Diff of the two buildlogs: -- --- b1/build.log 2024-05-14 11:01:37.173740978 +0000 +++ b2/build.log 2024-05-14 11:07:20.915132957 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 13 22:59:06 -12 2024 -I: pbuilder-time-stamp: 1715684346 +I: Current time: Tue Jun 17 07:24:42 +14 2025 +I: pbuilder-time-stamp: 1750094682 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ 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/560823/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/536396/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 16 17:24 /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/536396/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/536396/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='5f720cce02f648979fceda2821fa02e2' - 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='560823' - PS1='# ' - PS2='> ' + INVOCATION_ID=1ed2d2c34f6c42228d4164d35c0cac0b + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=536396 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.7RWC9vGM/pbuilderrc_aAgY --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.7RWC9vGM/b1 --logfile b1/build.log parsinsert_1.04-15.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.7RWC9vGM/pbuilderrc_JGTB --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.7RWC9vGM/b2 --logfile b2/build.log parsinsert_1.04-15.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 11 11:23 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/560823/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 15 17:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/536396/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] -Fetched 18.7 MB in 0s (207 MB/s) +Fetched 18.7 MB in 0s (102 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19744 files and directories currently installed.) @@ -276,7 +308,11 @@ 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/536396/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/536396/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 @@ -331,6 +367,61 @@ ParsInsert.cpp:417:25: note: in expansion of macro 'VERSION' 417 | DisplayT(USAGE, VERSION, APPNAME); | ^~~~~~~ +Taxonomy.cpp: In member function 'int CTaxEntry::Display(const char*, int)': +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"); + | ^~~~~ +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()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ParsInsert.h:29, from ParsInsert.cpp:34: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': @@ -343,6 +434,13 @@ ParsimonySet.h:432:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 432 | DisplayL("]\n"); | ^~~~~ +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"; @@ -481,18 +579,6 @@ ParsInsert.cpp:624:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 624 | DisplayL("[%d sec elapsed] Insert Locations Completed: %d sec\n", time(NULL)-start, time(NULL)-stage); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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"); - | ^~~~~ ParsInsert.cpp:642:14: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 642 | DisplayL("Writing Newick tree file: [%s]\n", treename.c_str()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -667,16 +753,6 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Taxonomy.cpp: In member function 'int CTaxEntry::Display(const char*, int)': -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 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); - | ^~~~~~ 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"); @@ -684,12 +760,6 @@ 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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:1893:26: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1893 | DisplayL("\tNO MATCHES found\n"); | ^~~~~~~~~~~~~~~~~~~~~~ @@ -736,10 +806,6 @@ ParsInsert.cpp:2121:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2121 | DisplayL("%12.12s\t Best[%s]\n", "", taxBest.c_str()); | ^~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp:2123:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2123 | DisplayL("\tFirst[%s]\n", taxFirst.c_str()); | ^~~~~~~~~~~~~~~ @@ -750,39 +816,16 @@ ParsInsert.cpp:2142:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2142 | DisplayL("\t%10.10s: %8d %8d (%6.2f%%) %8d %8d (%6.2f%%)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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: In function 'void OutputInsertLocations(CInsertPosArray&, int)': ParsInsert.cpp:2183:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2183 | DisplayL("======================================================================\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~ ParsInsert.cpp:2184:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2184 | DisplayL("\nInsertion: [%20.20s] [%5d sites]\n", name.c_str(), inserts[i]->nSites); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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:2188:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2188 | DisplayL("\tNO MATCHES found\n"); | ^~~~~~~~~~~~~~~~~~~~~~ -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:2232:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2232 | DisplayL("\t\t%5d [%5f] [%s][%s]\n", iterB->score, dist, iterB->node->title.c_str(), iterB->tax.c_str()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -851,13 +894,6 @@ 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 @@ -905,7 +941,7 @@ Duplicate sequence found [175015] Duplicate sequence found [290252] Loading sequence 998 [174865] -Insert Sequecne Read Completed: 998 sequences, 0 sec +Insert Sequecne Read Completed: 998 sequences, 1 sec Checking Taxa Taxonomy 318 of 20285 nodes are missing taxonomy 40556 131780 113792 97603 21481 98089 130706 112397 @@ -987,15 +1023,15 @@ [Thermotogae] 24 [Verrucomicrobia] 87 [WS3] 7 -Internal Taxonomy Completed: 4 sec +Internal Taxonomy Completed: 6 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 4 seconds, 5071 nodes per sec -Parsimony Calculation Completed: 3 sec -[8 sec elapsed] Searching for insertion points: +Processed 20285 nodes in 10 seconds, 2028 nodes per sec +Parsimony Calculation Completed: 9 sec +[17 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] @@ -1995,28 +2031,28 @@ 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: 1 sec} -[ 1000/20285] {9 sec} [I_1000] -[ 2000/20285] {17 sec} [7996] -[ 3000/20285] {23 sec} [39961] -[ 4000/20285] {30 sec} [81358] -[ 5000/20285] {37 sec} [I_5000] -[ 6000/20285] {43 sec} [4546] -[ 7000/20285] {49 sec} [67802] -[ 8000/20285] {55 sec} [135894] -[ 9000/20285] {59 sec} [I_9000] -[ 10000/20285] {63 sec} [137100] -[ 11000/20285] {67 sec} [I_11000] -[ 12000/20285] {71 sec} [63458] -[ 13000/20285] {77 sec} [47043] -[ 14000/20285] {81 sec} [I_14000] -[ 15000/20285] {85 sec} [44776] -[ 16000/20285] {88 sec} [16125] -[ 17000/20285] {90 sec} [I_17000] -[ 18000/20285] {92 sec} [99851] -[ 19000/20285] {94 sec} [104182] -[ 20000/20285] {95 sec} [63281] -Insertion of 957 sequences in [96 sec] -[103 sec elapsed] Insert Locations Completed: 95 sec +[ 1000/20285] {21 sec} [I_1000] +[ 2000/20285] {40 sec} [7996] +[ 3000/20285] {60 sec} [39961] +[ 4000/20285] {73 sec} [81358] +[ 5000/20285] {100 sec} [I_5000] +[ 6000/20285] {120 sec} [4546] +[ 7000/20285] {133 sec} [67802] +[ 8000/20285] {144 sec} [135894] +[ 9000/20285] {153 sec} [I_9000] +[ 10000/20285] {162 sec} [137100] +[ 11000/20285] {168 sec} [I_11000] +[ 12000/20285] {176 sec} [63458] +[ 13000/20285] {183 sec} [47043] +[ 14000/20285] {190 sec} [I_14000] +[ 15000/20285] {196 sec} [44776] +[ 16000/20285] {202 sec} [16125] +[ 17000/20285] {207 sec} [I_17000] +[ 18000/20285] {213 sec} [99851] +[ 19000/20285] {219 sec} [104182] +[ 20000/20285] {223 sec} [63281] +Insertion of 957 sequences in [224 sec] +[240 sec elapsed] Insert Locations Completed: 223 sec ====================================================================== Insertion: [ 100769] [ 1235 sites] @@ -9222,8 +9258,8 @@ 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 = 95, 36265 per hour -Process Completed: 103 sec +Insert Time = 223, 15449 per hour +Process Completed: 240 sec make[1]: Leaving directory '/build/reproducible-path/parsinsert-1.04' create-stamp debian/debhelper-build-stamp dh_prep @@ -9250,8 +9286,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-15_arm64.deb'. dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-15_arm64.deb'. +dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-15_arm64.deb'. dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-15_all.deb'. dpkg-genbuildinfo --build=binary -O../parsinsert_1.04-15_arm64.buildinfo dpkg-genchanges --build=binary -O../parsinsert_1.04-15_arm64.changes @@ -9260,12 +9296,14 @@ 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/536396/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/536396/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/560823 and its subdirectories -I: Current time: Mon May 13 23:01:35 -12 2024 -I: pbuilder-time-stamp: 1715684496 +I: removing directory /srv/workspace/pbuilder/536396 and its subdirectories +I: Current time: Tue Jun 17 07:30:19 +14 2025 +I: pbuilder-time-stamp: 1750095019