I: pbuilder: network access will be disabled during build
I: Current time: Sat Apr 15 08:33:50 +14 2023
I: pbuilder-time-stamp: 1681497230
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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: Copying source file
I: copying [gmap_2021-12-17+ds-3.dsc]
I: copying [./gmap_2021-12-17+ds.orig.tar.xz]
I: copying [./gmap_2021-12-17+ds-3.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Oct 4 08:26:58 2022 +14
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./gmap_2021-12-17+ds-3.dsc: no acceptable signature found
dpkg-source: info: extracting gmap in gmap-2021-12-17+ds
dpkg-source: info: unpacking gmap_2021-12-17+ds.orig.tar.xz
dpkg-source: info: unpacking gmap_2021-12-17+ds-3.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
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/849010/tmp/hooks/D01_modify_environment starting
debug: Running on ionos1-amd64.
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
lrwxrwxrwx 1 root root 4 Jan 6 03:20 /bin/sh -> dash
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/849010/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/849010/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME='pbuilder2'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='bb69f53a3ae64ed49f1093c65863ffa3'
LANG='C'
LANGUAGE='et_EE:et'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
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'
PPID='849010'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
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.5h1WZzeT/pbuilderrc_EC1J --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5h1WZzeT/b2 --logfile b2/build.log --extrapackages usrmerge gmap_2021-12-17+ds-3.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT-14'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://78.137.99.97:3128'
I: uname -a
Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash
-rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 21 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 21 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 21 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash
-rwxr-xr-x 1 root root 121904 Sep 21 2022 date
-rwxr-xr-x 1 root root 89240 Sep 21 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 21 2022 df
-rwxr-xr-x 1 root root 151344 Sep 21 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep
-rwxr-xr-x 1 root root 35664 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep
-rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt
-rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount
-rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep
-rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname
-rwxr-xr-x 1 root root 72824 Sep 21 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 24 02:40 login
-rwxr-xr-x 1 root root 151344 Sep 21 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk
-rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 24 00:02 more
-rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount
-rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 21 2022 mv
lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 21 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts
-rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed
lrwxrwxrwx 1 root root 4 Jan 6 03:20 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 21 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 24 00:02 su
-rwxr-xr-x 1 root root 39824 Sep 21 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar
-rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile
-rwxr-xr-x 1 root root 109616 Sep 21 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 21 2022 true
-rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount
-rwxr-xr-x 1 root root 43888 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 10 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 10 2022 znew
I: user script /srv/workspace/pbuilder/849010/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: amd64
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), help2man, libbz2-dev, zlib1g-dev, debhelper
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19596 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 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.
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:
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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{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, 34 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.9 MB of archives. After unpacking 74.5 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Fetched 19.9 MB in 1s (28.0 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ...
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(Reading database ... 19596 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_amd64.deb ...
Unpacking liblocale-gettext-perl (1.07-5) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../09-libpipeline1_1.5.7-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../10-man-db_2.11.2-2_amd64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.19-3_amd64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:amd64.
Preparing to unpack .../23-libelf1_0.188-2.1_amd64.deb ...
Unpacking libelf1:amd64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../24-dwz_0.15-1_amd64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../25-libicu72_72.1-3_amd64.deb ...
Unpacking libicu72:amd64 (72.1-3) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.21-12_amd64.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-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 .../29-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package help2man.
Preparing to unpack .../31-help2man_1.49.3_amd64.deb ...
Unpacking help2man (1.49.3) ...
Selecting previously unselected package libbz2-dev:amd64.
Preparing to unpack .../32-libbz2-dev_1.0.8-5+b1_amd64.deb ...
Unpacking libbz2-dev:amd64 (1.0.8-5+b1) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../33-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ...
Setting up libpipeline1:amd64 (1.5.7-1) ...
Setting up libicu72:amd64 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
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Setting up libuchardet0:amd64 (0.0.7-1) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-5) ...
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 (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.4) ...
Processing triggers for libc-bin (2.36-8) ...
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
Reading package lists...
Building dependency tree...
Reading state information...
usrmerge is already the newest version (35).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: user script /srv/workspace/pbuilder/849010/tmp/hooks/A99_set_merged_usr starting
Re-configuring usrmerge...
removed '/etc/unsupported-skip-usrmerge-conversion'
The system has been successfully converted.
I: user script /srv/workspace/pbuilder/849010/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/gmap-2021-12-17+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_2021-12-17+ds-3_source.changes
dpkg-buildpackage: info: source package gmap
dpkg-buildpackage: info: source version 2021-12-17+ds-3
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 amd64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
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configure.ac:87: installing 'config/config.guess'
configure.ac:87: installing 'config/config.sub'
configure.ac:111: installing 'config/install-sh'
configure.ac:111: installing 'config/missing'
Makefile.am: installing './INSTALL'
src/Makefile.am: installing 'config/depcomp'
src/Makefile.am:995: warning: variable 'dist_bulk_counts_SOURCES' is defined but no program or
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src/Makefile.am:911: warning: variable 'dist_iit_pileup_SOURCES' is defined but no program or
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src/Makefile.am:951: warning: variable 'dist_umi_correct_SOURCES' is defined but no program or
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src/Makefile.am:600: warning: variable 'uniqscan_LDADD' is defined but no program or
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src/Makefile.am:655: warning: variable 'uniqscanl_LDADD' is defined but no program or
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src/Makefile.am:969: warning: variable 'velocity_counts_LDADD' is defined but no program or
src/Makefile.am:969: library has 'velocity_counts' as canonical name (possible typo)
src/Makefile.am:993: warning: variable 'bulk_counts_LDFLAGS' is defined but no program or
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src/Makefile.am:909: warning: variable 'iit_pileup_LDFLAGS' is defined but no program or
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src/Makefile.am:949: warning: variable 'umi_correct_LDFLAGS' is defined but no program or
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src/Makefile.am:968: warning: variable 'velocity_counts_LDFLAGS' is defined but no program or
src/Makefile.am:968: 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/gmap-2021-12-17+ds'
dh_auto_configure -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2
./configure --build=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2
checking package version... 2021-12-17
loading default site script ./config.site
checking CFLAGS... -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-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 special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a 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 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 stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
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checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
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... 8
checking size of unsigned long long... 8
checking size of off_t... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether 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
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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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 for bsr instruction in assembly... yes
checking compiler is defective and requires an immediate in sse2 shift commands... no
checking for _mm_extract_epi64... yes
checking for _mm_popcnt_u64... yes
checking for whether simd is enabled... enabled
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... no
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 for user-selected SIMD level... sse2
checking gmapdb... /var/cache/gmap
checking MAX_STACK_READLENGTH... 300
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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security
checking standard linker flags to be used...
checking pthread compiler flags to be used...
checking popcnt flags to be used... -mpopcnt
checking compile level... sse2
checking SSE2 compiler flags to be used... -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2
make[1]: Leaving directory '/build/gmap-2021-12-17+ds'
dh_auto_build
make -j15
make[1]: Entering directory '/build/gmap-2021-12-17+ds'
Making all in src
make[2]: Entering directory '/build/gmap-2021-12-17+ds/src'
make all-am
make[3]: Entering directory '/build/gmap-2021-12-17+ds/src'
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo './'`gmap_select.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo './'`gmapl_select.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
In file included from compress-write.c:21:
compress-write.c: In function 'Compress_cat':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS'
877 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb.c: In function 'positions_read_multiple':
indexdb.c:1951:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1951 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-regiondb-write.o `test -f 'regiondb-write.c' || echo './'`regiondb-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c
In file included from regiondb-write.c:19:
regiondb-write.c: In function 'Region_read':
littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
regiondb-write.c:478:3: note: in expansion of macro 'FREAD_USHORTS'
478 | FREAD_USHORTS(buffer->offsets,offsets_size,fp);
| ^~~~~~~~~~~~~
littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
regiondb-write.c:479:3: note: in expansion of macro 'FREAD_USHORTS'
479 | FREAD_USHORTS(buffer->positions,REGION_LENGTH,fp);
| ^~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo './'`tableint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-list.o `test -f 'list.c' || echo './'`list.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb.c: In function 'positions_read_multiple':
indexdb.c:1951:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1951 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
In file included from compress-write.c:21:
compress-write.c: In function 'Compress_cat':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS'
877 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo './'`indexdb-cat.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
bigendian.c: In function 'Bigendian_write_char':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo './'`gsnap_select.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo './'`gsnapl_select.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c
In file included from compress-write.c:21:
compress-write.c: In function 'Compress_cat':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS'
877 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
indexdb.c: In function 'positions_read_multiple':
indexdb.c:1951:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1951 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
In file included from compress-write.c:21:
compress-write.c: In function 'Compress_cat':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS'
877 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function 'positions_read_multiple':
indexdb.c:1951:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1951 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-regiondb-write.o `test -f 'regiondb-write.c' || echo './'`regiondb-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
In file included from regiondb-write.c:19:
regiondb-write.c: In function 'Region_read':
littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
regiondb-write.c:478:3: note: in expansion of macro 'FREAD_USHORTS'
478 | FREAD_USHORTS(buffer->offsets,offsets_size,fp);
| ^~~~~~~~~~~~~
littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
regiondb-write.c:479:3: note: in expansion of macro 'FREAD_USHORTS'
479 | FREAD_USHORTS(buffer->positions,REGION_LENGTH,fp);
| ^~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-md5.o `test -f 'md5.c' || echo './'`md5.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-genome.o `test -f 'genome.c' || echo './'`genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
In file included from compress-write.c:21:
compress-write.c: In function 'Compress_cat':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS'
877 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb.c: In function 'positions_read_multiple':
indexdb.c:1951:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1951 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-regiondb-write.o `test -f 'regiondb-write.c' || echo './'`regiondb-write.c
In file included from regiondb-write.c:19:
regiondb-write.c: In function 'Region_read':
littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
regiondb-write.c:478:3: note: in expansion of macro 'FREAD_USHORTS'
478 | FREAD_USHORTS(buffer->offsets,offsets_size,fp);
| ^~~~~~~~~~~~~
littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
regiondb-write.c:479:3: note: in expansion of macro 'FREAD_USHORTS'
479 | FREAD_USHORTS(buffer->positions,REGION_LENGTH,fp);
| ^~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-md5.o `test -f 'md5.c' || echo './'`md5.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-genome.o `test -f 'genome.c' || echo './'`genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-access.o `test -f 'access.c' || echo './'`access.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-trindex.o `test -f 'trindex.c' || echo './'`trindex.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-list.o `test -f 'list.c' || echo './'`list.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-samread.o `test -f 'samread.c' || echo './'`samread.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-getline.o `test -f 'getline.c' || echo './'`getline.c
samheader.c: In function 'SAM_header_change_HD_tosorted':
samheader.c:231:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-sam_sort.o `test -f 'sam_sort.c' || echo './'`sam_sort.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
sam_sort.c: In function 'process_no_dedup':
sam_sort.c:1393:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1393 | fgets(line,linelen+1,fp_sam); /* Will read linelen characters with '\n' and then '\0' */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sam_sort.c: In function 'print_results':
sam_sort.c:1009:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1009 | fgets(line,linelen+1,fp_sam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sam_sort.c:1026:15: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1026 | fgets(line,linelen+1,fp_sam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sam_sort.c: In function 'read_sam_files_for_hashseq':
sam_sort.c:1602:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
1602 | fgets(line,linelen+1,fp_sam); /* Will read linelen characters with '\n' and then '\0' */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c
samread.c: In function 'Samread_flag_duplicate':
samread.c:1076:29: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
1076 | sprintf(newflag_string,"%u",flag | DUPLICATE_READ);
| ^
In file included from /usr/include/stdio.h:906,
from samread.c:6:
In function 'sprintf',
inlined from 'Samread_flag_duplicate' at samread.c:1076:3:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 11 bytes into a destination of size 10
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo './'`md5.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c
In file included from compress-write.c:21:
compress-write.c: In function 'Compress_cat':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS'
877 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo './'`genome_canonical.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function 'positions_read_multiple':
indexdb.c:1951:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1951 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-block.o `test -f 'block.c' || echo './'`block.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-match.o `test -f 'match.c' || echo './'`match.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo './'`diag.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo './'`pair.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo './'`translation.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-request.o `test -f 'request.c' || echo './'`request.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-result.o `test -f 'result.c' || echo './'`result.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-output.o `test -f 'output.c' || echo './'`output.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo './'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
samheader.c: In function 'SAM_header_change_HD_tosorted':
samheader.c:231:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo './'`md5.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo './'`genome_canonical.c
In file included from compress-write.c:21:
compress-write.c: In function 'Compress_cat':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS'
877 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo './'`block.c
indexdb.c: In function 'positions_read_multiple_large':
indexdb.c:1895:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1895 | read(positions_high_fd,buffer,1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
indexdb.c:1899:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1899 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo './'`match.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo './'`diag.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo './'`pair.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo './'`translation.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo './'`request.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo './'`result.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo './'`output.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
samheader.c: In function 'SAM_header_change_HD_tosorted':
samheader.c:231:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo './'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
In file included from transcriptome.c:28:
transcriptome.c: In function 'Transcriptome_new':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
transcriptome.c:132:5: note: in expansion of macro 'FREAD_INT'
132 | FREAD_INT(&divint,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo './'`mergeinfo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function 'positions_read_multiple':
indexdb.c:1951:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1951 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-cigar.o `test -f 'cigar.c' || echo './'`cigar.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-samprint.o `test -f 'samprint.c' || echo './'`samprint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-substring.o `test -f 'substring.c' || echo './'`substring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo './'`junction.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo './'`exon.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo './'`bitvector.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo './'`method.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-ladder.o `test -f 'ladder.c' || echo './'`ladder.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo './'`concordance.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo './'`uintlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo './'`listpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo './'`splice.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo './'`indel.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-intersect.o `test -f 'intersect.c' || echo './'`intersect.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-terminal.o `test -f 'terminal.c' || echo './'`terminal.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo './'`single-cell.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo './'`request.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo './'`output.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo './'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c
samheader.c: In function 'SAM_header_change_HD_tosorted':
samheader.c:231:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
In file included from transcriptome.c:28:
transcriptome.c: In function 'Transcriptome_new':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
transcriptome.c:132:5: note: in expansion of macro 'FREAD_INT'
132 | FREAD_INT(&divint,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo './'`mergeinfo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-diagonals-heap.o `test -f 'merge-diagonals-heap.c' || echo './'`merge-diagonals-heap.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo './'`merge-uint8.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo './'`merge-diagonals-simd-uint8.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
indexdb.c: In function 'positions_read_multiple_large':
indexdb.c:1895:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1895 | read(positions_high_fd,buffer,1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
indexdb.c:1899:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1899 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-cigar.o `test -f 'cigar.c' || echo './'`cigar.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-samprint.o `test -f 'samprint.c' || echo './'`samprint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-substring.o `test -f 'substring.c' || echo './'`substring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo './'`junction.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo './'`exon.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo './'`bitvector.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo './'`method.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-ladder.o `test -f 'ladder.c' || echo './'`ladder.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo './'`concordance.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo './'`uint8listpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo './'`listpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo './'`splice.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo './'`indel.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-intersect.o `test -f 'intersect.c' || echo './'`intersect.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo './'`intersect-large.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-terminal.o `test -f 'terminal.c' || echo './'`terminal.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo './'`single-cell.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo './'`request.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo './'`output.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
samheader.c: In function 'SAM_header_change_HD_tosorted':
samheader.c:231:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo './'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo './'`md5.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo './'`reader.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-compress.o `test -f 'compress.c' || echo './'`compress.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-genome.o `test -f 'genome.c' || echo './'`genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
In file included from compress-write.c:21:
compress-write.c: In function 'Compress_cat':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS'
877 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo './'`genome_canonical.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-block.o `test -f 'block.c' || echo './'`block.c
indexdb.c: In function 'positions_read_multiple':
indexdb.c:1951:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1951 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-match.o `test -f 'match.c' || echo './'`match.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-diag.o `test -f 'diag.c' || echo './'`diag.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-intron.o `test -f 'intron.c' || echo './'`intron.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-pair.o `test -f 'pair.c' || echo './'`pair.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-translation.o `test -f 'translation.c' || echo './'`translation.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-request.o `test -f 'request.c' || echo './'`request.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-result.o `test -f 'result.c' || echo './'`result.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-output.o `test -f 'output.c' || echo './'`output.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo './'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
samheader.c: In function 'SAM_header_change_HD_tosorted':
samheader.c:231:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-md5.o `test -f 'md5.c' || echo './'`md5.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-reader.o `test -f 'reader.c' || echo './'`reader.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-compress.o `test -f 'compress.c' || echo './'`compress.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-genome.o `test -f 'genome.c' || echo './'`genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
In file included from compress-write.c:21:
compress-write.c: In function 'Compress_cat':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS'
877 | FREAD_UINTS(Buffer,3,fp);
| ^~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo './'`genome_canonical.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
indexdb.c: In function 'positions_read_multiple_large':
indexdb.c:1895:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1895 | read(positions_high_fd,buffer,1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
indexdb.c:1899:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1899 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-block.o `test -f 'block.c' || echo './'`block.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-match.o `test -f 'match.c' || echo './'`match.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-diag.o `test -f 'diag.c' || echo './'`diag.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-intron.o `test -f 'intron.c' || echo './'`intron.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-pair.o `test -f 'pair.c' || echo './'`pair.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-translation.o `test -f 'translation.c' || echo './'`translation.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-request.o `test -f 'request.c' || echo './'`request.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-result.o `test -f 'result.c' || echo './'`result.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-output.o `test -f 'output.c' || echo './'`output.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo './'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
samheader.c: In function 'SAM_header_change_HD_tosorted':
samheader.c:231:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse2-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo './'`reader.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo './'`compress.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-genome.o `test -f 'genome.c' || echo './'`genome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
In file included from transcriptome.c:28:
transcriptome.c: In function 'Transcriptome_new':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
transcriptome.c:132:5: note: in expansion of macro 'FREAD_INT'
132 | FREAD_INT(&divint,fp);
| ^~~~~~~~~
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo './'`mergeinfo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
indexdb.c: In function 'positions_read_multiple':
indexdb.c:1951:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1951 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-cigar.o `test -f 'cigar.c' || echo './'`cigar.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-samprint.o `test -f 'samprint.c' || echo './'`samprint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-substring.o `test -f 'substring.c' || echo './'`substring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-junction.o `test -f 'junction.c' || echo './'`junction.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-exon.o `test -f 'exon.c' || echo './'`exon.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-bitvector.o `test -f 'bitvector.c' || echo './'`bitvector.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-method.o `test -f 'method.c' || echo './'`method.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-ladder.o `test -f 'ladder.c' || echo './'`ladder.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-concordance.o `test -f 'concordance.c' || echo './'`concordance.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo './'`uintlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-listpool.o `test -f 'listpool.c' || echo './'`listpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-intron.o `test -f 'intron.c' || echo './'`intron.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-splice.o `test -f 'splice.c' || echo './'`splice.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-indel.o `test -f 'indel.c' || echo './'`indel.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-intersect.o `test -f 'intersect.c' || echo './'`intersect.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-terminal.o `test -f 'terminal.c' || echo './'`terminal.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-single-cell.o `test -f 'single-cell.c' || echo './'`single-cell.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-request.o `test -f 'request.c' || echo './'`request.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-output.o `test -f 'output.c' || echo './'`output.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo './'`printbuffer.c
samheader.c: In function 'SAM_header_change_HD_tosorted':
samheader.c:231:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-except.o `test -f 'except.c' || echo './'`except.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-assert.o `test -f 'assert.c' || echo './'`assert.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-mem.o `test -f 'mem.c' || echo './'`mem.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-list.o `test -f 'list.c' || echo './'`list.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function 'Littleendian_write_char':
littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8':
littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
45 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
littleendian.c: In function 'Littleendian_write_uint8_as_uint':
littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
60 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
bigendian.c: In function 'Bigendian_write_char':
bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
16 | write(fd,buf,1);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
299 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_write_uint8':
bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
367 | write(fd,buf,8);
| ^~~~~~~~~~~~~~~
bigendian.c: In function 'Bigendian_fileio_read_uint8':
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. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-access.o `test -f 'access.c' || echo './'`access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
access.c: In function 'copy_memory_from_file':
access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c: In function 'copy_limited_from_file':
access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
606 | fread(p,sizeof(UINT2),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
614 | fread(p,sizeof(UINT4),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
622 | fread(p,sizeof(UINT8),filesize/eltsize,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-reader.o `test -f 'reader.c' || echo './'`reader.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
In file included from iit-read-univ.c:12:
iit-read-univ.c: In function 'read_tree_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT'
1068 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT'
1070 | FREAD_INT(&(new->nodes[i].a),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT'
1071 | FREAD_INT(&(new->nodes[i].b),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT'
1072 | FREAD_INT(&(new->nodes[i].leftindex),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT'
1073 | FREAD_INT(&(new->nodes[i].rightindex),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_intervals_univ':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8'
1121 | FREAD_UINT8(&(new->intervals[i].low),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8'
1122 | FREAD_UINT8(&(new->intervals[i].high),fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT'
1123 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT'
1132 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT'
1134 | FREAD_UINT(&uint4,fp);
| ^~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT'
1136 | FREAD_INT(&(new->intervals[i].type),fp);
| ^~~~~~~~~
iit-read-univ.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT'
1196 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read-univ.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT'
1278 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-compress.o `test -f 'compress.c' || echo './'`compress.c
In file included from iit-read.c:12:
iit-read.c: In function 'IIT_read_divint':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT'
2588 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function 'IIT_read':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT'
3103 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-genome.o `test -f 'genome.c' || echo './'`genome.c
iit-read.c: In function 'read_tree':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_intervals':
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'read_words':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8'
2144 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT'
2150 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c
iit-read.c: In function 'read_annotations':
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function 'IIT_debug':
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT'
3524 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function 'read_words_debug':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8'
2288 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT'
2293 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c
In file included from transcriptome.c:28:
transcriptome.c: In function 'Transcriptome_new':
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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
transcriptome.c:132:5: note: in expansion of macro 'FREAD_INT'
132 | FREAD_INT(&divint,fp);
| ^~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo './'`mergeinfo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-merge-diagonals-heap.o `test -f 'merge-diagonals-heap.c' || echo './'`merge-diagonals-heap.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-merge-uint8.o `test -f 'merge-uint8.c' || echo './'`merge-uint8.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo './'`merge-diagonals-simd-uint8.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c
indexdb.c: In function 'positions_read_multiple_large':
indexdb.c:1895:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1895 | read(positions_high_fd,buffer,1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
indexdb.c:1899:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
1899 | read(positions_fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-cigar.o `test -f 'cigar.c' || echo './'`cigar.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-samprint.o `test -f 'samprint.c' || echo './'`samprint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-substring.o `test -f 'substring.c' || echo './'`substring.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-junction.o `test -f 'junction.c' || echo './'`junction.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-exon.o `test -f 'exon.c' || echo './'`exon.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-bitvector.o `test -f 'bitvector.c' || echo './'`bitvector.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-method.o `test -f 'method.c' || echo './'`method.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-ladder.o `test -f 'ladder.c' || echo './'`ladder.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-concordance.o `test -f 'concordance.c' || echo './'`concordance.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-uint8listpool.o `test -f 'uint8listpool.c' || echo './'`uint8listpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-listpool.o `test -f 'listpool.c' || echo './'`listpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-intron.o `test -f 'intron.c' || echo './'`intron.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-splice.o `test -f 'splice.c' || echo './'`splice.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-indel.o `test -f 'indel.c' || echo './'`indel.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-intersect.o `test -f 'intersect.c' || echo './'`intersect.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-intersect-large.o `test -f 'intersect-large.c' || echo './'`intersect-large.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-terminal.o `test -f 'terminal.c' || echo './'`terminal.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-single-cell.o `test -f 'single-cell.c' || echo './'`single-cell.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-request.o `test -f 'request.c' || echo './'`request.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-output.o `test -f 'output.c' || echo './'`output.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
samheader.c: In function 'SAM_header_change_HD_tosorted':
samheader.c:231:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
231 | fread(buffer,sizeof(char),CHUNK,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
236 | fread(buffer,sizeof(char),headerlen,input);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo './'`printbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-getline.o `test -f 'getline.c' || echo './'`getline.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse2-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c
gcc -DMAIN=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm
gcc -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm
gcc -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-genome128_hr.o gmapindex-genome128_consec.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-regiondb.o gmapindex-regiondb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm
gcc -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-genome128_hr.o snpindex-genome128_consec.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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-genome128_hr.o cmetindex-genome128_consec.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-regiondb-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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-genome128_hr.o atoiindex-genome128_consec.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-regiondb-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 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm
gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o sam_sort sam_sort-except.o sam_sort-assert.o sam_sort-mem.o sam_sort-littleendian.o sam_sort-bigendian.o sam_sort-intlist.o sam_sort-list.o sam_sort-stopwatch.o sam_sort-semaphore.o sam_sort-access.o sam_sort-univinterval.o sam_sort-interval.o sam_sort-uintlist.o sam_sort-filestring.o sam_sort-parserange.o sam_sort-iit-read-univ.o sam_sort-iit-read.o sam_sort-samheader.o sam_sort-samread.o sam_sort-bzip2.o sam_sort-getline.o sam_sort-datadir.o sam_sort-sam_sort.o -lz -lbz2 -lm
gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-genome128_hr.o gsnap_nosimd-genome128_consec.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-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-regiondb.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mdprint.o gsnap_nosimd-cigar.o gsnap_nosimd-samprint.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-substring.o gsnap_nosimd-junction.o gsnap_nosimd-exon.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcript.o gsnap_nosimd-method.o gsnap_nosimd-stage3hr.o gsnap_nosimd-ladder.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-maxent.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-intersect.o gsnap_nosimd-kmer-search.o gsnap_nosimd-path-solve.o gsnap_nosimd-extension-search.o gsnap_nosimd-segment-search.o gsnap_nosimd-terminal.o gsnap_nosimd-distant-rna.o gsnap_nosimd-distant-dna.o gsnap_nosimd-uint8table_rh.o gsnap_nosimd-uinttable_rh.o gsnap_nosimd-stage1hr.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-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm
gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-genome128_hr.o gsnapl_nosimd-genome128_consec.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.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-regiondb.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mdprint.o gsnapl_nosimd-cigar.o gsnapl_nosimd-samprint.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-substring.o gsnapl_nosimd-junction.o gsnapl_nosimd-exon.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcript.o gsnapl_nosimd-method.o gsnapl_nosimd-stage3hr.o gsnapl_nosimd-ladder.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-maxent.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-intersect.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-segment-search.o gsnapl_nosimd-terminal.o gsnapl_nosimd-distant-rna.o gsnapl_nosimd-distant-dna.o gsnapl_nosimd-uint8table_rh.o gsnapl_nosimd-stage1hr.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-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm
gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmap.sse2 gmap_sse2-except.o gmap_sse2-assert.o gmap_sse2-mem.o gmap_sse2-intlist.o gmap_sse2-uintlist.o gmap_sse2-list.o gmap_sse2-littleendian.o gmap_sse2-bigendian.o gmap_sse2-univinterval.o gmap_sse2-interval.o gmap_sse2-stopwatch.o gmap_sse2-semaphore.o gmap_sse2-access.o gmap_sse2-filestring.o gmap_sse2-iit-read-univ.o gmap_sse2-iit-read.o gmap_sse2-md5.o gmap_sse2-bzip2.o gmap_sse2-fopen.o gmap_sse2-sequence.o gmap_sse2-reader.o gmap_sse2-genomicpos.o gmap_sse2-compress.o gmap_sse2-compress-write.o gmap_sse2-gbuffer.o gmap_sse2-genome.o gmap_sse2-popcount.o gmap_sse2-dinucl_bits.o gmap_sse2-genome_canonical.o gmap_sse2-genome-write.o gmap_sse2-bitpack64-read.o gmap_sse2-bitpack64-readtwo.o gmap_sse2-indexdb.o gmap_sse2-oligo.o gmap_sse2-block.o gmap_sse2-chrom.o gmap_sse2-segmentpos.o gmap_sse2-chrnum.o gmap_sse2-uinttable_rh.o gmap_sse2-gregion.o gmap_sse2-match.o gmap_sse2-matchpool.o gmap_sse2-diagnostic.o gmap_sse2-stage1.o gmap_sse2-diag.o gmap_sse2-diagpool.o gmap_sse2-cmet.o gmap_sse2-atoi.o gmap_sse2-orderstat.o gmap_sse2-oligoindex_hr.o gmap_sse2-intron.o gmap_sse2-maxent.o gmap_sse2-maxent_hr.o gmap_sse2-pair.o gmap_sse2-pairpool.o gmap_sse2-cellpool.o gmap_sse2-stage2.o gmap_sse2-doublelist.o gmap_sse2-smooth.o gmap_sse2-splicestringpool.o gmap_sse2-splicetrie_build.o gmap_sse2-splicetrie.o gmap_sse2-boyer-moore.o gmap_sse2-dynprog.o gmap_sse2-dynprog_simd.o gmap_sse2-dynprog_single.o gmap_sse2-dynprog_genome.o gmap_sse2-dynprog_cdna.o gmap_sse2-dynprog_end.o gmap_sse2-translation.o gmap_sse2-pbinom.o gmap_sse2-changepoint.o gmap_sse2-stage3.o gmap_sse2-request.o gmap_sse2-result.o gmap_sse2-output.o gmap_sse2-inbuffer.o gmap_sse2-samheader.o gmap_sse2-printbuffer.o gmap_sse2-outbuffer.o gmap_sse2-chimera.o gmap_sse2-datadir.o gmap_sse2-parserange.o gmap_sse2-getline.o gmap_sse2-gmap.o -lz -lbz2 -lm
gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmapl.sse2 gmapl_sse2-except.o gmapl_sse2-assert.o gmapl_sse2-mem.o gmapl_sse2-intlist.o gmapl_sse2-uintlist.o gmapl_sse2-uint8list.o gmapl_sse2-list.o gmapl_sse2-littleendian.o gmapl_sse2-bigendian.o gmapl_sse2-univinterval.o gmapl_sse2-interval.o gmapl_sse2-stopwatch.o gmapl_sse2-semaphore.o gmapl_sse2-access.o gmapl_sse2-filestring.o gmapl_sse2-iit-read-univ.o gmapl_sse2-iit-read.o gmapl_sse2-md5.o gmapl_sse2-bzip2.o gmapl_sse2-fopen.o gmapl_sse2-sequence.o gmapl_sse2-reader.o gmapl_sse2-genomicpos.o gmapl_sse2-compress.o gmapl_sse2-compress-write.o gmapl_sse2-gbuffer.o gmapl_sse2-genome.o gmapl_sse2-popcount.o gmapl_sse2-dinucl_bits.o gmapl_sse2-genome_canonical.o gmapl_sse2-genome-write.o gmapl_sse2-bitpack64-read.o gmapl_sse2-bitpack64-readtwo.o gmapl_sse2-indexdb.o gmapl_sse2-oligo.o gmapl_sse2-block.o gmapl_sse2-chrom.o gmapl_sse2-segmentpos.o gmapl_sse2-chrnum.o gmapl_sse2-uinttable_rh.o gmapl_sse2-gregion.o gmapl_sse2-match.o gmapl_sse2-matchpool.o gmapl_sse2-diagnostic.o gmapl_sse2-stage1.o gmapl_sse2-diag.o gmapl_sse2-diagpool.o gmapl_sse2-cmet.o gmapl_sse2-atoi.o gmapl_sse2-orderstat.o gmapl_sse2-oligoindex_hr.o gmapl_sse2-intron.o gmapl_sse2-maxent.o gmapl_sse2-maxent_hr.o gmapl_sse2-pair.o gmapl_sse2-pairpool.o gmapl_sse2-cellpool.o gmapl_sse2-stage2.o gmapl_sse2-doublelist.o gmapl_sse2-smooth.o gmapl_sse2-splicestringpool.o gmapl_sse2-splicetrie_build.o gmapl_sse2-splicetrie.o gmapl_sse2-boyer-moore.o gmapl_sse2-dynprog.o gmapl_sse2-dynprog_simd.o gmapl_sse2-dynprog_single.o gmapl_sse2-dynprog_genome.o gmapl_sse2-dynprog_cdna.o gmapl_sse2-dynprog_end.o gmapl_sse2-translation.o gmapl_sse2-pbinom.o gmapl_sse2-changepoint.o gmapl_sse2-stage3.o gmapl_sse2-request.o gmapl_sse2-result.o gmapl_sse2-output.o gmapl_sse2-inbuffer.o gmapl_sse2-samheader.o gmapl_sse2-printbuffer.o gmapl_sse2-outbuffer.o gmapl_sse2-chimera.o gmapl_sse2-datadir.o gmapl_sse2-parserange.o gmapl_sse2-getline.o gmapl_sse2-gmap.o -lz -lbz2 -lm
gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnap.sse2 gsnap_sse2-except.o gsnap_sse2-assert.o gsnap_sse2-mem.o gsnap_sse2-intlist.o gsnap_sse2-uintlist.o gsnap_sse2-list.o gsnap_sse2-littleendian.o gsnap_sse2-bigendian.o gsnap_sse2-univinterval.o gsnap_sse2-interval.o gsnap_sse2-stopwatch.o gsnap_sse2-semaphore.o gsnap_sse2-access.o gsnap_sse2-filestring.o gsnap_sse2-iit-read-univ.o gsnap_sse2-iit-read.o gsnap_sse2-bzip2.o gsnap_sse2-reader.o gsnap_sse2-genomicpos.o gsnap_sse2-compress.o gsnap_sse2-genome.o gsnap_sse2-transcriptome.o gsnap_sse2-popcount.o gsnap_sse2-genome128_hr.o gsnap_sse2-genome128_consec.o gsnap_sse2-dinucl_bits.o gsnap_sse2-genome_sites.o gsnap_sse2-bitpack64-read.o gsnap_sse2-bitpack64-readtwo.o gsnap_sse2-mergeinfo.o gsnap_sse2-merge-uint4.o gsnap_sse2-merge-diagonals-simd-uint4.o gsnap_sse2-indexdb.o gsnap_sse2-regiondb.o gsnap_sse2-oligo.o gsnap_sse2-chrnum.o gsnap_sse2-maxent_hr.o gsnap_sse2-mdprint.o gsnap_sse2-cigar.o gsnap_sse2-samprint.o gsnap_sse2-mapq.o gsnap_sse2-fopen.o gsnap_sse2-shortread.o gsnap_sse2-substring.o gsnap_sse2-junction.o gsnap_sse2-exon.o gsnap_sse2-doublelist.o gsnap_sse2-bitvector.o gsnap_sse2-transcript.o gsnap_sse2-method.o gsnap_sse2-stage3hr.o gsnap_sse2-ladder.o gsnap_sse2-concordance.o gsnap_sse2-simplepair.o gsnap_sse2-maxent.o gsnap_sse2-orderstat.o gsnap_sse2-intlistpool.o gsnap_sse2-uintlistpool.o gsnap_sse2-listpool.o gsnap_sse2-hitlistpool.o gsnap_sse2-intron.o gsnap_sse2-gbuffer.o gsnap_sse2-knownsplicing.o gsnap_sse2-splice.o gsnap_sse2-indel.o gsnap_sse2-bitpack64-access.o gsnap_sse2-univdiag.o gsnap_sse2-univdiagpool.o gsnap_sse2-sedgesort.o gsnap_sse2-intersect.o gsnap_sse2-kmer-search.o gsnap_sse2-path-solve.o gsnap_sse2-extension-search.o gsnap_sse2-segment-search.o gsnap_sse2-terminal.o gsnap_sse2-distant-rna.o gsnap_sse2-distant-dna.o gsnap_sse2-uint8table_rh.o gsnap_sse2-uinttable_rh.o gsnap_sse2-stage1hr.o gsnap_sse2-tableuint.o gsnap_sse2-single-cell.o gsnap_sse2-request.o gsnap_sse2-resulthr.o gsnap_sse2-output.o gsnap_sse2-inbuffer.o gsnap_sse2-samheader.o gsnap_sse2-printbuffer.o gsnap_sse2-outbuffer.o gsnap_sse2-datadir.o gsnap_sse2-parserange.o gsnap_sse2-getline.o gsnap_sse2-gsnap.o -lz -lbz2 -lm
gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -g -O2 -ffile-prefix-map=/build/gmap-2021-12-17+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnapl.sse2 gsnapl_sse2-except.o gsnapl_sse2-assert.o gsnapl_sse2-mem.o gsnapl_sse2-intlist.o gsnapl_sse2-uintlist.o gsnapl_sse2-uint8list.o gsnapl_sse2-list.o gsnapl_sse2-littleendian.o gsnapl_sse2-bigendian.o gsnapl_sse2-univinterval.o gsnapl_sse2-interval.o gsnapl_sse2-stopwatch.o gsnapl_sse2-semaphore.o gsnapl_sse2-access.o gsnapl_sse2-filestring.o gsnapl_sse2-iit-read-univ.o gsnapl_sse2-iit-read.o gsnapl_sse2-bzip2.o gsnapl_sse2-reader.o gsnapl_sse2-genomicpos.o gsnapl_sse2-compress.o gsnapl_sse2-genome.o gsnapl_sse2-transcriptome.o gsnapl_sse2-popcount.o gsnapl_sse2-genome128_hr.o gsnapl_sse2-genome128_consec.o gsnapl_sse2-dinucl_bits.o gsnapl_sse2-genome_sites.o gsnapl_sse2-bitpack64-read.o gsnapl_sse2-bitpack64-readtwo.o gsnapl_sse2-mergeinfo.o gsnapl_sse2-merge-diagonals-heap.o gsnapl_sse2-merge-uint8.o gsnapl_sse2-merge-diagonals-simd-uint8.o gsnapl_sse2-merge-uint4.o gsnapl_sse2-merge-diagonals-simd-uint4.o gsnapl_sse2-indexdb.o gsnapl_sse2-regiondb.o gsnapl_sse2-oligo.o gsnapl_sse2-chrnum.o gsnapl_sse2-maxent_hr.o gsnapl_sse2-mdprint.o gsnapl_sse2-cigar.o gsnapl_sse2-samprint.o gsnapl_sse2-mapq.o gsnapl_sse2-fopen.o gsnapl_sse2-shortread.o gsnapl_sse2-substring.o gsnapl_sse2-junction.o gsnapl_sse2-exon.o gsnapl_sse2-doublelist.o gsnapl_sse2-bitvector.o gsnapl_sse2-transcript.o gsnapl_sse2-method.o gsnapl_sse2-stage3hr.o gsnapl_sse2-ladder.o gsnapl_sse2-concordance.o gsnapl_sse2-simplepair.o gsnapl_sse2-maxent.o gsnapl_sse2-orderstat.o gsnapl_sse2-intlistpool.o gsnapl_sse2-uint8listpool.o gsnapl_sse2-listpool.o gsnapl_sse2-hitlistpool.o gsnapl_sse2-intron.o gsnapl_sse2-gbuffer.o gsnapl_sse2-knownsplicing.o gsnapl_sse2-splice.o gsnapl_sse2-indel.o gsnapl_sse2-bitpack64-access.o gsnapl_sse2-univdiag.o gsnapl_sse2-univdiagpool.o gsnapl_sse2-sedgesort.o gsnapl_sse2-intersect.o gsnapl_sse2-intersect-large.o gsnapl_sse2-kmer-search.o gsnapl_sse2-path-solve.o gsnapl_sse2-extension-search.o gsnapl_sse2-segment-search.o gsnapl_sse2-terminal.o gsnapl_sse2-distant-rna.o gsnapl_sse2-distant-dna.o gsnapl_sse2-uint8table_rh.o gsnapl_sse2-stage1hr.o gsnapl_sse2-tableuint.o gsnapl_sse2-single-cell.o gsnapl_sse2-request.o gsnapl_sse2-resulthr.o gsnapl_sse2-output.o gsnapl_sse2-inbuffer.o gsnapl_sse2-samheader.o gsnapl_sse2-printbuffer.o gsnapl_sse2-outbuffer.o gsnapl_sse2-datadir.o gsnapl_sse2-parserange.o gsnapl_sse2-getline.o gsnapl_sse2-gsnap.o -lz -lbz2 -lm
make[3]: Leaving directory '/build/gmap-2021-12-17+ds/src'
make[2]: Leaving directory '/build/gmap-2021-12-17+ds/src'
Making all in util
make[2]: Entering directory '/build/gmap-2021-12-17+ds/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
chmod +x gmap_process
chmod +x gmap_build
chmod +x gmap_cat
cp ensembl_genes.pl ensembl_genes
chmod +x md_coords
cp gtf_splicesites.pl gtf_splicesites
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
cp gff3_genes.pl gff3_genes
cp dbsnp_iit.pl dbsnp_iit
cp gvf_iit.pl gvf_iit
cp vcf_iit.pl vcf_iit
chmod +x gtf_introns
chmod +x gtf_genes
chmod +x gtf_transcript_splicesites
chmod +x gff3_splicesites
chmod +x gff3_introns
chmod +x gff3_genes
chmod +x dbsnp_iit
chmod +x gvf_iit
chmod +x vcf_iit
make[2]: Leaving directory '/build/gmap-2021-12-17+ds/util'
Making all in tests
make[2]: Entering directory '/build/gmap-2021-12-17+ds/tests'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/build/gmap-2021-12-17+ds/tests'
make[2]: Entering directory '/build/gmap-2021-12-17+ds'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/build/gmap-2021-12-17+ds'
make[1]: Leaving directory '/build/gmap-2021-12-17+ds'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/gmap-2021-12-17+ds'
dh_auto_test --no-parallel
make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1
make[2]: Entering directory '/build/gmap-2021-12-17+ds'
Making check in src
make[3]: Entering directory '/build/gmap-2021-12-17+ds/src'
make[3]: Leaving directory '/build/gmap-2021-12-17+ds/src'
Making check in util
make[3]: Entering directory '/build/gmap-2021-12-17+ds/util'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/gmap-2021-12-17+ds/util'
Making check in tests
make[3]: Entering directory '/build/gmap-2021-12-17+ds/tests'
make check-TESTS
make[4]: Entering directory '/build/gmap-2021-12-17+ds/tests'
make[5]: Entering directory '/build/gmap-2021-12-17+ds/tests'
PASS: align.test
PASS: coords1.test
PASS: setup1.test
PASS: iit.test
============================================================================
Testsuite summary for gmap 2021-12-17
============================================================================
# TOTAL: 4
# PASS: 4
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[5]: Leaving directory '/build/gmap-2021-12-17+ds/tests'
make[4]: Leaving directory '/build/gmap-2021-12-17+ds/tests'
make[3]: Leaving directory '/build/gmap-2021-12-17+ds/tests'
make[3]: Entering directory '/build/gmap-2021-12-17+ds'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/build/gmap-2021-12-17+ds'
make[2]: Leaving directory '/build/gmap-2021-12-17+ds'
make[1]: Leaving directory '/build/gmap-2021-12-17+ds'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/gmap-2021-12-17+ds'
mkdir -p /build/gmap-2021-12-17+ds/debian/gmap/usr/share/man/man1
/usr/bin/help2man --no-info --version-string=2021-12-17+ds-3 --name='Genomic Mapping and Alignment Program' \
/build/gmap-2021-12-17+ds/src/gmap |debian/filter.pl >/build/gmap-2021-12-17+ds/debian/gmap/usr/share/man/man1/gmap.1
/usr/bin/help2man --no-info --version-string=2021-12-17+ds-3 --name='Genomic Short-read Nucleotide Alignment Program' \
/build/gmap-2021-12-17+ds/src/gsnap |debian/filter.pl >/build/gmap-2021-12-17+ds/debian/gmap/usr/share/man/man1/gsnap.1
/usr/bin/help2man --no-info --version-string=2021-12-17+ds-3 --name='Tool for genome database creation for GMAP or GSNAP' \
/build/gmap-2021-12-17+ds/util/gmap_build |debian/filter.pl >/build/gmap-2021-12-17+ds/debian/gmap/usr/share/man/man1/gmap_build.1
dh_auto_install
make -j15 install DESTDIR=/build/gmap-2021-12-17\+ds/debian/gmap AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/gmap-2021-12-17+ds'
Making install in src
make[3]: Entering directory '/build/gmap-2021-12-17+ds/src'
make[4]: Entering directory '/build/gmap-2021-12-17+ds/src'
make[4]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/gmap-2021-12-17+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 sam_sort gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse2 gmapl.sse2 gsnap.sse2 gsnapl.sse2 '/build/gmap-2021-12-17+ds/debian/gmap/usr/lib/gmap'
make[4]: Leaving directory '/build/gmap-2021-12-17+ds/src'
make[3]: Leaving directory '/build/gmap-2021-12-17+ds/src'
Making install in util
make[3]: Entering directory '/build/gmap-2021-12-17+ds/util'
make[4]: Entering directory '/build/gmap-2021-12-17+ds/util'
make[4]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/gmap-2021-12-17+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/gmap-2021-12-17+ds/debian/gmap/usr/lib/gmap'
make[4]: Leaving directory '/build/gmap-2021-12-17+ds/util'
make[3]: Leaving directory '/build/gmap-2021-12-17+ds/util'
Making install in tests
make[3]: Entering directory '/build/gmap-2021-12-17+ds/tests'
make[4]: Entering directory '/build/gmap-2021-12-17+ds/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/gmap-2021-12-17+ds/tests'
make[3]: Leaving directory '/build/gmap-2021-12-17+ds/tests'
make[3]: Entering directory '/build/gmap-2021-12-17+ds'
make[4]: Entering directory '/build/gmap-2021-12-17+ds'
make[4]: Nothing to be done for 'install-exec-am'.
/bin/bash /build/gmap-2021-12-17+ds/config/install-sh -d /build/gmap-2021-12-17+ds/debian/gmap/var/cache/gmap
make[4]: Leaving directory '/build/gmap-2021-12-17+ds'
make[3]: Leaving directory '/build/gmap-2021-12-17+ds'
make[2]: Leaving directory '/build/gmap-2021-12-17+ds'
make[1]: Leaving directory '/build/gmap-2021-12-17+ds'
debian/rules override_dh_install
make[1]: Entering directory '/build/gmap-2021-12-17+ds'
mkdir -p debian/gmap/usr/bin
dh_install
for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \
cd /build/gmap-2021-12-17+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/gmap-2021-12-17+ds'
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installexamples
make[1]: Entering directory '/build/gmap-2021-12-17+ds'
mkdir /build/gmap-2021-12-17+ds/debian/gmap/usr/share/doc/gmap/examples
find tests/ -type f -print0 | xargs -0r sed -i \
-e 's@/build/gmap-2021-12-17+ds@«buildpath»@g' \
-e 's@\#! /bin/bash@\#! /bin/sh@g'
tar --sort=name \
--mtime="@1664818591" \
--owner=root --group=root --numeric-owner \
--mode=go=rX,u+rw,a-s \
--exclude='*/align.log' \
--exclude='*/Makefile' \
--exclude='*/Makefile.in' \
-cJf /build/gmap-2021-12-17+ds/debian/gmap/usr/share/doc/gmap/examples/tests.tar.xz tests
make[1]: Leaving directory '/build/gmap-2021-12-17+ds'
dh_installman
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'gmap' in '../gmap_2021-12-17+ds-3_amd64.deb'.
dpkg-deb: building package 'gmap-dbgsym' in '../gmap-dbgsym_2021-12-17+ds-3_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../gmap_2021-12-17+ds-3_amd64.buildinfo
dpkg-genchanges --build=binary -O../gmap_2021-12-17+ds-3_amd64.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/849010/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/849010/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/849010 and its subdirectories
I: Current time: Sat Apr 15 08:37:51 +14 2023
I: pbuilder-time-stamp: 1681497471