Diff of the two buildlogs: -- --- b1/build.log 2025-09-12 15:45:49.736019908 +0000 +++ b2/build.log 2025-09-12 15:49:08.132269017 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Sep 12 03:42:58 -12 2025 -I: pbuilder-time-stamp: 1757691778 +I: Current time: Fri Oct 16 12:08:58 +14 2026 +I: pbuilder-time-stamp: 1792102138 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ dpkg-source: info: applying fix-gcc13-ftbfs.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3487565/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/198980/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 15 22:09 /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/198980/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/198980/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=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='dbadd048af634df9b5ec9425fd1e609d' - 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='3487565' - PS1='# ' - PS2='> ' + INVOCATION_ID=5b01543cceee4bce96b7385305759c2a + 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=198980 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.Q0BrcaxJ/pbuilderrc_BApq --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.Q0BrcaxJ/b1 --logfile b1/build.log mecat2_0.0+git20200428.f54c542+ds-4.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - 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.Q0BrcaxJ/pbuilderrc_9n3V --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.Q0BrcaxJ/b2 --logfile b2/build.log mecat2_0.0+git20200428.f54c542+ds-4.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + 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 ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3487565/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/198980/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -139,7 +171,7 @@ Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 12.1 MB in 8s (1559 kB/s) +Fetched 12.1 MB in 8s (1562 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -274,7 +306,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mecat2-0.0+git20200428.f54c542+ds/ && 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 > ../mecat2_0.0+git20200428.f54c542+ds-4_source.changes +I: user script /srv/workspace/pbuilder/198980/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/198980/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mecat2-0.0+git20200428.f54c542+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mecat2_0.0+git20200428.f54c542+ds-4_source.changes dpkg-buildpackage: info: source package mecat2 dpkg-buildpackage: info: source version 0.0+git20200428.f54c542+ds-4 dpkg-buildpackage: info: source distribution unstable @@ -284,7 +320,7 @@ debian/rules clean dh clean dh_auto_clean - make -j40 clean + make -j42 clean make[1]: Entering directory '/build/reproducible-path/mecat2-0.0+git20200428.f54c542+ds' cd src && make clean make[2]: Entering directory '/build/reproducible-path/mecat2-0.0+git20200428.f54c542+ds/src' @@ -322,7 +358,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j40 "INSTALL=install --strip-program=true" + make -j42 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/mecat2-0.0+git20200428.f54c542+ds' cd src && make make[2]: Entering directory '/build/reproducible-path/mecat2-0.0+git20200428.f54c542+ds/src' @@ -383,6 +419,8 @@ g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_allow.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_desc.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_types.cpp +g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr_util.cpp +g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr.cpp corelib/hbn_aux.c: In function ‘hbn_get_cpu_count’: corelib/hbn_aux.c:357:9: warning: unused variable ‘allCPUNum_’ [-Wunused-variable] 357 | int allCPUNum_ = sysconf(_SC_NPROCESSORS_CONF); @@ -396,8 +434,6 @@ corelib/seq_tag.c:7:12: warning: ‘RepeatSeq’ defined but not used [-Wunused-variable] 7 | static int RepeatSeq = 0; | ^~~~~~~~~ -g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr_util.cpp -g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/str_cmp.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/numeric_str_interconv.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/str_util.cpp @@ -405,41 +441,29 @@ cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_hits.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_message.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_options.c -ncbi_blast/setup/blast_hits.c:3897:1: warning: ‘s_TrimResultsByTotalHSPLimitEx’ defined but not used [-Wunused-function] - 3897 | s_TrimResultsByTotalHSPLimitEx(BlastHSPResults* results, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbi_blast/setup/blast_hits.c:3815:1: warning: ‘s_TrimResultsByTotalHSPLimit’ defined but not used [-Wunused-function] - 3815 | s_TrimResultsByTotalHSPLimit(BlastHSPResults* results, Uint4 total_hsp_limit) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbi_blast/setup/blast_hits.c:3580:12: warning: ‘s_SortHspWrapRawScore’ defined but not used [-Wunused-function] - 3580 | static int s_SortHspWrapRawScore(const void *x, const void *y) - | ^~~~~~~~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_stat.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_parameters.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_program.c g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/setup/blast_types.cpp cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/boost_erf.c -algo/chain_dp.c: In function ‘find_best_kmer_match’: -algo/chain_dp.c:164:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] - 164 | memset(t, 0, sizeof(int) * n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -algo/chain_dp.c: In function ‘chaining_find_candidates’: -algo/chain_dp.c:257:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] - 257 | memset(t, 0, sizeof(int) * n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -algo/diff_gapalign.cpp:375:1: warning: ‘void dump_subseq(const u8*, int)’ defined but not used [-Wunused-function] - 375 | dump_subseq(const u8* seq, int len) - | ^~~~~~~~~~~ g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/setup/hsp2string.cpp cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/ncbi_math.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_query_info.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_sequence_blk.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/gapinfo.c +ncbi_blast/setup/blast_hits.c:3897:1: warning: ‘s_TrimResultsByTotalHSPLimitEx’ defined but not used [-Wunused-function] + 3897 | s_TrimResultsByTotalHSPLimitEx(BlastHSPResults* results, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbi_blast/setup/blast_hits.c:3815:1: warning: ‘s_TrimResultsByTotalHSPLimit’ defined but not used [-Wunused-function] + 3815 | s_TrimResultsByTotalHSPLimit(BlastHSPResults* results, Uint4 total_hsp_limit) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbi_blast/setup/blast_hits.c:3580:12: warning: ‘s_SortHspWrapRawScore’ defined but not used [-Wunused-function] + 3580 | static int s_SortHspWrapRawScore(const void *x, const void *y) + | ^~~~~~~~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2pcan app/mecat2pcan/pcan.c g++ -o ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/map app/map/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_align_one_volume.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_build_seqdb.c -cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_extend_subseq_hit.c In file included from ncbi_blast/setup/ncbi_math.c:498: ncbi_blast/setup/ncbi_erf.c: In function ‘s_IEEE754_Exp’: ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] @@ -455,7 +479,6 @@ ncbi_blast/setup/ncbi_erf.c:401:9: note: in expansion of macro ‘__LO’ 401 | __LO(z) = 0; | ^~~~ -cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_find_subseq_hit.c ncbi_blast/setup/ncbi_erf.c: In function ‘BLAST_ErfC’: ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 40 | #define __LO(x) *(int*)&x @@ -463,11 +486,21 @@ ncbi_blast/setup/ncbi_erf.c:462:13: note: in expansion of macro ‘__LO’ 462 | __LO(z) = 0; | ^~~~ +cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_extend_subseq_hit.c +cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_find_subseq_hit.c +algo/chain_dp.c: In function ‘find_best_kmer_match’: +algo/chain_dp.c:164:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] + 164 | memset(t, 0, sizeof(int) * n); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_job_control.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_options.c -cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_task_struct.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_subseq_hit.c +cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_task_struct.c cc -o ../Linux-amd64/obj/mecat2map/app/map/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/main.c +algo/chain_dp.c: In function ‘chaining_find_candidates’: +algo/chain_dp.c:257:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] + 257 | memset(t, 0, sizeof(int) * n); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2map/app/map/mecat_results.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/mecat_results.c g++ -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_aux.c @@ -477,13 +510,16 @@ cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns_align_tag.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns_aux.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns.c +algo/diff_gapalign.cpp:375:1: warning: ‘void dump_subseq(const u8*, int)’ defined but not used [-Wunused-function] + 375 | dump_subseq(const u8* seq, int len) + | ^~~~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/hbn_task_struct.c -cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/main.c -cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/raw_reads_reader.c app/mecat2cns/fccns_aux.c: In function ‘consensus_backbone_segment’: app/mecat2cns/fccns_aux.c:137:9: warning: variable ‘g_best_ck’ set but not used [-Wunused-but-set-variable] 137 | int g_best_ck = 0; | ^~~~~~~~~ +cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/main.c +cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/raw_reads_reader.c cc -o ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/hbndb app/hbndb/viewhbndb.c g++ -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/largest_cover_range.c @@ -493,31 +529,31 @@ g++ -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/main.c cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/split_reads.c -cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/common/m4_aux.c cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/common/range_list.c +cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/common/m4_aux.c cc -o ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/3_trim_bases app/mecat2trim/3_trim_bases/main.c cc -o ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2pm4 app/mecat2pm4/main.c -ncbi_blast/cmdline_args/ncbiargs_allow.cpp:85:15: warning: ‘std::string ncbi::s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass)’ defined but not used [-Wunused-function] - 85 | static string s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass symbol_class) - | ^~~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2extseqs -Iapp/mecat2extseqs/libboost app/mecat2extseqs/main.c g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/argument_parser.cpp cc -o ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/fsa app/fsa/getopt.c g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/logger.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/read_store.cpp +ncbi_blast/cmdline_args/ncbiargs_allow.cpp:85:15: warning: ‘std::string ncbi::s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass)’ defined but not used [-Wunused-function] + 85 | static string s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass symbol_class) + | ^~~~~~~~~~~~~~~~ g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/sequence.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/utility.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fasta_reader.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fastq_reader.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_store.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/simple_align.cpp +g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_filter.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_stat.cpp g++ -o ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_ol_filter.cpp -g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_filter.cpp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_assemble.cpp -g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/assembly.cpp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/graph.cpp +g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/assembly.cpp app/mecat2cns/cns_one_read.cpp: In function ‘BOOL meap_consensus_one_segment(FCCnsData*, int*, int*, int, int, kstring_t*)’: app/mecat2cns/cns_one_read.cpp:34:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 34 | if (ks_size(*cns_seq) < min_size) return FALSE; @@ -532,14 +568,13 @@ app/mecat2cns/cns_one_read.cpp:242:9: note: in expansion of macro ‘hbn_assert’ 242 | hbn_assert(read_length == kv_size(*fwd_read_v)); | ^~~~~~~~~~ -g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/string_graph.cpp -g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/path_graph.cpp app/map/cmdline_args.cpp:74:20: warning: ‘ncbi::kGroupExtension’ defined but not used [-Wunused-variable] 74 | static const char* kGroupExtension = "Extension options"; | ^~~~~~~~~~~~~~~ +g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/string_graph.cpp +g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/path_graph.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_ctg_bridge.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_bridge.cpp -g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_graph.cpp app/fsa/simple_align.cpp: In member function ‘SimpleAlign::Result SimpleAlign::Align(const std::string&, const std::string&, int, bool)’: app/fsa/simple_align.cpp:153:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 153 | if ( node.x + node.len >= query.size() || node.y + node.len >= target_.size()) { @@ -547,10 +582,18 @@ app/fsa/simple_align.cpp:153:75: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 153 | if ( node.x + node.len >= query.size() || node.y + node.len >= target_.size()) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_graph.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_link.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_link_store.cpp g++ -o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_rd_stat.cpp g++ -o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/read_stat.cpp +app/fsa/overlap_filter.cpp: In member function ‘void OverlapFilter::FilterLocalStep(Seq::Id, const std::unordered_map&)’: +app/fsa/overlap_filter.cpp:413:18: warning: unused variable ‘loc’ [-Wunused-variable] + 413 | auto loc = o.Location(max_overhang_); + | ^~~ +app/fsa/overlap_filter.cpp:447:22: warning: unused variable ‘loc’ [-Wunused-variable] + 447 | auto loc = o.Location(max_overhang_); + | ^~~ app/fsa/string_graph.cpp: In member function ‘std::vector StringNode::GetAllOutNodes()’: app/fsa/string_graph.cpp:39:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 39 | return std::move(nodes); @@ -561,13 +604,6 @@ 49 | return std::move(nodes); | ~~~~~~~~~^~~~~~~ app/fsa/string_graph.cpp:49:21: note: remove ‘std::move’ call -app/fsa/overlap_filter.cpp: In member function ‘void OverlapFilter::FilterLocalStep(Seq::Id, const std::unordered_map&)’: -app/fsa/overlap_filter.cpp:413:18: warning: unused variable ‘loc’ [-Wunused-variable] - 413 | auto loc = o.Location(max_overhang_); - | ^~~ -app/fsa/overlap_filter.cpp:447:22: warning: unused variable ‘loc’ [-Wunused-variable] - 447 | auto loc = o.Location(max_overhang_); - | ^~~ ncbi_blast/str_util/numeric_str_interconv.cpp: In function ‘ncbi::SIZE_TYPE ns_hbnstr::DoubleToString_Ecvt(double, unsigned int, char*, ncbi::SIZE_TYPE, int*, int*)’: ncbi_blast/str_util/numeric_str_interconv.cpp:2175:20: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 0 and 15 bytes from a string of length 31 [-Wstringop-truncation] 2175 | strncpy(buffer,digits,digits_len); @@ -654,8 +690,8 @@ g++ -o ../Linux-amd64/bin/mecat2lcr -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/bin/mecat2splitreads -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/bin/mecat2trimbases -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp -cc -o ../Linux-amd64/bin/mecat2pm4 -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/bin/mecat2extseqs -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp +cc -o ../Linux-amd64/bin/mecat2pm4 -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp ar -rv ../Linux-amd64/bin/libfsa.a ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o ar: creating ../Linux-amd64/bin/libfsa.a a - ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o @@ -732,12 +768,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/198980/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/198980/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/3487565 and its subdirectories -I: Current time: Fri Sep 12 03:45:49 -12 2025 -I: pbuilder-time-stamp: 1757691949 +I: removing directory /srv/workspace/pbuilder/198980 and its subdirectories +I: Current time: Fri Oct 16 12:12:07 +14 2026 +I: pbuilder-time-stamp: 1792102327