Diff of the two buildlogs: -- --- b1/build.log 2025-08-26 08:07:41.532346250 +0000 +++ b2/build.log 2025-08-26 08:18:23.525069819 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 25 20:02:43 -12 2025 -I: pbuilder-time-stamp: 1756195363 +I: Current time: Tue Sep 29 04:31:51 +14 2026 +I: pbuilder-time-stamp: 1790605911 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -29,53 +29,85 @@ dpkg-source: info: applying fix_linking.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/677875/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2114695/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Sep 28 14:31 /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/2114695/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2114695/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='ba531f18763e4d21b7c4933527c43bcd' - 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='677875' - PS1='# ' - PS2='> ' + INVOCATION_ID=55e1ffb904624a079a57a709ccdfdbfc + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=2114695 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.91M2S2eU/pbuilderrc_zNv5 --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.91M2S2eU/b1 --logfile b1/build.log mothur_1.48.1-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.91M2S2eU/pbuilderrc_rb0j --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.91M2S2eU/b2 --logfile b2/build.log mothur_1.48.1-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/677875/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2114695/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -168,7 +200,7 @@ Get: 47 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 libreadline-dev arm64 8.2-6 [155 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 55.1 MB in 0s (235 MB/s) +Fetched 55.1 MB in 1s (105 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19969 files and directories currently installed.) @@ -385,7 +417,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mothur-1.48.1/ && 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 > ../mothur_1.48.1-1_source.changes +I: user script /srv/workspace/pbuilder/2114695/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2114695/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mothur-1.48.1/ && 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 > ../mothur_1.48.1-1_source.changes dpkg-buildpackage: info: source package mothur dpkg-buildpackage: info: source version 1.48.1-1 dpkg-buildpackage: info: source distribution unstable @@ -549,11 +585,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)': source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 456 | fscanf(fp, "%ld\n", &dmat->ntaxa); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp source/clearcut/distclearcut.cpp: In function 'DMAT* NJ_compute_dmat(NJ_ARGS*, NJ_alignment*)': source/clearcut/distclearcut.cpp:155:41: warning: 'char* __builtin_strncat(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 155 | *dmat->taxaname[i] = '\0'; strncat(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i])+1); @@ -569,11 +605,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp source/commands/alignmusclecommand.cpp: In member function 'void AlignMuscleCommand::wrapperFunction()': source/commands/alignmusclecommand.cpp:297:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 297 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp @@ -585,11 +621,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)': source/commands/chimerauchimecommand.cpp:517:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 517 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp source/commands/chimeravsearchcommand.cpp: In function 'void driver(vsearchData*)': source/commands/chimeravsearchcommand.cpp:412:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -620,11 +656,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distsharedcommand.o source/commands/distsharedcommand.cpp source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()': source/commands/distancecommand.cpp:323:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 323 | system(("gzip -v " + outputFile).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distsharedcommand.o source/commands/distsharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/fastaqinfocommand.o source/commands/fastaqinfocommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp @@ -661,12 +697,12 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::string)': source/commands/makefilecommand.cpp:473:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 473 | system(findCommand.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makesharedcommand.o source/commands/makesharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp @@ -687,14 +723,14 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()': source/commands/pairwiseseqscommand.cpp:339:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 339 | system(("gzip -v " + outputFile).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp @@ -738,11 +774,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/translateseqscommand.o source/commands/translateseqscommand.cpp source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()': source/commands/systemcommand.cpp:97:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | system(command.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/translateseqscommand.o source/commands/translateseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treesharedcommand.o source/commands/treesharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp @@ -871,8 +907,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/utils.o source/utils.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validcalculator.o source/validcalculator.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp source/utils.cpp: In member function 'bool Utils::findTool(std::string&, std::string&, std::vector >&, std::vector > >)': source/utils.cpp:952:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 952 | system(versionTestCommand.c_str()); @@ -881,6 +915,8 @@ source/utils.cpp:1514:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1514 | system(command.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd .. @@ -907,6 +943,8 @@ g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tracebackbit.o tracebackbit.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o uchime_main.o uchime_main.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o usort.o usort.cpp +g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o viterbifast.o viterbifast.cpp +g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o writechhit.o writechhit.cpp myutils.cpp: In function 'const char* SecsToHHMMSS(int)': myutils.cpp:728:36: warning: '%02d' directive writing between 2 and 9 bytes into a region of size between 8 and 13 [-Wformat-overflow=] 728 | sprintf(Str, "%02d:%02d:%02d", HH, MM, SS); @@ -952,8 +990,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o viterbifast.o viterbifast.cpp -g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o writechhit.o writechhit.cpp myutils.cpp: In function 'void Progress(const char*, ...)': myutils.cpp:728:36: warning: '%02d' directive writing between 2 and 9 bytes into a region of size between 8 and 13 [-Wformat-overflow=] 728 | sprintf(Str, "%02d:%02d:%02d", HH, MM, SS); @@ -1056,12 +1092,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2114695/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2114695/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/677875 and its subdirectories -I: Current time: Mon Aug 25 20:07:40 -12 2025 -I: pbuilder-time-stamp: 1756195660 +I: removing directory /srv/workspace/pbuilder/2114695 and its subdirectories +I: Current time: Tue Sep 29 04:41:22 +14 2026 +I: pbuilder-time-stamp: 1790606482