Diff of the two buildlogs: -- --- b1/build.log 2025-10-25 21:02:22.414834001 +0000 +++ b2/build.log 2025-10-25 21:05:16.447055254 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 27 15:23:32 -12 2026 -I: pbuilder-time-stamp: 1795836212 +I: Current time: Sun Oct 26 11:02:23 +14 2025 +I: pbuilder-time-stamp: 1761426143 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying build-flags.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20815/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1203008/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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 25 21:03 /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/1203008/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1203008/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + 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=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8d8d82d7743c4ec3ace069857d5fcd36' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='20815' - PS1='# ' - PS2='> ' + INVOCATION_ID=f3fa420ed15747338db6916cd3873b74 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=1203008 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ulwvnQt7/pbuilderrc_wPZZ --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ulwvnQt7/b1 --logfile b1/build.log soapdenovo_1.05-7.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.ulwvnQt7/pbuilderrc_4qke --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ulwvnQt7/b2 --logfile b2/build.log soapdenovo_1.05-7.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/20815/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1203008/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -140,7 +172,7 @@ Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 rename all 2.02-1 [21.8 kB] -Fetched 11.3 MB in 5s (2148 kB/s) +Fetched 11.3 MB in 5s (2409 kB/s) Preconfiguring packages ... 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 ... 19900 files and directories currently installed.) @@ -281,7 +313,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/soapdenovo-1.05/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../soapdenovo_1.05-7_source.changes +I: user script /srv/workspace/pbuilder/1203008/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1203008/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/soapdenovo-1.05/ && 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 > ../soapdenovo_1.05-7_source.changes dpkg-buildpackage: info: source package soapdenovo dpkg-buildpackage: info: source version 1.05-7 dpkg-buildpackage: info: source distribution unstable @@ -291,7 +327,7 @@ debian/rules clean dh clean dh_auto_clean - make -j42 clean + make -j40 clean make[1]: Entering directory '/build/reproducible-path/soapdenovo-1.05' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/31mer' SOAPdenovo-31mer cleaning done. @@ -310,53 +346,55 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j42 INSTALL="install --strip-program=true" + make -j40 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/soapdenovo-1.05' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/31mer' -Compiling arc.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c" -Compiling attachPEinfo.c... Compiling bubble.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c" -gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c" +Compiling arc.c... Compiling attachPEinfo.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c" +Compiling bubble.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c" Compiling check.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c" Compiling compactEdge.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c" -Compiling concatenateEdge.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c" -Compiling connect.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c" +Compiling concatenateEdge.c... Compiling connect.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c" Compiling contig.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c" Compiling cutTipPreGraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c" Compiling cutTip_graph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c" -Compiling darray.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c" -Compiling dfib.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c" -Compiling dfibHeap.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c" -Compiling fib.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c" -Compiling fibHeap.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c" +Compiling darray.c... Compiling dfib.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c" +Compiling dfibHeap.c... Compiling fib.c... Compiling fibHeap.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c" Compiling hashFunction.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c" Compiling kmer.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c" -Compiling lib.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c" -Compiling loadGraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c" -Compiling loadPath.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c" -Compiling loadPreGraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c" -Compiling localAsm.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c" -Compiling main.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c" -Compiling map.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c" -Compiling mem_manager.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c" -Compiling newhash.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c" -Compiling node2edge.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c" -Compiling orderContig.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c" -Compiling output_contig.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c" -Compiling output_pregraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c" +Compiling lib.c... Compiling loadGraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c" +Compiling loadPath.c... Compiling loadPreGraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c" +Compiling localAsm.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c" +Compiling main.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c" +Compiling map.c... Compiling mem_manager.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c" +Compiling newhash.c... Compiling orderContig.c... Compiling node2edge.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c" +Compiling output_contig.c... Compiling output_pregraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c" Compiling output_scaffold.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c" -Compiling pregraph.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c" -Compiling prlHashCtg.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c" +Compiling pregraph.c... Compiling prlHashCtg.c... Compiling prlRead2Ctg.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c" Compiling prlHashReads.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c" -Compiling prlRead2Ctg.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c" -Compiling prlRead2path.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c" -Compiling prlReadFillGap.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c" -Compiling read2scaf.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c" -Compiling readInterval.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c" +Compiling prlRead2path.c... attachPEinfo.c: In function 'loadPEgrads': +Compiling read2scaf.c... Compiling prlReadFillGap.c... attachPEinfo.c:86:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 86 | fgets ( line, sizeof ( line ), fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Compiling readInterval.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c" +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c" Compiling stack.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c" -Compiling readseq1by1.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c" -Compiling scaffold.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c" loadPath.c: In function 'loadPath': -loadPath.c:58:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] +Compiling readseq1by1.c... loadPath.c:58:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 58 | fscanf ( fp, "%d", &num1 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ loadPath.c:62:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -369,18 +407,26 @@ loadPath.c:168:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 168 | fscanf ( fp, "%d", &num2 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -attachPEinfo.c: In function 'loadPEgrads': -attachPEinfo.c:86:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 86 | fgets ( line, sizeof ( line ), fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -prlRead2Ctg.c: In function 'basicContigInfo': -prlRead2Ctg.c:494:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 494 | fgets ( lldne, sizeof ( lldne ), fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -prlRead2Ctg.c:499:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 499 | fgets ( lldne, sizeof ( lldne ), fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c" +Compiling scaffold.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c" +Compiling searchPath.c... loadGraph.c: In function 'loadUpdatedVertex': +loadGraph.c:57:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 57 | fscanf ( fp, "%llx ", &word ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c" +read2scaf.c: In function 'locateReadOnScaf': +read2scaf.c:282:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 282 | fgets ( line, 1024, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +Compiling seq.c... loadPreGraph.c: In function 'loadVertex': +loadPreGraph.c:77:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 77 | fscanf ( fp, "%llx ", &word ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +orderContig.c: In function 'PE2Links': map.c: In function 'getMinOverlap.constprop': +orderContig.c:2765:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2765 | fgets ( line, lineLen, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ map.c:40:28: warning: '.preGraphBasic' directive writing 14 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 40 | sprintf ( name, "%s.preGraphBasic", gfile ); | ^~~~~~~~~~~~~~ @@ -396,107 +442,76 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -loadGraph.c: In function 'loadUpdatedVertex': -loadGraph.c:57:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 57 | fscanf ( fp, "%llx ", &word ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -loadPreGraph.c: In function 'loadVertex': -loadPreGraph.c:77:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 77 | fscanf ( fp, "%llx ", &word ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +orderContig.c: In function 'Links2Scaf': readseq1by1.c: In function 'read1seqfq': readseq1by1.c:213:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 213 | fgets ( str, 4950, fp ); // pass quality value line | ^~~~~~~~~~~~~~~~~~~~~~~ -read2scaf.c: In function 'locateReadOnScaf': -read2scaf.c:282:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 282 | fgets ( line, 1024, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -orderContig.c: In function 'PE2Links': -orderContig.c:2765:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2765 | fgets ( line, lineLen, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -orderContig.c: In function 'Links2Scaf': +gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c" orderContig.c:2891:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2891 | fgets ( line, lineLen, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -Compiling searchPath.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c" -Compiling seq.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c" Compiling splitReps.c... gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c" +prlRead2Ctg.c: In function 'basicContigInfo': +prlRead2Ctg.c:494:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 494 | fgets ( lldne, sizeof ( lldne ), fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +prlRead2Ctg.c:499:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 499 | fgets ( lldne, sizeof ( lldne ), fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -Wl,-z,relro -Wl,-z,now -o SOAPdenovo-31mer arc.o attachPEinfo.o bubble.o check.o compactEdge.o concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o darray.o dfib.o dfibHeap.o fib.o fibHeap.o hashFunction.o kmer.o lib.o loadGraph.o loadPath.o loadPreGraph.o localAsm.o main.o map.o mem_manager.o newhash.o node2edge.o orderContig.o output_contig.o output_pregraph.o output_scaffold.o pregraph.o prlHashCtg.o prlHashReads.o prlRead2Ctg.o prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o -pthread -lm Linking... SOAPdenovo-31mer compilation done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/31mer' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/63mer' -Compiling arc.c... Compiling attachPEinfo.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c" -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c" -Compiling bubble.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c" -Compiling check.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c" -Compiling compactEdge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c" +Compiling arc.c... Compiling attachPEinfo.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c" +Compiling bubble.c... Compiling check.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c" +Compiling compactEdge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c" Compiling concatenateEdge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c" -Compiling connect.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c" -Compiling contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c" +Compiling connect.c... Compiling contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c" Compiling cutTipPreGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c" Compiling cutTip_graph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c" -Compiling darray.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c" -Compiling dfib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c" -Compiling dfibHeap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c" -Compiling fib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c" -Compiling fibHeap.c... Compiling hashFunction.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c" -Compiling kmer.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c" -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c" +Compiling darray.c... Compiling dfib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c" +Compiling dfibHeap.c... Compiling fib.c... Compiling fibHeap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c" +Compiling hashFunction.c... Compiling kmer.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c" Compiling lib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c" Compiling loadGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c" Compiling loadPath.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c" Compiling loadPreGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c" Compiling localAsm.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c" -Compiling main.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c" -Compiling map.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c" -Compiling mem_manager.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c" -Compiling newhash.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c" -Compiling node2edge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c" -Compiling orderContig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c" -Compiling output_contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c" -Compiling output_pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c" -Compiling output_scaffold.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c" -Compiling pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c" -Compiling prlHashCtg.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c" -Compiling prlHashReads.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c" -Compiling prlRead2Ctg.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c" -Compiling prlRead2path.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c" -Compiling prlReadFillGap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c" -Compiling read2scaf.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c" -Compiling readInterval.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c" -Compiling stack.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c" -Compiling readseq1by1.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c" -Compiling scaffold.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c" +Compiling main.c... Compiling map.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c" +Compiling mem_manager.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c" +Compiling newhash.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c" +Compiling node2edge.c... Compiling orderContig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c" +Compiling output_contig.c... Compiling output_pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c" +Compiling output_scaffold.c... Compiling pregraph.c... Compiling prlHashReads.c... Compiling prlHashCtg.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c" +Compiling prlRead2Ctg.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c" +Compiling prlRead2path.c... Compiling prlReadFillGap.c... Compiling read2scaf.c... Compiling readInterval.c... Compiling stack.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c" attachPEinfo.c: In function 'loadPEgrads': attachPEinfo.c:86:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | fgets ( line, sizeof ( line ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Compiling searchPath.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c" read2scaf.c: In function 'locateReadOnScaf': read2scaf.c:286:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fgets ( line, 1024, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ -readseq1by1.c: In function 'read1seqfq': -readseq1by1.c:213:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 213 | fgets ( str, 4950, fp ); // pass quality value line - | ^~~~~~~~~~~~~~~~~~~~~~~ -Compiling seq.c... loadPath.c: In function 'loadPath': -loadPath.c:58:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 58 | fscanf ( fp, "%d", &num1 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -loadPath.c:62:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 62 | fscanf ( fp, "%d", &num2 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -loadPath.c: In function 'loadPathBin': -loadPath.c:164:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 164 | fscanf ( fp, "%d", &num1 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -loadPath.c:168:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 168 | fscanf ( fp, "%d", &num2 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c" +Compiling readseq1by1.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c" map.c: In function 'getMinOverlap.constprop': map.c:40:28: warning: '.preGraphBasic' directive writing 14 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 40 | sprintf ( name, "%s.preGraphBasic", gfile ); @@ -513,7 +528,35 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +Compiling scaffold.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c" +loadPreGraph.c: In function 'loadVertex': +loadPreGraph.c:77:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 77 | fscanf ( fp, "%llx %llx", & ( word.high ), & ( word.low ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Compiling searchPath.c... Compiling seq.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c" Compiling splitReps.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c || echo "Error in command: gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c" +loadPath.c: In function 'loadPath': +loadPath.c:58:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 58 | fscanf ( fp, "%d", &num1 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +loadPath.c:62:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 62 | fscanf ( fp, "%d", &num2 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +loadPath.c: In function 'loadPathBin': +loadPath.c:164:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 164 | fscanf ( fp, "%d", &num1 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +loadPath.c:168:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 168 | fscanf ( fp, "%d", &num2 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +prlRead2Ctg.c: In function 'basicContigInfo': +prlRead2Ctg.c:493:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 493 | fgets ( lldne, sizeof ( lldne ), fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +prlRead2Ctg.c:498:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 498 | fgets ( lldne, sizeof ( lldne ), fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ orderContig.c: In function 'PE2Links': orderContig.c:2765:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2765 | fgets ( line, lineLen, fp ); @@ -522,84 +565,74 @@ orderContig.c:2890:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2890 | fgets ( line, lineLen, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -prlRead2Ctg.c: In function 'basicContigInfo': -prlRead2Ctg.c:493:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 493 | fgets ( lldne, sizeof ( lldne ), fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -prlRead2Ctg.c:498:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 498 | fgets ( lldne, sizeof ( lldne ), fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -loadPreGraph.c: In function 'loadVertex': -loadPreGraph.c:77:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 77 | fscanf ( fp, "%llx %llx", & ( word.high ), & ( word.low ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseq1by1.c: In function 'read1seqfq': +readseq1by1.c:213:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 213 | fgets ( str, 4950, fp ); // pass quality value line + | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -Wl,-z,relro -Wl,-z,now -o SOAPdenovo-63mer arc.o attachPEinfo.o bubble.o check.o compactEdge.o concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o darray.o dfib.o dfibHeap.o fib.o fibHeap.o hashFunction.o kmer.o lib.o loadGraph.o loadPath.o loadPreGraph.o localAsm.o main.o map.o mem_manager.o newhash.o node2edge.o orderContig.o output_contig.o output_pregraph.o output_scaffold.o pregraph.o prlHashCtg.o prlHashReads.o prlRead2Ctg.o prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o -pthread -lm Linking... SOAPdenovo-63mer compilation done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/63mer' make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/127mer' -Compiling arc.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c" -Compiling attachPEinfo.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c" -Compiling bubble.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c" -Compiling check.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c" -Compiling compactEdge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c" -Compiling concatenateEdge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c" -Compiling connect.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c" -Compiling contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c" -Compiling cutTipPreGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c" -Compiling cutTip_graph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c" -Compiling darray.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c" -Compiling dfib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c" -Compiling dfibHeap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c" -Compiling fib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c" -Compiling fibHeap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c" -Compiling hashFunction.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c" +Compiling arc.c... Compiling attachPEinfo.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc arc.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc attachPEinfo.c" +Compiling bubble.c... Compiling check.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc bubble.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc check.c" +Compiling compactEdge.c... Compiling concatenateEdge.c... Compiling connect.c... Compiling contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc compactEdge.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc concatenateEdge.c" +Compiling cutTipPreGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc connect.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc contig.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTipPreGraph.c" +Compiling cutTip_graph.c... Compiling darray.c... Compiling dfib.c... Compiling dfibHeap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc cutTip_graph.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc darray.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfib.c" +Compiling fib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc dfibHeap.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fib.c" +Compiling fibHeap.c... Compiling hashFunction.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc fibHeap.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc hashFunction.c" Compiling kmer.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc kmer.c" Compiling lib.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc lib.c" -Compiling loadGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c" -Compiling loadPath.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c" +Compiling loadGraph.c... Compiling loadPath.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadGraph.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPath.c" Compiling loadPreGraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc loadPreGraph.c" Compiling localAsm.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc localAsm.c" -Compiling main.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c" -Compiling map.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c" -Compiling mem_manager.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c" -Compiling newhash.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c" -Compiling node2edge.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c" -Compiling orderContig.c... Compiling output_contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c" -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c" +Compiling main.c... Compiling map.c... Compiling mem_manager.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc map.c" +Compiling newhash.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc main.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc newhash.c" +Compiling node2edge.c... Compiling orderContig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc mem_manager.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc node2edge.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc orderContig.c" +Compiling output_contig.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_contig.c" Compiling output_pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_pregraph.c" -Compiling output_scaffold.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c" -Compiling pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c" -Compiling prlHashCtg.c... Compiling prlHashReads.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c" -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c" +Compiling output_scaffold.c... Compiling pregraph.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc output_scaffold.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc pregraph.c" +Compiling prlHashCtg.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashCtg.c" +Compiling prlHashReads.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlHashReads.c" Compiling prlRead2Ctg.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2Ctg.c" Compiling prlRead2path.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlRead2path.c" Compiling prlReadFillGap.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc prlReadFillGap.c" Compiling read2scaf.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc read2scaf.c" -Compiling readInterval.c... Compiling stack.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c" -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c" -Compiling readseq1by1.c... Compiling scaffold.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c" -gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c" attachPEinfo.c: In function 'loadPEgrads': attachPEinfo.c:86:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 86 | fgets ( line, sizeof ( line ), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Compiling searchPath.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c" -Compiling seq.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c" -loadPath.c: In function 'loadPath': -loadPath.c:58:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 58 | fscanf ( fp, "%d", &num1 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -loadPath.c:62:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 62 | fscanf ( fp, "%d", &num2 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -loadPath.c: In function 'loadPathBin': -loadPath.c:164:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 164 | fscanf ( fp, "%d", &num1 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -loadPath.c:168:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 168 | fscanf ( fp, "%d", &num2 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -Compiling splitReps.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c" +Compiling stack.c... Compiling readInterval.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc stack.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readInterval.c" +Compiling readseq1by1.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc readseq1by1.c" +prlRead2Ctg.c: In function 'basicContigInfo': +prlRead2Ctg.c:493:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 493 | fgets ( lldne, sizeof ( lldne ), fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +prlRead2Ctg.c:498:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 498 | fgets ( lldne, sizeof ( lldne ), fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +orderContig.c: In function 'PE2Links': +orderContig.c:2765:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2765 | fgets ( line, lineLen, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +orderContig.c: In function 'Links2Scaf': +orderContig.c:2890:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2890 | fgets ( line, lineLen, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ map.c: In function 'getMinOverlap.constprop': map.c:40:28: warning: '.preGraphBasic' directive writing 14 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 40 | sprintf ( name, "%s.preGraphBasic", gfile ); @@ -616,33 +649,36 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -orderContig.c: In function 'PE2Links': -read2scaf.c: In function 'locateReadOnScaf': -read2scaf.c:286:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fgets ( line, 1024, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -orderContig.c:2765:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2765 | fgets ( line, lineLen, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -prlRead2Ctg.c: In function 'basicContigInfo': -orderContig.c: In function 'Links2Scaf': -orderContig.c:2890:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2890 | fgets ( line, lineLen, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -prlRead2Ctg.c:493:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 493 | fgets ( lldne, sizeof ( lldne ), fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -prlRead2Ctg.c:498:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 498 | fgets ( lldne, sizeof ( lldne ), fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadPreGraph.c: In function 'loadVertex': loadPreGraph.c:77:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 77 | fscanf ( fp, "%llx %llx %llx %llx", & ( word.high1 ), & ( word.low1 ), & ( word.high2 ), & ( word.low2 ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Compiling scaffold.c... loadPath.c: In function 'loadPath': +loadPath.c:58:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 58 | fscanf ( fp, "%d", &num1 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +loadPath.c:62:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 62 | fscanf ( fp, "%d", &num2 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +loadPath.c: In function 'loadPathBin': +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc scaffold.c" +loadPath.c:164:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 164 | fscanf ( fp, "%d", &num1 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +Compiling searchPath.c... Compiling seq.c... loadPath.c:168:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 168 | fscanf ( fp, "%d", &num2 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc searchPath.c" +gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc seq.c" readseq1by1.c: In function 'read1seqfq': readseq1by1.c:213:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 213 | fgets ( str, 4950, fp ); // pass quality value line | ^~~~~~~~~~~~~~~~~~~~~~~ +read2scaf.c: In function 'locateReadOnScaf': +read2scaf.c:286:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 286 | fgets ( line, 1024, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +Compiling splitReps.c... gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c || echo "Error in command: gcc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -g -Iinc splitReps.c" gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64 -Wl,-z,relro -Wl,-z,now -o SOAPdenovo-127mer arc.o attachPEinfo.o bubble.o check.o compactEdge.o concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o darray.o dfib.o dfibHeap.o fib.o fibHeap.o hashFunction.o kmer.o lib.o loadGraph.o loadPath.o loadPreGraph.o localAsm.o main.o map.o mem_manager.o newhash.o node2edge.o orderContig.o output_contig.o output_pregraph.o output_scaffold.o pregraph.o prlHashCtg.o prlHashReads.o prlRead2Ctg.o prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o -pthread -lm Linking... SOAPdenovo-127mer compilation done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/127mer' @@ -652,7 +688,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/soapdenovo/ - make -j42 install DESTDIR=/build/reproducible-path/soapdenovo-1.05/debian/soapdenovo AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + make -j40 install DESTDIR=/build/reproducible-path/soapdenovo-1.05/debian/soapdenovo AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/soapdenovo-1.05' Installation done. make[1]: Leaving directory '/build/reproducible-path/soapdenovo-1.05' @@ -687,12 +723,14 @@ 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/1203008/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1203008/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/20815 and its subdirectories -I: Current time: Fri Nov 27 15:25:21 -12 2026 -I: pbuilder-time-stamp: 1795836321 +I: removing directory /srv/workspace/pbuilder/1203008 and its subdirectories +I: Current time: Sun Oct 26 11:05:16 +14 2025 +I: pbuilder-time-stamp: 1761426316