Diff of the two buildlogs: -- --- b1/build.log 2025-08-30 07:47:26.253926276 +0000 +++ b2/build.log 2025-08-30 07:58:26.222823585 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 2 02:07:09 -12 2026 -I: pbuilder-time-stamp: 1790950029 +I: Current time: Sat Aug 30 21:47:29 +14 2025 +I: pbuilder-time-stamp: 1756540049 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying gcc-12.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2283948/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/710830/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Aug 30 07:47 /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/710830/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/710830/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="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=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='ac586c25200b4bc5bec62e6b665d31a1' - 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='2283948' - PS1='# ' - PS2='> ' + INVOCATION_ID=0d27c704ffe94b35af0bc86ec051e5d4 + 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=710830 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.lfPpubuv/pbuilderrc_ZjOd --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.lfPpubuv/b1 --logfile b1/build.log parsinsert_1.04-15.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://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lfPpubuv/pbuilderrc_UCQn --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.lfPpubuv/b2 --logfile b2/build.log parsinsert_1.04-15.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://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2283948/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/710830/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -137,7 +169,7 @@ Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] 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] -Fetched 11.2 MB in 4s (2800 kB/s) +Fetched 11.2 MB in 0s (30.7 MB/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 ... 19855 files and directories currently installed.) @@ -268,7 +300,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/parsinsert-1.04/ && 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 > ../parsinsert_1.04-15_source.changes +I: user script /srv/workspace/pbuilder/710830/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/710830/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/parsinsert-1.04/ && 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 > ../parsinsert_1.04-15_source.changes dpkg-buildpackage: info: source package parsinsert dpkg-buildpackage: info: source version 1.04-15 dpkg-buildpackage: info: source distribution unstable @@ -282,7 +318,7 @@ mv parsinsert ParsInsert || true mv: cannot stat 'parsinsert': No such file or directory dh_auto_clean - make -j42 clean + make -j40 clean make[2]: Entering directory '/build/reproducible-path/parsinsert-1.04' rm -f ParsInsert AttrList.o Knox_Stddef.o PNode.o SeqList.o Taxonomy.o ParsInsert.o *.fasta *.log *.results *.tree make[2]: Leaving directory '/build/reproducible-path/parsinsert-1.04' @@ -297,7 +333,7 @@ make[1]: Entering directory '/build/reproducible-path/parsinsert-1.04' blhc: ignore-line-regexp: ^g\+\+ .* -fPIE.*$ dh_auto_build - make -j42 "INSTALL=install --strip-program=true" + make -j40 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/parsinsert-1.04' g++ -Wdate-time -g -O2 -ffile-prefix-map=/build/reproducible-path/parsinsert-1.04=. -specs=/usr/share/dpkg/no-pie-compile.specs -fPIE -c -o AttrList.o AttrList.cpp g++ -Wdate-time -g -O2 -ffile-prefix-map=/build/reproducible-path/parsinsert-1.04=. -specs=/usr/share/dpkg/no-pie-compile.specs -fPIE -c -o Knox_Stddef.o Knox_Stddef.cpp @@ -327,30 +363,6 @@ Taxonomy.cpp:96:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 96 | DisplayL("%s[%s] %d\n", leader, name.c_str(), count); | ^~~~~~~~~~~~~ -In file included from PNode.h:31, - from SeqList.cpp:27: -ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': -ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 429 | DisplayL("%s [", label); - | ^~~~~~ -ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 431 | DisplayL(" %3d", segCounts[k]); - | ^~~~~~ -ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 432 | DisplayL("]\n"); - | ^~~~~ -In file included from PNode.h:31, - from PNode.cpp:27: -ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': -ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 429 | DisplayL("%s [", label); - | ^~~~~~ -ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 431 | DisplayL(" %3d", segCounts[k]); - | ^~~~~~ -ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 432 | DisplayL("]\n"); - | ^~~~~ In file included from ParsInsert.h:29, from ParsInsert.cpp:34: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': @@ -363,40 +375,6 @@ ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 432 | DisplayL("]\n"); | ^~~~~ -SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceIndexFile(const char*)': -SeqList.cpp:490:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 490 | DisplayT("Loading sequence %d [%s]\n", count, name); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp:492:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 492 | DisplayT("Loading sequence %d\n", count); - | ^~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp:496:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 496 | DisplayT("Loaded %d sequences from [%s]\n", count, filename); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp: In member function 'int CSequenceFile::ReadTaxonomyFile()': -SeqList.cpp:529:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 529 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp:531:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 531 | DisplayT("Loading sequence %d\n", seqCount); - | ^~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceFile(int)': -SeqList.cpp:565:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 565 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp:580:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 580 | DisplayL("Duplicate sequence found [%s]\n", seq->name.c_str()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SeqList.cpp:605:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 605 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -PNode.cpp: In member function 'void CPTree::Parse(const char*)': -PNode.cpp:299:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 299 | DisplayL("Could not process all the chars in NEWICK file\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -PNode.cpp:304:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 304 | DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: At global scope: ParsInsert.cpp:93:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 93 | char *statsName = "PI_Results.log"; @@ -587,6 +565,18 @@ ParsInsert.cpp:958:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 958 | DisplayL("\n"); | ^~~~ +In file included from PNode.h:31, + from PNode.cpp:27: +ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': +ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 429 | DisplayL("%s [", label); + | ^~~~~~ +ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 431 | DisplayL(" %3d", segCounts[k]); + | ^~~~~~ +ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 432 | DisplayL("]\n"); + | ^~~~~ ParsInsert.cpp: In function 'int SetInternalTaxonomy(CPTree*)': ParsInsert.cpp:1092:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1092 | DisplayT("\rSetting Internal Taxonomy %d nodes remaining ", nSeqRemaining); @@ -709,10 +699,22 @@ ParsInsert.cpp:1830:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1830 | DisplayT("\r %d nodes remaining to be written ", nSeqRemaining); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from PNode.h:31, + from SeqList.cpp:27: +ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': +ParsimonySet.h:429:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 429 | DisplayL("%s [", label); + | ^~~~~~ ParsInsert.cpp: In function 'void DisplayInsertLocations(CInsertPosArray&, int)': ParsInsert.cpp:1881:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1881 | DisplayL("======================================================================\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ParsimonySet.h:431:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 431 | DisplayL(" %3d", segCounts[k]); + | ^~~~~~ +ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 432 | DisplayL("]\n"); + | ^~~~~ ParsInsert.cpp:1883:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1883 | DisplayL("\nInsertion of [%s][%5d sites] [%d matches] Taxonomy[%s]:\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -834,12 +836,39 @@ ParsInsert.cpp:3038:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 3038 | DisplayL("\nDistance to Insertion: [%20.20s] [%5d sites]\n", name.c_str(), inserts[i]->best.list.size()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceIndexFile(const char*)': +SeqList.cpp:490:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 490 | DisplayT("Loading sequence %d [%s]\n", count, name); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:492:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 492 | DisplayT("Loading sequence %d\n", count); + | ^~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:496:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 496 | DisplayT("Loaded %d sequences from [%s]\n", count, filename); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp:3042:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 3042 | DisplayL("\tNO MATCHES found for [%s]\n", name.c_str()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp: In member function 'int CSequenceFile::ReadTaxonomyFile()': +SeqList.cpp:529:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 529 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:531:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 531 | DisplayT("Loading sequence %d\n", seqCount); + | ^~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceFile(int)': +SeqList.cpp:565:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 565 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp:3055:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 3055 | DisplayL("\tDistance error from [%20.20s] = %d\n", pname.c_str(), dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:580:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 580 | DisplayL("Duplicate sequence found [%s]\n", seq->name.c_str()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SeqList.cpp:605:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 605 | DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'int FullTree_Initialization()': ParsInsert.cpp:3070:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 3070 | DisplayL("Reading Newick Tree: [%s]\n", fullTreeName); @@ -850,6 +879,13 @@ ParsInsert.cpp:3078:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 3078 | DisplayL("Newick Tree Read Completed: %d taxa\n", (fullTree->nodeList.size()+1)/2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +PNode.cpp: In member function 'void CPTree::Parse(const char*)': +PNode.cpp:299:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 299 | DisplayL("Could not process all the chars in NEWICK file\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +PNode.cpp:304:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 304 | DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -g -O2 -ffile-prefix-map=/build/reproducible-path/parsinsert-1.04=. -specs=/usr/share/dpkg/no-pie-compile.specs -fPIE -o ParsInsert AttrList.o Knox_Stddef.o PNode.o SeqList.o Taxonomy.o ParsInsert.o -lm -lc -specs=/usr/share/dpkg/no-pie-link.specs make[2]: Leaving directory '/build/reproducible-path/parsinsert-1.04' mv ParsInsert parsinsert @@ -892,7 +928,7 @@ Newick Tree Read Completed: 10143 taxa, 0 sec Tree Sequence Reading: [core_rdp.fasta] Loading sequence 10143 [51224] -Tree Sequence Read Completed: 10143 sequences, 1 sec +Tree Sequence Read Completed: 10143 sequences, 0 sec Reading sequences for insertion: [set1000.fasta] Duplicate sequence found [175015] Duplicate sequence found [290252] @@ -979,15 +1015,15 @@ [Thermotogae] 24 [Verrucomicrobia] 87 [WS3] 7 -Internal Taxonomy Completed: 2 sec +Internal Taxonomy Completed: 4 sec Setting internal parsimony sequences ... Calculating internal parsimony sequences ... Calculating Parsimony ... CalcParsimony 20000 nodes remaining CalcParsimony 19000 nodes remaining CalcParsimony 18000 nodes remaining CalcParsimony 17000 nodes remaining CalcParsimony 16000 nodes remaining CalcParsimony 15000 nodes remaining CalcParsimony 14000 nodes remaining CalcParsimony 13000 nodes remaining CalcParsimony 12000 nodes remaining CalcParsimony 11000 nodes remaining CalcParsimony 10000 nodes remaining CalcParsimony 9000 nodes remaining CalcParsimony 8000 nodes remaining CalcParsimony 7000 nodes remaining CalcParsimony 6000 nodes remaining CalcParsimony 5000 nodes remaining CalcParsimony 4000 nodes remaining CalcParsimony 3000 nodes remaining CalcParsimony 2000 nodes remaining CalcParsimony 1000 nodes remaining CalcParsimony 0 nodes remaining Applying parsimonious selections back down the tree. 10147 nodes were modified -Processed 20285 nodes in 3 seconds, 6762 nodes per sec -Parsimony Calculation Completed: 2 sec -[5 sec elapsed] Searching for insertion points: +Processed 20285 nodes in 5 seconds, 4057 nodes per sec +Parsimony Calculation Completed: 4 sec +[9 sec elapsed] Searching for insertion points: **** Sequence is already in core tree: 100403 **** Sequence is already in core tree: 100628 Insert [ 100769](len=7683) [ 1235 sites] (147 - 6732) [Bacteria;Actinobacteria;Actinobacteria;Actinomycetales;Streptosporangineae;Nocardiopsaceae;Nocardiopsis] @@ -1987,28 +2023,28 @@ Insert [ 99538](len=7683) [ 1184 sites] (137 - 6427) [Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;Chryseobacterium] Insert [ 99764](len=7683) [ 1261 sites] (130 - 6790) [Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Brucellaceae;Brucella] Searching for position to insert 957 sequences in tree of 20285 nodes. {Setup: 2 sec} -[ 1000/20285] {10 sec} [I_1000] -[ 2000/20285] {18 sec} [7996] -[ 3000/20285] {25 sec} [39961] -[ 4000/20285] {32 sec} [81358] -[ 5000/20285] {40 sec} [I_5000] -[ 6000/20285] {48 sec} [4546] -[ 7000/20285] {56 sec} [67802] -[ 8000/20285] {62 sec} [135894] -[ 9000/20285] {66 sec} [I_9000] -[ 10000/20285] {70 sec} [137100] -[ 11000/20285] {75 sec} [I_11000] -[ 12000/20285] {79 sec} [63458] -[ 13000/20285] {83 sec} [47043] -[ 14000/20285] {88 sec} [I_14000] -[ 15000/20285] {92 sec} [44776] -[ 16000/20285] {95 sec} [16125] -[ 17000/20285] {98 sec} [I_17000] -[ 18000/20285] {100 sec} [99851] -[ 19000/20285] {102 sec} [104182] -[ 20000/20285] {104 sec} [63281] -Insertion of 957 sequences in [104 sec] -[108 sec elapsed] Insert Locations Completed: 103 sec +[ 1000/20285] {12 sec} [I_1000] +[ 2000/20285] {38 sec} [7996] +[ 3000/20285] {64 sec} [39961] +[ 4000/20285] {93 sec} [81358] +[ 5000/20285] {113 sec} [I_5000] +[ 6000/20285] {158 sec} [4546] +[ 7000/20285] {185 sec} [67802] +[ 8000/20285] {204 sec} [135894] +[ 9000/20285] {248 sec} [I_9000] +[ 10000/20285] {271 sec} [137100] +[ 11000/20285] {310 sec} [I_11000] +[ 12000/20285] {332 sec} [63458] +[ 13000/20285] {347 sec} [47043] +[ 14000/20285] {356 sec} [I_14000] +[ 15000/20285] {378 sec} [44776] +[ 16000/20285] {397 sec} [16125] +[ 17000/20285] {407 sec} [I_17000] +[ 18000/20285] {419 sec} [99851] +[ 19000/20285] {441 sec} [104182] +[ 20000/20285] {454 sec} [63281] +Insertion of 957 sequences in [457 sec] +[465 sec elapsed] Insert Locations Completed: 456 sec ====================================================================== Insertion: [ 100769] [ 1235 sites] @@ -9214,8 +9250,8 @@ Family: 830 821 ( 98.92%) 821 876 ( 93.72%) Genus: 573 563 ( 98.25%) 563 706 ( 79.75%) Species: 49 49 (100.00%) 49 53 ( 92.45%) -Insert Time = 103, 33448 per hour -Process Completed: 108 sec +Insert Time = 456, 7555 per hour +Process Completed: 467 sec make[1]: Leaving directory '/build/reproducible-path/parsinsert-1.04' create-stamp debian/debhelper-build-stamp dh_prep @@ -9252,12 +9288,14 @@ 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/710830/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/710830/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/2283948 and its subdirectories -I: Current time: Fri Oct 2 02:10:25 -12 2026 -I: pbuilder-time-stamp: 1790950225 +I: removing directory /srv/workspace/pbuilder/710830 and its subdirectories +I: Current time: Sat Aug 30 21:58:25 +14 2025 +I: pbuilder-time-stamp: 1756540705