I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 29 16:13:52 +14 2024 I: pbuilder-time-stamp: 1711678432 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [lagan_2.0-10.dsc] I: copying [./lagan_2.0.orig.tar.gz] I: copying [./lagan_2.0-10.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 25 07:06:21 2024 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lagan_2.0-10.dsc: no acceptable signature found dpkg-source: info: extracting lagan in lagan-2.0 dpkg-source: info: unpacking lagan_2.0.orig.tar.gz dpkg-source: info: unpacking lagan_2.0-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_define_conflicting_getline.patch dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying ambiuousEnd.patch dpkg-source: info: applying addTest.patch dpkg-source: info: applying adjustPerlPaths.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying gcc9.patch dpkg-source: info: applying gcc10.patch dpkg-source: info: applying gcc-lto.patch dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/13297/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Mar 29 02:14 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/13297/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/13297/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=2b3f33a21a3c480fbffc2741a118bb38 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=13297 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.NXej4L6K/pbuilderrc_HPVa --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NXej4L6K/b2 --logfile b2/build.log lagan_2.0-10.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 28 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/13297/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team 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), libboost-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19816 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 libboost-dev; however: Package libboost-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: 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} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{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} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 29.9 MB of archives. After unpacking 235 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.14.1 [85.6 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.14.1 [890 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libboost1.83-dev i386 1.83.0-2+b2 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main i386 libboost-dev i386 1.83.0.2+b2 [3840 B] Fetched 29.9 MB in 1s (48.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19816 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_i386.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-1+b2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-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 .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.14.1_all.deb ... Unpacking libdebhelper-perl (13.14.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-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 .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.190-1+b1_i386.deb ... Unpacking libelf1:i386 (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.14.1_all.deb ... Unpacking debhelper (13.14.1) ... Selecting previously unselected package libboost1.83-dev:i386. Preparing to unpack .../30-libboost1.83-dev_1.83.0-2+b2_i386.deb ... Unpacking libboost1.83-dev:i386 (1.83.0-2+b2) ... Selecting previously unselected package libboost-dev:i386. Preparing to unpack .../31-libboost-dev_1.83.0.2+b2_i386.deb ... Unpacking libboost-dev:i386 (1.83.0.2+b2) ... Setting up libpipeline1:i386 (1.5.7-1+b2) ... Setting up libboost1.83-dev:i386 (1.83.0-2+b2) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.14.1) ... Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libboost-dev:i386 (1.83.0.2+b2) ... Setting up libelf1:i386 (0.190-1+b1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... 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 (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.14.1) ... Processing triggers for libc-bin (2.37-15) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/13297/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/13297/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/lagan-2.0/ && 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 > ../lagan_2.0-10_source.changes dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_clean make -j7 clean make[2]: Entering directory '/build/reproducible-path/lagan-2.0' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src' rm -f *.o *~ utils/*~ mlagan.purify core (cd glocal; make clean) make[4]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' rm -f *.o ./*~ *~ core make[4]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0' rm -f prolagan make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_build --sourcedirectory=src cd src && make -j7 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../anchors anchors.c skiplist.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../order order.c diagmatrix.c filebuffer.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2mf utils/bin2mf.c -Wl,-z,relro anchors.c: In function 'anchors_getline': anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 232 | fgets(temp, 1024, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2bl utils/bin2bl.c -Wl,-z,relro order.c: In function 'readfile': order.c:63:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readSubstMatrix': order.c:147:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 147 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:151:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 151 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:152:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 152 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function 'readfile': mlagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readfile': fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function 'readSubstMatrix': fchaos.c:622:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:627:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fscanf (file, "%d", &gappenstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function 'readfile': prolagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p utils/cextract.c: In function 'getLength': utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function 'readfile': utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-z,relro utils/cstat.c: In function 'cntlets': utils/cstat.c:45:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function 'readseq': utils/cstat.c:68:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 68 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c:26:25: warning: unknown conversion type character '&' in format [-Wformat=] 26 | fscanf (file, "%&d", &dummy); | ^ utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 52 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:19:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fscanf (file, "numContigs = %d\n", numContigs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fscanf (file, "seqLen = %d\n", seqLen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:26:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | fscanf (file, "%&d", &dummy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:56:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fscanf (file, "numContigs = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:57:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fscanf (file, "seqLen = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:63:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf (file, "%d", &((*score)[i][j])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getbounds.c: In function 'getLength': utils/getbounds.c:18:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 18 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro utils/getlength.c: In function 'main': utils/getlength.c:20:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 20 | fgets (buffer, BUF_SIZE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro utils/rc.c: In function 'main': utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | fgets(temp, 255, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/seqmerge.c: In function 'main': utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro utils/scorealign.c: In function 'getSequence': utils/scorealign.c:266:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 266 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'readScoreMatrix': utils/scorealign.c:415:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 415 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:423:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 423 | fscanf (file, "%1s", &(line[0])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:425:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:430:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 430 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function 'getLength': utils/getcontigpos.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function 'readfile': utils/getcontigpos.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'main': utils/scorecontigs.c:385:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=] 385 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] utils/scorecontigs.c: In function 'cntlets': utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fgets(temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'readseq': utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets (temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: 'gapcache' is static but used in inline function 'endGap1' which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: 'gapcache' is static but used in inline function 'endGap0' which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro utils/fa2xfa.c: In function 'getLength': utils/fa2xfa.c:30:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function 'readfile': utils/fa2xfa.c:55:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 55 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -Wl,-z,relro g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro utils/dotplot.cpp: In function 'int main(int, char**)': utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/overlay.c: In function 'read_align': utils/overlay.c:110:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 110 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p utils/Glue.cpp: In function 'void calculateScoreMatrix(int)': utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 64 | char *alpha = "ATCG"; | ^~~~~~ utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ^~~~~~~~~~~~~~~ utils/Glue.cpp:72:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE' 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function 'void readScoreMatrix(char*)': utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 44 | fgets (line, 1024, file); | ~~~~~~^~~~~~~~~~~~~~~~~~ utils/Glue.cpp:52:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | fscanf (file, "%1s", &(line[0])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp:54:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | fscanf (file, "%d", &k); | ~~~~~~~^~~~~~~~~~~~~~~~ utils/Glue.cpp:59:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fscanf (file, "%d%d", &gapopen, &gapcont); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c glocal.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c rightinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c score.cpp -Wl,-z,relro io.cpp: In function 'long long int getline(FILE*, hll*)': io.cpp:60:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fgets(temp, 1024, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_auto_test make -j7 test make[1]: Entering directory '/build/reproducible-path/lagan-2.0' make -C src make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' (cd glocal; make LDFLAGS="-Wl,-z,relro") make[3]: Entering directory '/build/reproducible-path/lagan-2.0/src/glocal' g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-z,relro make[3]: Leaving directory '/build/reproducible-path/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]" [ok] make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/lagan/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_fixperms find debian -name flipchaos.pl -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lagan' in '../lagan_2.0-10_i386.deb'. dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_i386.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_i386.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/13297/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/13297/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/13297 and its subdirectories I: Current time: Fri Mar 29 16:14:55 +14 2024 I: pbuilder-time-stamp: 1711678495