting previously unselected package libelf1t64:i386.
Preparing to unpack .../23-libelf1t64_0.192-4_i386.deb ...
Unpacking libelf1t64:i386 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../24-dwz_0.15-1+b1_i386.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:i386.
Preparing to unpack .../25-libunistring5_1.3-1_i386.deb ...
Unpacking libunistring5:i386 (1.3-1) ...
Selecting previously unselected package libicu72:i386.
Preparing to unpack .../26-libicu72_72.1-6_i386.deb ...
Unpacking libicu72:i386 (72.1-6) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_i386.deb ...
Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../28-gettext_0.23.1-1_i386.deb ...
Unpacking gettext (0.23.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../31-debhelper_13.24.1_all.deb ...
Unpacking debhelper (13.24.1) ...
Selecting previously unselected package help2man.
Preparing to unpack .../32-help2man_1.49.3_i386.deb ...
Unpacking help2man (1.49.3) ...
Selecting previously unselected package libbz2-dev:i386.
Preparing to unpack .../33-libbz2-dev_1.0.8-6_i386.deb ...
Unpacking libbz2-dev:i386 (1.0.8-6) ...
Selecting previously unselected package libsimde-dev.
Preparing to unpack .../34-libsimde-dev_0.8.2-2_all.deb ...
Unpacking libsimde-dev (0.8.2-2) ...
Selecting previously unselected package zlib1g-dev:i386.
Preparing to unpack .../35-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_i386.deb ...
Unpacking zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libpipeline1:i386 (1.5.8-1) ...
Setting up libsimde-dev (0.8.2-2) ...
Setting up libicu72:i386 (72.1-6) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up architecture-properties:i386 (0.2.6) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:i386 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up liblocale-gettext-perl (1.07-7+b1) ...
Setting up libbz2-dev:i386 (1.0.8-6) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up help2man (1.49.3) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/11997/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/11997/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/gmap-2024-11-20+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gmap_2024-11-20+ds-2_source.changes
dpkg-buildpackage: info: source package gmap
dpkg-buildpackage: info: source version 2024-11-20+ds-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --builddir build
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds'
dh_auto_clean
make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds'
dh_autoreconf_clean -O--builddir=build
dh_clean -O--builddir=build
debian/rules binary
dh binary --builddir build
dh_update_autotools_config -O--builddir=build
dh_autoreconf -O--builddir=build
configure.ac:104: installing 'config/compile'
configure.ac:85: installing 'config/config.guess'
configure.ac:85: installing 'config/config.sub'
configure.ac:109: installing 'config/install-sh'
configure.ac:109: installing 'config/missing'
Makefile.am: installing './INSTALL'
src/Makefile.am: installing 'config/depcomp'
src/Makefile.am:870: warning: variable 'dist_compare2truth_SOURCES' is defined but no program or
src/Makefile.am:870: library has 'compare2truth' as canonical name (possible typo)
src/Makefile.am:1216: warning: variable 'dist_gcount_bulk_SOURCES' is defined but no program or
src/Makefile.am:1216: library has 'gcount_bulk' as canonical name (possible typo)
src/Makefile.am:1242: warning: variable 'dist_gcount_sc_SOURCES' is defined but no program or
src/Makefile.am:1242: library has 'gcount_sc' as canonical name (possible typo)
src/Makefile.am:216: warning: variable 'dist_gexact_SOURCES' is defined but no program or
src/Makefile.am:216: library has 'gexact' as canonical name (possible typo)
src/Makefile.am:742: warning: variable 'dist_gexact_arm_SOURCES' is defined but no program or
src/Makefile.am:742: library has 'gexact_arm' as canonical name (possible typo)
src/Makefile.am:772: warning: variable 'dist_gexact_avx2_SOURCES' is defined but no program or
src/Makefile.am:772: library has 'gexact_avx2' as canonical name (possible typo)
src/Makefile.am:778: warning: variable 'dist_gexact_avx512_SOURCES' is defined but no program or
src/Makefile.am:778: library has 'gexact_avx512' as canonical name (possible typo)
src/Makefile.am:784: warning: variable 'dist_gexact_avx512bw_SOURCES' is defined but no program or
src/Makefile.am:784: library has 'gexact_avx512bw' as canonical name (possible typo)
src/Makefile.am:736: warning: variable 'dist_gexact_nosimd_SOURCES' is defined but no program or
src/Makefile.am:736: library has 'gexact_nosimd' as canonical name (possible typo)
src/Makefile.am:748: warning: variable 'dist_gexact_sse2_SOURCES' is defined but no program or
src/Makefile.am:748: library has 'gexact_sse2' as canonical name (possible typo)
src/Makefile.am:760: warning: variable 'dist_gexact_sse41_SOURCES' is defined but no program or
src/Makefile.am:760: library has 'gexact_sse41' as canonical name (possible typo)
src/Makefile.am:766: warning: variable 'dist_gexact_sse42_SOURCES' is defined but no program or
src/Makefile.am:766: library has 'gexact_sse42' as canonical name (possible typo)
src/Makefile.am:754: warning: variable 'dist_gexact_ssse3_SOURCES' is defined but no program or
src/Makefile.am:754: library has 'gexact_ssse3' as canonical name (possible typo)
src/Makefile.am:223: warning: variable 'dist_gfilter_SOURCES' is defined but no program or
src/Makefile.am:223: library has 'gfilter' as canonical name (possible typo)
src/Makefile.am:816: warning: variable 'dist_gfilter_arm_SOURCES' is defined but no program or
src/Makefile.am:816: library has 'gfilter_arm' as canonical name (possible typo)
src/Makefile.am:846: warning: variable 'dist_gfilter_avx2_SOURCES' is defined but no program or
src/Makefile.am:846: library has 'gfilter_avx2' as canonical name (possible typo)
src/Makefile.am:852: warning: variable 'dist_gfilter_avx512_SOURCES' is defined but no program or
src/Makefile.am:852: library has 'gfilter_avx512' as canonical name (possible typo)
src/Makefile.am:858: warning: variable 'dist_gfilter_avx512bw_SOURCES' is defined but no program or
src/Makefile.am:858: library has 'gfilter_avx512bw' as canonical name (possible typo)
src/Makefile.am:810: warning: variable 'dist_gfilter_nosimd_SOURCES' is defined but no program or
src/Makefile.am:810: library has 'gfilter_nosimd' as canonical name (possible typo)
src/Makefile.am:822: warning: variable 'dist_gfilter_sse2_SOURCES' is defined but no program or
src/Makefile.am:822: library has 'gfilter_sse2' as canonical name (possible typo)
src/Makefile.am:834: warning: variable 'dist_gfilter_sse41_SOURCES' is defined but no program or
src/Makefile.am:834: library has 'gfilter_sse41' as canonical name (possible typo)
src/Makefile.am:840: warning: variable 'dist_gfilter_sse42_SOURCES' is defined but no program or
src/Makefile.am:840: library has 'gfilter_sse42' as canonical name (possible typo)
src/Makefile.am:828: warning: variable 'dist_gfilter_ssse3_SOURCES' is defined but no program or
src/Makefile.am:828: library has 'gfilter_ssse3' as canonical name (possible typo)
src/Makefile.am:1132: warning: variable 'dist_iit_pileup_SOURCES' is defined but no program or
src/Makefile.am:1132: library has 'iit_pileup' as canonical name (possible typo)
src/Makefile.am:1154: warning: variable 'dist_sam_sort_SOURCES' is defined but no program or
src/Makefile.am:1154: library has 'sam_sort' as canonical name (possible typo)
src/Makefile.am:1172: warning: variable 'dist_umi_correct_SOURCES' is defined but no program or
src/Makefile.am:1172: library has 'umi_correct' as canonical name (possible typo)
src/Makefile.am:1191: warning: variable 'dist_velocity_counts_SOURCES' is defined but no program or
src/Makefile.am:1191: library has 'velocity_counts' as canonical name (possible typo)
src/Makefile.am:869: warning: variable 'compare2truth_LDADD' is defined but no program or
src/Makefile.am:869: library has 'compare2truth' as canonical name (possible typo)
src/Makefile.am:1215: warning: variable 'gcount_bulk_LDADD' is defined but no program or
src/Makefile.am:1215: library has 'gcount_bulk' as canonical name (possible typo)
src/Makefile.am:1241: warning: variable 'gcount_sc_LDADD' is defined but no program or
src/Makefile.am:1241: library has 'gcount_sc' as canonical name (possible typo)
src/Makefile.am:215: warning: variable 'gexact_LDADD' is defined but no program or
src/Makefile.am:215: library has 'gexact' as canonical name (possible typo)
src/Makefile.am:741: warning: variable 'gexact_arm_LDADD' is defined but no program or
src/Makefile.am:741: library has 'gexact_arm' as canonical name (possible typo)
src/Makefile.am:771: warning: variable 'gexact_avx2_LDADD' is defined but no program or
src/Makefile.am:771: library has 'gexact_avx2' as canonical name (possible typo)
src/Makefile.am:777: warning: variable 'gexact_avx512_LDADD' is defined but no program or
src/Makefile.am:777: library has 'gexact_avx512' as canonical name (possible typo)
src/Makefile.am:783: warning: variable 'gexact_avx512bw_LDADD' is defined but no program or
src/Makefile.am:783: library has 'gexact_avx512bw' as canonical name (possible typo)
src/Makefile.am:735: warning: variable 'gexact_nosimd_LDADD' is defined but no program or
src/Makefile.am:735: library has 'gexact_nosimd' as canonical name (possible typo)
src/Makefile.am:747: warning: variable 'gexact_sse2_LDADD' is defined but no program or
src/Makefile.am:747: library has 'gexact_sse2' as canonical name (possible typo)
src/Makefile.am:759: warning: variable 'gexact_sse41_LDADD' is defined but no program or
src/Makefile.am:759: library has 'gexact_sse41' as canonical name (possible typo)
src/Makefile.am:765: warning: variable 'gexact_sse42_LDADD' is defined but no program or
src/Makefile.am:765: library has 'gexact_sse42' as canonical name (possible typo)
src/Makefile.am:753: warning: variable 'gexact_ssse3_LDADD' is defined but no program or
src/Makefile.am:753: library has 'gexact_ssse3' as canonical name (possible typo)
src/Makefile.am:222: warning: variable 'gfilter_LDADD' is defined but no program or
src/Makefile.am:222: library has 'gfilter' as canonical name (possible typo)
src/Makefile.am:815: warning: variable 'gfilter_arm_LDADD' is defined but no program or
src/Makefile.am:815: library has 'gfilter_arm' as canonical name (possible typo)
src/Makefile.am:845: warning: variable 'gfilter_avx2_LDADD' is defined but no program or
src/Makefile.am:845: library has 'gfilter_avx2' as canonical name (possible typo)
src/Makefile.am:851: warning: variable 'gfilter_avx512_LDADD' is defined but no program or
src/Makefile.am:851: library has 'gfilter_avx512' as canonical name (possible typo)
src/Makefile.am:857: warning: variable 'gfilter_avx512bw_LDADD' is defined but no program or
src/Makefile.am:857: library has 'gfilter_avx512bw' as canonical name (possible typo)
src/Makefile.am:809: warning: variable 'gfilter_nosimd_LDADD' is defined but no program or
src/Makefile.am:809: library has 'gfilter_nosimd' as canonical name (possible typo)
src/Makefile.am:821: warning: variable 'gfilter_sse2_LDADD' is defined but no program or
src/Makefile.am:821: library has 'gfilter_sse2' as canonical name (possible typo)
src/Makefile.am:833: warning: variable 'gfilter_sse41_LDADD' is defined but no program or
src/Makefile.am:833: library has 'gfilter_sse41' as canonical name (possible typo)
src/Makefile.am:839: warning: variable 'gfilter_sse42_LDADD' is defined but no program or
src/Makefile.am:839: library has 'gfilter_sse42' as canonical name (possible typo)
src/Makefile.am:827: warning: variable 'gfilter_ssse3_LDADD' is defined but no program or
src/Makefile.am:827: library has 'gfilter_ssse3' as canonical name (possible typo)
src/Makefile.am:1131: warning: variable 'iit_pileup_LDADD' is defined but no program or
src/Makefile.am:1131: library has 'iit_pileup' as canonical name (possible typo)
src/Makefile.am:1153: warning: variable 'sam_sort_LDADD' is defined but no program or
src/Makefile.am:1153: library has 'sam_sort' as canonical name (possible typo)
src/Makefile.am:1171: warning: variable 'umi_correct_LDADD' is defined but no program or
src/Makefile.am:1171: library has 'umi_correct' as canonical name (possible typo)
src/Makefile.am:1190: warning: variable 'velocity_counts_LDADD' is defined but no program or
src/Makefile.am:1190: library has 'velocity_counts' as canonical name (possible typo)
src/Makefile.am:868: warning: variable 'compare2truth_LDFLAGS' is defined but no program or
src/Makefile.am:868: library has 'compare2truth' as canonical name (possible typo)
src/Makefile.am:1214: warning: variable 'gcount_bulk_LDFLAGS' is defined but no program or
src/Makefile.am:1214: library has 'gcount_bulk' as canonical name (possible typo)
src/Makefile.am:1240: warning: variable 'gcount_sc_LDFLAGS' is defined but no program or
src/Makefile.am:1240: library has 'gcount_sc' as canonical name (possible typo)
src/Makefile.am:214: warning: variable 'gexact_LDFLAGS' is defined but no program or
src/Makefile.am:214: library has 'gexact' as canonical name (possible typo)
src/Makefile.am:740: warning: variable 'gexact_arm_LDFLAGS' is defined but no program or
src/Makefile.am:740: library has 'gexact_arm' as canonical name (possible typo)
src/Makefile.am:770: warning: variable 'gexact_avx2_LDFLAGS' is defined but no program or
src/Makefile.am:770: library has 'gexact_avx2' as canonical name (possible typo)
src/Makefile.am:776: warning: variable 'gexact_avx512_LDFLAGS' is defined but no program or
src/Makefile.am:776: library has 'gexact_avx512' as canonical name (possible typo)
src/Makefile.am:782: warning: variable 'gexact_avx512bw_LDFLAGS' is defined but no program or
src/Makefile.am:782: library has 'gexact_avx512bw' as canonical name (possible typo)
src/Makefile.am:734: warning: variable 'gexact_nosimd_LDFLAGS' is defined but no program or
src/Makefile.am:734: library has 'gexact_nosimd' as canonical name (possible typo)
src/Makefile.am:746: warning: variable 'gexact_sse2_LDFLAGS' is defined but no program or
src/Makefile.am:746: library has 'gexact_sse2' as canonical name (possible typo)
src/Makefile.am:758: warning: variable 'gexact_sse41_LDFLAGS' is defined but no program or
src/Makefile.am:758: library has 'gexact_sse41' as canonical name (possible typo)
src/Makefile.am:764: warning: variable 'gexact_sse42_LDFLAGS' is defined but no program or
src/Makefile.am:764: library has 'gexact_sse42' as canonical name (possible typo)
src/Makefile.am:752: warning: variable 'gexact_ssse3_LDFLAGS' is defined but no program or
src/Makefile.am:752: library has 'gexact_ssse3' as canonical name (possible typo)
src/Makefile.am:221: warning: variable 'gfilter_LDFLAGS' is defined but no program or
src/Makefile.am:221: library has 'gfilter' as canonical name (possible typo)
src/Makefile.am:814: warning: variable 'gfilter_arm_LDFLAGS' is defined but no program or
src/Makefile.am:814: library has 'gfilter_arm' as canonical name (possible typo)
src/Makefile.am:844: warning: variable 'gfilter_avx2_LDFLAGS' is defined but no program or
src/Makefile.am:844: library has 'gfilter_avx2' as canonical name (possible typo)
src/Makefile.am:850: warning: variable 'gfilter_avx512_LDFLAGS' is defined but no program or
src/Makefile.am:850: library has 'gfilter_avx512' as canonical name (possible typo)
src/Makefile.am:856: warning: variable 'gfilter_avx512bw_LDFLAGS' is defined but no program or
src/Makefile.am:856: library has 'gfilter_avx512bw' as canonical name (possible typo)
src/Makefile.am:808: warning: variable 'gfilter_nosimd_LDFLAGS' is defined but no program or
src/Makefile.am:808: library has 'gfilter_nosimd' as canonical name (possible typo)
src/Makefile.am:820: warning: variable 'gfilter_sse2_LDFLAGS' is defined but no program or
src/Makefile.am:820: library has 'gfilter_sse2' as canonical name (possible typo)
src/Makefile.am:832: warning: variable 'gfilter_sse41_LDFLAGS' is defined but no program or
src/Makefile.am:832: library has 'gfilter_sse41' as canonical name (possible typo)
src/Makefile.am:838: warning: variable 'gfilter_sse42_LDFLAGS' is defined but no program or
src/Makefile.am:838: library has 'gfilter_sse42' as canonical name (possible typo)
src/Makefile.am:826: warning: variable 'gfilter_ssse3_LDFLAGS' is defined but no program or
src/Makefile.am:826: library has 'gfilter_ssse3' as canonical name (possible typo)
src/Makefile.am:1130: warning: variable 'iit_pileup_LDFLAGS' is defined but no program or
src/Makefile.am:1130: library has 'iit_pileup' as canonical name (possible typo)
src/Makefile.am:1152: warning: variable 'sam_sort_LDFLAGS' is defined but no program or
src/Makefile.am:1152: library has 'sam_sort' as canonical name (possible typo)
src/Makefile.am:1170: warning: variable 'umi_correct_LDFLAGS' is defined but no program or
src/Makefile.am:1170: library has 'umi_correct' as canonical name (possible typo)
src/Makefile.am:1189: warning: variable 'velocity_counts_LDFLAGS' is defined but no program or
src/Makefile.am:1189: library has 'velocity_counts' as canonical name (possible typo)
parallel-tests: installing 'config/test-driver'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds'
rm -Rf src/simde
dh_auto_configure -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap --disable-simd
cd build && ../configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --disable-simd
checking package version... 2024-11-20
checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking target system type... i686-pc-linux-gnu
checking for non-Intel CPU... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking for gcc option to enable large file support... -D_FILE_OFFSET_BITS=64
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports the include directive... yes (GNU style)
checking whether make supports nested variables... yes
checking xargs -n works... yes
checking dependency style of gcc... none
checking whether to enable maintainer-specific portions of Makefiles... no
checking bindir... /usr/lib/gmap
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking for C compiler vendor... gnu
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... 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 dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for fcntl.h... yes
checking for limits.h... 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 for inline... inline
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... 4
checking size of unsigned long long... 8
checking size of off_t... 8
checking for declarations of fseeko and ftello... yes
checking whether alloca is enabled... not specified so disabled by default
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 MADV_SEQUENTIAL in madvise... yes
checking for SHM_NORESERVE in shmget... 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... no
checking for sigaction... yes
checking for shmget... yes
checking for shmctl... yes
checking for shmat... yes
checking for shmdt... yes
checking for semget... yes
checking for semctl... yes
checking for semop... 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 gcc options needed to detect all undeclared functions... none needed
checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes
checking whether __builtin_popcount is declared... yes
checking whether __builtin_popcount works... yes
checking whether __builtin_clz is declared... yes
checking whether __builtin_clz works... yes
checking whether __builtin_ctz is declared... yes
checking whether __builtin_ctz works... yes
checking whether __builtin_clzll is declared... yes
checking whether __builtin_clzll works... yes
checking whether __builtin_ctzll is declared... yes
checking whether __builtin_ctzll works... yes
checking for bsr instruction in assembly... no
checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... yes
checking if compiler has STTNI commands... yes
checking for _mm_extract_epi64... yes
checking for _mm_popcnt_u64... yes
checking for whether simd is enabled... disabled
checking for sse2 support... yes
checking for ssse3 support... yes
checking for sse4.1 support... yes
checking for sse4.2 support... yes
checking for popcnt support... yes
checking for bmi1 support... no
checking for avx2 support... yes
checking for bmi2 support... no
checking for avx512 support... no
checking for avx512bw and avx512vl support... no
checking whether C compiler accepts -msse2... yes
checking for emmintrin.h header file... yes
checking whether C compiler accepts -msse2 -mssse3... yes
checking for tmmintrin.h header file... yes
checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes
checking for smmintrin.h header file... yes
checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes
checking for nmmintrin.h header file... yes
checking for mm_popcnt run support... yes
checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes
checking for immintrin.h header file... yes
checking gmapdb... /var/cache/gmap
checking for zlib support... enabled
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... yes
checking for bzlib support... enabled
checking for bzlib.h... yes
checking for BZ2_bzReadOpen in -lbz2... yes
checking for BZ2_bzRead in -lbz2... yes
checking for BZ2_bzReadClose in -lbz2... yes
checking if bzlib package is complete... working
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating util/Makefile
config.status: creating util/gmap_process.pl
config.status: creating util/gmap_build.pl
config.status: creating util/gmap_cat.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/ensembl_genes.pl
config.status: creating util/gtf_splicesites.pl
config.status: creating util/gtf_transcript_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/gvf_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
checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration
checking standard linker flags to be used...
checking pthread compiler flags to be used...
checking popcnt flags to be used... -mpopcnt
checking compile level... none
make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds'
dh_auto_build
cd build && make -j21
make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
Making all in src
make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
make all-am
make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
In function 'update',
inlined from 'finish' at ../../src/md5.c:241:3,
inlined from 'MD5_compute' at ../../src/md5.c:273:10:
../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 8 [-Wstringop-overflow=]
212 | transform(state,&(input[i]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]'
../../src/md5.c: In function 'MD5_compute':
../../src/md5.c:104:1: note: in a call to function 'transform'
104 | transform (UINT4 state[4], unsigned char block[64]) {
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
In file included from ../../src/compress-write.c:21:
../../src/compress-write.c: In function 'Compress_cat':
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS'
847 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c
In function 'update',
inlined from 'finish' at ../../src/md5.c:241:3,
inlined from 'MD5_compute' at ../../src/md5.c:273:10:
../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 8 [-Wstringop-overflow=]
212 | transform(state,&(input[i]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]'
../../src/md5.c: In function 'MD5_compute':
../../src/md5.c:104:1: note: in a call to function 'transform'
104 | transform (UINT4 state[4], unsigned char block[64]) {
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c
../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack':
../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n",
| ~~^
| |
| long int
| %d
936 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING);
| ~~~
| |
| int
../../src/indexdb.c: In function 'positions_read_multiple':
../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1953 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c
In file included from ../../src/sarray-write.c:34:
../../src/sarray-write.c: In function 'Sarray_write_csa':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT'
808 | FREAD_UINT(&sa_i,sa_fp);
| ^~~~~~~~~~
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS'
815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT'
828 | FREAD_UINT(&sa_i,sa_fp);
| ^~~~~~~~~~
../../src/sarray-write.c: In function 'Sarray_compute_lcp':
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS'
1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT'
1033 | FREAD_UINT(&SA_i,fp);
| ^~~~~~~~~~
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS'
1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT'
1080 | FREAD_UINT(&rank_i,fp);
| ^~~~~~~~~~
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS'
1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS'
1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT'
1140 | FREAD_UINT(&rank_i,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT'
1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */
| ^~~~~~~~~~
../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes':
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS'
1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT'
1257 | FREAD_UINT(&SA_i,fp);
| ^~~~~~~~~~
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS'
1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT'
1304 | FREAD_UINT(&rank_i,fp);
| ^~~~~~~~~~
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS'
1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS'
1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT'
1370 | FREAD_UINT(&rank_i,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT'
1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */
| ^~~~~~~~~~
../../src/sarray-write.c: In function 'Sarray_discriminating_chars':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT'
2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */
| ^~~~~~~~~~
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS'
2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT'
2443 | FREAD_UINT(&SA_i,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack':
../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n",
| ~~^
| |
| long int
| %d
936 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING);
| ~~~
| |
| int
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
../../src/indexdb.c: In function 'positions_read_multiple':
../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1953 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/compress-write.c:21:
../../src/compress-write.c: In function 'Compress_cat':
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS'
847 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c
In file included from ../../src/compress-write.c:21:
../../src/compress-write.c: In function 'Compress_cat':
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS'
847 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c
../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack':
../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n",
| ~~^
| |
| long int
| %d
936 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING);
| ~~~
| |
| int
../../src/indexdb.c: In function 'positions_read_multiple':
../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1953 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
In function 'update',
inlined from 'finish' at ../../src/md5.c:241:3,
inlined from 'MD5_compute' at ../../src/md5.c:273:10:
../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 8 [-Wstringop-overflow=]
212 | transform(state,&(input[i]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]'
../../src/md5.c: In function 'MD5_compute':
../../src/md5.c:104:1: note: in a call to function 'transform'
104 | transform (UINT4 state[4], unsigned char block[64]) {
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
In file included from ../../src/compress-write.c:21:
../../src/compress-write.c: In function 'Compress_cat':
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS'
847 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c
../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack':
../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n",
| ~~^
| |
| long int
| %d
936 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING);
| ~~~
| |
| int
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c
../../src/indexdb.c: In function 'positions_read_multiple':
../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1953 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
In function 'update',
inlined from 'finish' at ../../src/md5.c:241:3,
inlined from 'MD5_compute' at ../../src/md5.c:273:10:
../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 8 [-Wstringop-overflow=]
212 | transform(state,&(input[i]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]'
../../src/md5.c: In function 'MD5_compute':
../../src/md5.c:104:1: note: in a call to function 'transform'
104 | transform (UINT4 state[4], unsigned char block[64]) {
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
In file included from ../../src/compress-write.c:21:
../../src/compress-write.c: In function 'Compress_cat':
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS'
847 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c
../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack':
../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n",
| ~~^
| |
| long int
| %d
936 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING);
| ~~~
| |
| int
../../src/indexdb.c: In function 'positions_read_multiple':
../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1953 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c
In function 'update',
inlined from 'finish' at ../../src/md5.c:241:3,
inlined from 'MD5_compute' at ../../src/md5.c:273:10:
../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 8 [-Wstringop-overflow=]
212 | transform(state,&(input[i]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]'
../../src/md5.c: In function 'MD5_compute':
../../src/md5.c:104:1: note: in a call to function 'transform'
104 | transform (UINT4 state[4], unsigned char block[64]) {
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
In file included from ../../src/transcriptome.c:29:
../../src/transcriptome.c: In function 'Transcriptome_new':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT'
159 | FREAD_INT(&trnum,fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT'
184 | FREAD_INT(&divint,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
In file included from ../../src/compress-write.c:21:
../../src/compress-write.c: In function 'Compress_cat':
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS'
847 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c
In function 'update',
inlined from 'finish' at ../../src/md5.c:241:3,
inlined from 'MD5_compute' at ../../src/md5.c:273:10:
../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 8 [-Wstringop-overflow=]
212 | transform(state,&(input[i]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]'
../../src/md5.c: In function 'MD5_compute':
../../src/md5.c:104:1: note: in a call to function 'transform'
104 | transform (UINT4 state[4], unsigned char block[64]) {
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c
../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack':
../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n",
| ~~^
| |
| long int
| %d
936 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING);
| ~~~
| |
| int
../../src/indexdb.c: In function 'positions_read_multiple':
../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1953 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c
../../src/samheader.c: In function 'SAM_header_change_HD_tosorted':
../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
241 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
In file included from ../../src/compress-write.c:21:
../../src/compress-write.c: In function 'Compress_cat':
../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS'
847 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c
In function 'update',
inlined from 'finish' at ../../src/md5.c:241:3,
inlined from 'MD5_compute' at ../../src/md5.c:273:10:
../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 8 [-Wstringop-overflow=]
212 | transform(state,&(input[i]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]'
../../src/md5.c: In function 'MD5_compute':
../../src/md5.c:104:1: note: in a call to function 'transform'
104 | transform (UINT4 state[4], unsigned char block[64]) {
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c
../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack':
../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n",
| ~~^
| |
| long int
| %d
936 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING);
| ~~~
| |
| int
../../src/indexdb.c: In function 'positions_read_multiple_large':
../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1897 | read(positions_high_fd,buffer,1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1901 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c
../../src/samheader.c: In function 'SAM_header_change_HD_tosorted':
../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
241 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c
In file included from ../../src/transcriptome.c:29:
../../src/transcriptome.c: In function 'Transcriptome_new':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT'
159 | FREAD_INT(&trnum,fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT'
184 | FREAD_INT(&divint,fp);
| ^~~~~~~~~
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c
../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack':
../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n",
| ~~^
| |
| long int
| %d
936 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING);
| ~~~
| |
| int
../../src/indexdb.c: In function 'positions_read_multiple':
../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1953 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c
In file included from /usr/include/stdio.h:970,
from ../../src/shortread.h:8,
from ../../src/shortread.c:12:
In function 'fgets',
inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14:
/usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
316 | return __fgets_chk_warn (__s, __sz, __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c
../../src/samheader.c: In function 'SAM_header_change_HD_tosorted':
../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
241 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c
In file included from /usr/include/stdio.h:970,
from ../../src/filestring.h:5,
from ../../src/single-cell.h:9,
from ../../src/single-cell.c:12:
In function 'fgets',
inlined from 'input_oneline' at ../../src/single-cell.c:169:14,
inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25,
inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10,
inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10:
/usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
316 | return __fgets_chk_warn (__s, __sz, __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'fgets',
inlined from 'input_oneline' at ../../src/single-cell.c:169:14,
inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4,
inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10,
inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10:
/usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
316 | return __fgets_chk_warn (__s, __sz, __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c
../../src/littleendian.c: In function 'Littleendian_write_char':
../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint':
../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8':
../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint':
../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_char':
../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint':
../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint':
../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_write_uint8':
../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8':
../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c
../../src/access.c: In function 'Access_allocate_shared':
../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
| ~~^
| |
| long unsigned int
| %u
885 | filename,*len);
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap':
../../src/access.c:1012:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1012 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1013 | filename,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_offset':
../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1085 | fd,offset,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'Access_mmap_and_preload':
../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~
| |
| size_t {aka unsigned int}
../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n",
| ~~^
| |
| long long int
| %d
1318 | filename,*len,length,errno,strerror(errno));
| ~~~~~~
| |
| size_t {aka unsigned int}
../../src/access.c: In function 'copy_memory_from_file':
../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c: In function 'copy_limited_from_file':
../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
599 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
607 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
615 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c
In file included from ../../src/iit-read-univ.c:12:
../../src/iit-read-univ.c: In function 'read_tree_univ':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_intervals_univ':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c
../../src/iit-read-univ.c: In function 'read_annotations':
../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1397 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c: In function 'read_words_debug':
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c
In file included from ../../src/iit-read.c:12:
../../src/iit-read.c: In function 'IIT_read_divint':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'IIT_read':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_tree':
../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_intervals':
../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'read_words':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
../../src/iit-read.c: In function 'read_annotations':
../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2486 | read(new->fd,new->values,new->value_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2513 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c: In function 'IIT_debug':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
../../src/iit-read.c: In function 'read_words_debug':
../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
In file included from ../../src/transcriptome.c:29:
../../src/transcriptome.c: In function 'Transcriptome_new':
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT'
159 | FREAD_INT(&trnum,fp);
| ^~~~~~~~~
../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT'
184 | FREAD_INT(&divint,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c
../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack':
../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n",
| ~~^
| |
| long int
| %d
936 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING);
| ~~~
| |
| int
../../src/indexdb.c: In function 'positions_read_multiple_large':
../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1897 | read(positions_high_fd,buffer,1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1901 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c
In file included from /usr/include/stdio.h:970,
from ../../src/shortread.h:8,
from ../../src/shortread.c:12:
In function 'fgets',
inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14:
/usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
316 | return __fgets_chk_warn (__s, __sz, __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c
../../src/altsplice.c: In function 'Altsplice_print':
../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
124 | printf(":%u,len:%d,%llu(%d,%d)",
| ~^
| |
| int
| %lld
125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]);
| ~~~~~~~~~~~~~~~~~~~~~~
| |
| Univcoord_T {aka long long unsigned int}
../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=]
124 | printf(":%u,len:%d,%llu(%d,%d)",
| ~~~^
| |
| long long unsigned int
| %u
125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]);
| ~~~~~~~~~~~~~
| |
| int
../../src/path.c: In function 'Path_print':
../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int Univcoord_T {aka long long unsigned int}
| %llu
../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
3336 | printf("%d[%u..%u]:%s ",
| ~^
| |
| unsigned int
| %llu
3337 | this->chrnum,this->chroffset,this->chrhigh,
| ~~~~~~~~~~~~~~~
| |
| Univcoord_T {aka long long unsigned int}
../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
3336 | printf("%d[%u..%u]:%s ",
| ~^
| |
| unsigned int
| %llu
3337 | this->chrnum,this->chroffset,this->chrhigh,
| ~~~~~~~~~~~~~
| |
| Univcoord_T {aka long long unsigned int}
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c
../../src/stage1hr.c: In function 'Stage1_list_extension':
../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int Univcoord_T {aka long long unsigned int}
| %llu
../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int Univcoord_T {aka long long unsigned int}
| %llu
../../src/stage1hr.c: In function 'Stage1_list_exhaustive':
../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
1333 | printf("%u %d..%d %d\n",
| ~^
| |
| unsigned int
| %llu
1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i],
| ~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| Univcoord_T {aka long long unsigned int}
../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
1339 | printf("%u %d..%d %d\n",
| ~^
| |
| unsigned int
| %llu
1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| Univcoord_T {aka long long unsigned int}
../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals':
../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int Univcoord_T {aka long long unsigned int}
| %llu
../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int Univcoord_T {aka long long unsigned int}
| %llu
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c
../../src/samheader.c: In function 'SAM_header_change_HD_tosorted':
../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
241 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c
../../src/support.c: In function 'Support_dump':
../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */
| ~^
| |
| unsigned int
| %llu
../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */
| ~^
| |
| unsigned int
| %llu
../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */
| ~^
| |
| unsigned int
| %llu
../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=]
1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */
| ~^
| |
| unsigned int
| %llu
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c
gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c
In file included from /usr/include/stdio.h:970,
from ../../src/filestring.h:5,
from ../../src/single-cell.h:9,
from ../../src/single-cell.c:12:
In function 'fgets',
inlined from 'input_oneline' at ../../src/single-cell.c:169:14,
inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25,
inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10,
inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10:
/usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
316 | return __fgets_chk_warn (__s, __sz, __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'fgets',
inlined from 'input_oneline' at ../../src/single-cell.c:169:14,
inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4,
inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10,
inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10:
/usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
316 | return __fgets_chk_warn (__s, __sz, __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm
gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -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-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm
gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -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-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm
gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm
gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -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-semaphore.o iit_store-access.o iit_store-doublelist.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-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm
gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -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-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm
gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -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-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm
gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -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-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm
gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm
gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm
gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm
gcc -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm
gcc -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm
gcc -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm
gcc -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm
make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
Making all in util
make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util'
cp gmap_process.pl gmap_process
cp gmap_build.pl gmap_build
cp gmap_cat.pl gmap_cat
cp md_coords.pl md_coords
cp fa_coords.pl fa_coords
cp psl_splicesites.pl psl_splicesites
cp psl_introns.pl psl_introns
cp psl_genes.pl psl_genes
cp ensembl_genes.pl ensembl_genes
cp gtf_splicesites.pl gtf_splicesites
chmod +x gmap_cat
chmod +x gmap_process
chmod +x gmap_build
chmod +x md_coords
chmod +x fa_coords
chmod +x psl_splicesites
chmod +x psl_introns
chmod +x psl_genes
chmod +x ensembl_genes
chmod +x gtf_splicesites
cp gtf_introns.pl gtf_introns
cp gtf_genes.pl gtf_genes
cp gtf_transcript_splicesites.pl gtf_transcript_splicesites
cp gff3_splicesites.pl gff3_splicesites
cp gff3_introns.pl gff3_introns
chmod +x gtf_introns
chmod +x gtf_genes
cp gff3_genes.pl gff3_genes
chmod +x gtf_transcript_splicesites
chmod +x gff3_splicesites
cp dbsnp_iit.pl dbsnp_iit
chmod +x gff3_introns
cp gvf_iit.pl gvf_iit
cp vcf_iit.pl vcf_iit
chmod +x gff3_genes
chmod +x dbsnp_iit
chmod +x gvf_iit
chmod +x vcf_iit
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Making all in tests
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make[3]: Nothing to be done for 'all-am'.
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make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds'
dh_auto_test --no-parallel
cd build && make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
Making check in src
make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
Making check in util
make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util'
Making check in tests
make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests'
make check-TESTS
make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests'
make[5]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests'
PASS: align.test
PASS: coords1.test
PASS: setup1.test
PASS: iit.test
============================================================================
Testsuite summary for gmap 2024-11-20
============================================================================
# TOTAL: 4
# PASS: 4
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
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make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--builddir=build
dh_prep -O--builddir=build
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds'
mkdir -p /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1
/usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Mapping and Alignment Program' \
/build/reproducible-path/gmap-2024-11-20+ds/build/src/gmap |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap.1
/usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Short-read Nucleotide Alignment Program' \
/build/reproducible-path/gmap-2024-11-20+ds/build/src/gsnap |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnap.1
/usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Mapping and Alignment Program' \
/build/reproducible-path/gmap-2024-11-20+ds/build/src/gmapl |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmapl.1
/usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Short-read Nucleotide Alignment Program' \
/build/reproducible-path/gmap-2024-11-20+ds/build/src/gsnapl |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnapl.1
/usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Tool for genome database creation for GMAP or GSNAP' \
/build/reproducible-path/gmap-2024-11-20+ds/build/util/gmap_build |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap_build.1
dh_auto_install
cd build && make -j21 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
Making install in src
make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
make[4]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap'
/usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap'
make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src'
Making install in util
make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util'
make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util'
make[4]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap'
/usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap'
make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util'
make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util'
Making install in tests
make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests'
make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/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/reproducible-path/gmap-2024-11-20+ds/build/tests'
make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests'
make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
make[4]: Nothing to be done for 'install-exec-am'.
/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap
make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build'
make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds'
mkdir -p debian/gmap/usr/bin
dh_install
for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \
cd /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap/; \
ls -1 gmap*.* gsnap*.* `; do \
ln -s /usr/lib/gmap/$bin debian/gmap/usr/bin/$bin; \
done
make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds'
dh_installdocs -O--builddir=build
dh_installchangelogs -O--builddir=build
debian/rules override_dh_installexamples
make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds'
mkdir /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples
find tests/ -type f -print0 | xargs -0r sed -i \
-e 's@/build/reproducible-path/gmap-2024-11-20+ds@«buildpath»@g' \
-e 's@\#! /bin/bash@\#! /bin/sh@g'
tar --sort=name \
--mtime="@1740521462" \
--owner=root --group=root --numeric-owner \
--mode=go=rX,u+rw,a-s \
--exclude='*/align.log' \
--exclude='*/Makefile' \
--exclude='*/Makefile.in' \
-cJf /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples/tests.tar.xz tests
make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds'
dh_installman -O--builddir=build
dh_installsystemduser -O--builddir=build
dh_lintian -O--builddir=build
dh_perl -O--builddir=build
dh_link -O--builddir=build
dh_strip_nondeterminism -O--builddir=build
dh_compress -O--builddir=build
dh_fixperms -O--builddir=build
dh_missing -O--builddir=build
dh_dwz -a -O--builddir=build
dh_strip -a -O--builddir=build
dh_makeshlibs -a -O--builddir=build
dh_shlibdeps -a -O--builddir=build
dh_installdeb -O--builddir=build
dh_gencontrol -O--builddir=build
dh_md5sums -O--builddir=build
dh_builddeb -O--builddir=build
dpkg-deb: building package 'gmap-dbgsym' in '../gmap-dbgsym_2024-11-20+ds-2_i386.deb'.
dpkg-deb: building package 'gmap' in '../gmap_2024-11-20+ds-2_i386.deb'.
dpkg-genbuildinfo --build=binary -O../gmap_2024-11-20+ds-2_i386.buildinfo
dpkg-genchanges --build=binary -O../gmap_2024-11-20+ds-2_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/11997/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/11997/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/11997 and its subdirectories
I: Current time: Sun Apr 5 05:52:24 +14 2026
I: pbuilder-time-stamp: 1775317944