Diff of the two buildlogs: -- --- b1/build.log 2024-05-08 21:03:47.272375397 +0000 +++ b2/build.log 2024-05-08 21:06:12.490191157 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 8 08:50:51 -12 2024 -I: pbuilder-time-stamp: 1715201451 +I: Current time: Wed Jun 11 17:26:50 +14 2025 +I: pbuilder-time-stamp: 1749612410 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/3536167/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3880415/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 Jun 11 03:26 /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/3880415/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3880415/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='unstable' - 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]="21" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='976b9740ebe1498bab8bc6e2bf51d691' - 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='3536167' - PS1='# ' - PS2='> ' + INVOCATION_ID=28f87957c4d04ed89f49a6c51670f562 + 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=3880415 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.0f5jMIuo/pbuilderrc_qnaO --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0f5jMIuo/b1 --logfile b1/build.log parsinsert_1.04-15.dsc' - SUDO_GID='110' - 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.0f5jMIuo/pbuilderrc_HzWP --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0f5jMIuo/b2 --logfile b2/build.log parsinsert_1.04-15.dsc' + SUDO_GID=111 + 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 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 7 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3536167/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 10 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3880415/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 unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] -Fetched 19.0 MB in 2s (9175 kB/s) +Fetched 19.0 MB in 1s (17.6 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 ... 19699 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/3880415/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3880415/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 @@ -290,7 +326,7 @@ mv parsinsert ParsInsert || true mv: cannot stat 'parsinsert': No such file or directory dh_auto_clean - make -j20 clean + make -j42 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' @@ -305,7 +341,7 @@ make[1]: Entering directory '/build/reproducible-path/parsinsert-1.04' blhc: ignore-line-regexp: ^g\+\+ .* -fPIE.*$ dh_auto_build - make -j20 "INSTALL=install --strip-program=true" + make -j42 "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 @@ -331,6 +367,34 @@ 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"); + | ^~~~~ In file included from ParsInsert.h:29, from ParsInsert.cpp:34: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': @@ -343,6 +407,40 @@ 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"; @@ -533,10 +631,6 @@ ParsInsert.cpp:958:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 958 | DisplayL("\n"); | ^~~~ -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); - | ^~~~~~~~~~~~~ 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); @@ -694,18 +788,6 @@ ParsInsert.cpp:2013:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2013 | DisplayL("\nInsertion of [%s][%5d sites] [%d matches] Taxonomy[%s]:\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:2022:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2022 | DisplayL("\tNO MATCHES found\n"); | ^~~~~~~~~~~~~~~~~~~~~~ @@ -756,21 +838,9 @@ ParsInsert.cpp:2307:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2307 | DisplayL("\t %6d (%4d diffs, %4d partials, %4d indels) [%s] \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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:2325:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2325 | DisplayL("%18s[%s]\n", leader.c_str(), taxVoteList[knox].c_str()); | ^~~~~~~~~~~~ -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:2332:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2332 | DisplayL("%18s[%s]\n", leader.c_str(), taxBest.c_str()); | ^~~~~~~~~~~~ @@ -824,40 +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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 @@ -900,7 +936,7 @@ Newick Tree Read Completed: 10143 taxa, 0 sec Tree Sequence Reading: [core_rdp.fasta] Loading sequence 10143 [51224] -Tree Sequence Read Completed: 10143 sequences, 2 sec +Tree Sequence Read Completed: 10143 sequences, 0 sec Reading sequences for insertion: [set1000.fasta] Duplicate sequence found [175015] Duplicate sequence found [290252] @@ -987,15 +1023,15 @@ [Thermotogae] 24 [Verrucomicrobia] 87 [WS3] 7 -Internal Taxonomy Completed: 13 sec +Internal Taxonomy Completed: 2 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 12 seconds, 1690 nodes per sec -Parsimony Calculation Completed: 12 sec -[29 sec elapsed] Searching for insertion points: +Processed 20285 nodes in 4 seconds, 5071 nodes per sec +Parsimony Calculation Completed: 3 sec +[5 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] @@ -1994,29 +2030,29 @@ **** Sequence is already in core tree: 9947 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] {47 sec} [I_1000] -[ 2000/20285] {94 sec} [7996] -[ 3000/20285] {125 sec} [39961] -[ 4000/20285] {152 sec} [81358] -[ 5000/20285] {180 sec} [I_5000] -[ 6000/20285] {213 sec} [4546] -[ 7000/20285] {250 sec} [67802] -[ 8000/20285] {283 sec} [135894] -[ 9000/20285] {313 sec} [I_9000] -[ 10000/20285] {340 sec} [137100] -[ 11000/20285] {362 sec} [I_11000] -[ 12000/20285] {382 sec} [63458] -[ 13000/20285] {411 sec} [47043] -[ 14000/20285] {441 sec} [I_14000] -[ 15000/20285] {470 sec} [44776] -[ 16000/20285] {491 sec} [16125] -[ 17000/20285] {510 sec} [I_17000] -[ 18000/20285] {523 sec} [99851] -[ 19000/20285] {536 sec} [104182] -[ 20000/20285] {546 sec} [63281] -Insertion of 957 sequences in [548 sec] -[576 sec elapsed] Insert Locations Completed: 547 sec +Searching for position to insert 957 sequences in tree of 20285 nodes. {Setup: 1 sec} +[ 1000/20285] {8 sec} [I_1000] +[ 2000/20285] {15 sec} [7996] +[ 3000/20285] {22 sec} [39961] +[ 4000/20285] {28 sec} [81358] +[ 5000/20285] {34 sec} [I_5000] +[ 6000/20285] {40 sec} [4546] +[ 7000/20285] {46 sec} [67802] +[ 8000/20285] {51 sec} [135894] +[ 9000/20285] {55 sec} [I_9000] +[ 10000/20285] {59 sec} [137100] +[ 11000/20285] {63 sec} [I_11000] +[ 12000/20285] {66 sec} [63458] +[ 13000/20285] {70 sec} [47043] +[ 14000/20285] {74 sec} [I_14000] +[ 15000/20285] {78 sec} [44776] +[ 16000/20285] {81 sec} [16125] +[ 17000/20285] {83 sec} [I_17000] +[ 18000/20285] {85 sec} [99851] +[ 19000/20285] {87 sec} [104182] +[ 20000/20285] {88 sec} [63281] +Insertion of 957 sequences in [89 sec] +[93 sec elapsed] Insert Locations Completed: 88 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 = 547, 6298 per hour -Process Completed: 577 sec +Insert Time = 88, 39150 per hour +Process Completed: 93 sec make[1]: Leaving directory '/build/reproducible-path/parsinsert-1.04' create-stamp debian/debhelper-build-stamp dh_prep @@ -9250,9 +9286,9 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-15_amd64.deb'. dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-15_amd64.deb'. dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-15_all.deb'. -dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-15_amd64.deb'. dpkg-genbuildinfo --build=binary -O../parsinsert_1.04-15_amd64.buildinfo dpkg-genchanges --build=binary -O../parsinsert_1.04-15_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -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/3880415/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3880415/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/3536167 and its subdirectories -I: Current time: Wed May 8 09:03:45 -12 2024 -I: pbuilder-time-stamp: 1715202226 +I: removing directory /srv/workspace/pbuilder/3880415 and its subdirectories +I: Current time: Wed Jun 11 17:29:12 +14 2025 +I: pbuilder-time-stamp: 1749612552