Diff of the two buildlogs: -- --- b1/build.log 2025-03-06 08:35:15.775638546 +0000 +++ b2/build.log 2025-03-06 08:38:47.462151281 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Mar 5 20:23:59 -12 2025 -I: pbuilder-time-stamp: 1741249439 +I: Current time: Thu Apr 9 04:58:18 +14 2026 +I: pbuilder-time-stamp: 1775660298 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ 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/3572391/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3900949/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Apr 8 14:58 /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/3900949/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3900949/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=20 ' - DISTRIBUTION='trixie' - 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]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='988735a03da04e7cb8e9bfd759c3356a' - 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='3572391' - PS1='# ' - PS2='> ' + INVOCATION_ID=0c09eb55dcba414f9596ab99a31f14d1 + 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=3900949 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.a6obupnU/pbuilderrc_BKGQ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.a6obupnU/b1 --logfile b1/build.log mothur_1.48.1-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.a6obupnU/pbuilderrc_0MAA --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.a6obupnU/b2 --logfile b2/build.log mothur_1.48.1-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3572391/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3900949/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -167,7 +199,7 @@ Get: 47 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libreadline-dev amd64 8.2-6 [153 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 57.9 MB in 2s (24.6 MB/s) +Fetched 57.9 MB in 3s (17.4 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 ... 19800 files and directories currently installed.) @@ -384,7 +416,11 @@ 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/3900949/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3900949/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 @@ -410,7 +446,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/mothur-1.48.1' dh_auto_build -- 64BIT_VERSION=yes - make -j20 "INSTALL=install --strip-program=true" 64BIT_VERSION=yes + make -j42 "INSTALL=install --strip-program=true" 64BIT_VERSION=yes make[2]: Entering directory '/build/reproducible-path/mothur-1.48.1' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/calculators/accuracy.o source/calculators/accuracy.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/calculators/ace.o source/calculators/ace.cpp @@ -550,18 +586,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/getopt_long.o source/clearcut/getopt_long.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/aligncheckcommand.o source/commands/aligncheckcommand.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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^ -source/clearcut/distclearcut.cpp:155:89: note: length computed here - 155 | *dmat->taxaname[i] = '\0'; strncat(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i])+1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/aligncheckcommand.o source/commands/aligncheckcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/aligncommand.o source/commands/aligncommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/alignmusclecommand.o source/commands/alignmusclecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/amovacommand.o source/commands/amovacommand.cpp @@ -571,48 +600,55 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 +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); + | ^ +source/clearcut/distclearcut.cpp:155:89: note: length computed here + 155 | *dmat->taxaname[i] = '\0'; strncat(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i])+1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/chimerapintailcommand.o source/commands/chimerapintailcommand.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 -fcf-protection -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/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/chopseqscommand.o source/commands/chopseqscommand.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 -fcf-protection -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 -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] - 412 | 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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/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 -fcf-protection -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/clustercommand.o source/commands/clustercommand.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 -fcf-protection -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/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/clusterfitcommand.o source/commands/clusterfitcommand.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] + 412 | 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 -fcf-protection -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/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp +source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)': +source/commands/clustercommand.cpp:542:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 542 | 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 -fcf-protection -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/clustersplitcommand.o source/commands/clustersplitcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/collectcommand.o source/commands/collectcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/collectsharedcommand.o source/commands/collectsharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/consensusseqscommand.o source/commands/consensusseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/corraxescommand.o source/commands/corraxescommand.cpp -source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)': -source/commands/clustercommand.cpp:542:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 542 | 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 -fcf-protection -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/countgroupscommand.o source/commands/countgroupscommand.cpp source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::string, std::string, std::string, double, clusterData*)': source/commands/clustersplitcommand.cpp:1050:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1050 | 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 -fcf-protection -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/countgroupscommand.o source/commands/countgroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/countseqscommand.o source/commands/countseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/createdatabasecommand.o source/commands/createdatabasecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/degapseqscommand.o source/commands/degapseqscommand.cpp @@ -625,12 +661,12 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/filtersharedcommand.o source/commands/filtersharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/getcurrentcommand.o source/commands/getcurrentcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/getdistscommand.o source/commands/getdistscommand.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 -fcf-protection -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/getcurrentcommand.o source/commands/getcurrentcommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/getdistscommand.o source/commands/getdistscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/getgroupcommand.o source/commands/getgroupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/getgroupscommand.o source/commands/getgroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/getlabelcommand.o source/commands/getlabelcommand.cpp @@ -662,15 +698,15 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/mergecountcommand.o source/commands/mergecountcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/mergefilecommand.o source/commands/mergefilecommand.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 -fcf-protection -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/mergegroupscommand.o source/commands/mergegroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/mergeotuscommand.o source/commands/mergeotuscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/mergesfffilecommand.o source/commands/mergesfffilecommand.cpp @@ -686,10 +722,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 @@ -697,6 +729,10 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 +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 -fcf-protection -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/quitcommand.o source/commands/quitcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rarefactcommand.o source/commands/rarefactcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp @@ -727,23 +763,23 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/splitgroupscommand.o source/commands/splitgroupscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/sracommand.o source/commands/sracommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/srainfocommand.o source/commands/srainfocommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/subsamplecommand.o source/commands/subsamplecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/summarycommand.o source/commands/summarycommand.cpp source/commands/srainfocommand.cpp: In member function 'void SRAInfoCommand::runSystemCommand(std::string)': source/commands/srainfocommand.cpp:487:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | system(inputString.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 -fcf-protection -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/subsamplecommand.o source/commands/subsamplecommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/summarycommand.o source/commands/summarycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/summaryqualcommand.o source/commands/summaryqualcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp @@ -874,14 +910,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -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()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -source/utils.cpp: In member function 'std::string Utils::sortFile(std::string, std::string)': -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()); - | ~~~~~~^~~~~~~~~~~~~~~~~ cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd .. make[3]: Entering directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src' make[3]: Leaving directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src' @@ -901,6 +929,14 @@ 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 path.o path.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 searchchime.o searchchime.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 seqdb.o seqdb.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()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +source/utils.cpp: In member function 'std::string Utils::sortFile(std::string, std::string)': +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++ -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 setnucmx.o setnucmx.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 sfasta.o sfasta.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 tracebackbit.o tracebackbit.cpp @@ -1087,12 +1123,14 @@ 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/3900949/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3900949/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/3572391 and its subdirectories -I: Current time: Wed Mar 5 20:35:15 -12 2025 -I: pbuilder-time-stamp: 1741250115 +I: removing directory /srv/workspace/pbuilder/3900949 and its subdirectories +I: Current time: Thu Apr 9 05:01:46 +14 2026 +I: pbuilder-time-stamp: 1775660506