Diff of the two buildlogs: -- --- b1/build.log 2019-06-12 17:40:38.480433891 +0000 +++ b2/build.log 2019-06-12 17:42:06.820376888 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 12 05:25:48 -12 2019 -I: pbuilder-time-stamp: 1560360348 +I: Current time: Wed Jul 15 14:03:40 +14 2020 +I: pbuilder-time-stamp: 1594771420 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Oct 25 02:39:56 2018 -12 +gpgv: Signature made Fri Oct 26 04:39:56 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,6 +30,18 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/2376/tmp/hooks/D01_modify_environment starting +disorder-fs debug: Running on profitbricks-build16-i386. +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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/2376/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -98,7 +110,7 @@ Get: 31 http://cdn-fastly.deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://cdn-fastly.deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://cdn-fastly.deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] -Fetched 19.3 MB in 14s (1416 kB/s) +Fetched 19.3 MB in 4s (4799 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) @@ -251,9 +263,41 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 182 kB of additional disk space will be used. +Get:1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libnumber-compare-perl all 0.03-1 [7642 B] +Get:2 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtext-glob-perl all 0.10-1 [8362 B] +Get:3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://cdn-fastly.deb.debian.org/debian buster/main i386 usrmerge all 21 [12.8 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 1s (102 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 21275 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.10-1_all.deb ... +Unpacking libtext-glob-perl (0.10-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_21_all.deb ... +Unpacking usrmerge (21) ... +Setting up libtext-glob-perl (0.10-1) ... +Setting up libnumber-compare-perl (0.03-1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (21) ... +The system has been successfully converted. +Processing triggers for man-db (2.8.5-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/rate4site-3.0.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/rate4site-3.0.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package rate4site dpkg-buildpackage: info: source version 3.0.0-6 dpkg-buildpackage: info: source distribution unstable @@ -273,7 +317,7 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -296,8 +340,8 @@ checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes @@ -333,7 +377,7 @@ config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build - make -j10 + make -j18 make[1]: Entering directory '/build/rate4site-3.0.0' make all-recursive make[2]: Entering directory '/build/rate4site-3.0.0' @@ -353,10 +397,6 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o errorMsg.o errorMsg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nucleotide.o nucleotide.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o amino.o amino.cpp -someUtil.cpp: In function 'void createDir(const string&, const string&)': -someUtil.cpp:507:16: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - system(sysCall.c_str()); - ~~~~~~^~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o geneticCodeHolder.o geneticCodeHolder.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o codon.o codon.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o doubleRep.o doubleRep.cpp @@ -370,6 +410,10 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o aaJC.o aaJC.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gtrModel.o gtrModel.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fromQtoPt.o fromQtoPt.cpp +someUtil.cpp: In function 'void createDir(const string&, const string&)': +someUtil.cpp:507:16: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + system(sysCall.c_str()); + ~~~~~~^~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o distanceTable.o distanceTable.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nj.o nj.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o njConstrain.o njConstrain.cpp @@ -447,7 +491,7 @@ make[2]: Leaving directory '/build/rate4site-3.0.0' make[1]: Leaving directory '/build/rate4site-3.0.0' dh_auto_test - make -j10 check VERBOSE=1 + make -j18 check VERBOSE=1 make[1]: Entering directory '/build/rate4site-3.0.0' Making check in src/phylogeny make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' @@ -466,14 +510,14 @@ dh_testroot dh_prep dh_auto_install - make -j10 install DESTDIR=/build/rate4site-3.0.0/debian/rate4site AM_UPDATE_INFO_DIR=no + make -j18 install DESTDIR=/build/rate4site-3.0.0/debian/rate4site AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/rate4site-3.0.0' Making install in src/phylogeny make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' make[3]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' - /bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/lib/i386-linux-gnu' + /usr/bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/lib/i386-linux-gnu' /usr/bin/install -c -m 644 libphylo.a '/build/rate4site-3.0.0/debian/rate4site/usr/lib/i386-linux-gnu' - /bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' + /usr/bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' /usr/bin/install -c -m 644 replacementMatrixSource/mitochondriaAscidian.code replacementMatrixSource/mitochondriaProtozoan.code replacementMatrixSource/nuclearCiliate.code replacementMatrixSource/mitochondriaEchinoderm.code replacementMatrixSource/mitochondriaVertebrate.code replacementMatrixSource/nuclearEuplotid.code replacementMatrixSource/mitochondriaFlatworm.code replacementMatrixSource/mitochondriaYeast.code replacementMatrixSource/nuclearStandard.code replacementMatrixSource/mitochondriaInvertebrate.code replacementMatrixSource/nuclearBlepharisma.code cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q adrianCodon.dat.q LG.dat.q replacementMatrixSource/cpREV45.dat replacementMatrixSource/dayhoff.dat replacementMatrixSource/jones.dat replacementMatrixSource/mtREV24.dat replacementMatrixSource/wag.dat getopt.h errorMsg.h definitions.h doubleRep.h ConversionUtils.h sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h pijAccelerator.h replacementModel.h distribution.h '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' /usr/bin/install -c -m 644 readTree.h nucleotide.h amino.h geneticCodeHolder.h codon.h evaluateCharacterFreq.h uniDistribution.h generalGammaDistribution.h readDatMatrix.h datMatrixHolder.h chebyshevAccelerator.h nucJC.h aaJC.h gtrModel.h fromQtoPt.h trivialAccelerator.h distanceMethod.h distanceTable.h nj.h njConstrain.h distances2Tree.h numRec.h uniformDistribution.h checkcovFanctors.h likelihoodComputation.h computePijComponent.h stochasticProcess.h suffStatComponent.h unObservableData.h likeDist.h countTableComponent.h jcDistance.h fastStartTree.h checkcovFanctorsWithFactors.h likelihoodComputationFactors.h bestAlpha.h gammaDistribution.h siteSpecificRate.h recognizeFormat.h bblEM.h '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' /usr/bin/install -c -m 644 bestGtrModelParams.h tamura92.h bestHKYparam.h hky.h bestTamura92param.h talRandom.h computeSubstitutionCounts.h fromCountTableComponentToDistance.h computeCounts.h computeDownAlg.h computeUpAlg.h gammaUtilities.h seqContainerTreeMap.h treeUtil.h matrixUtils.h computePosteriorExpectationOfSubstitutions.h computePosteriorExpectationOfSubstitutions_nonReversibleSp.h multipleStochasticProcess.h simulateJumps.h simulateJumpsAbstract.h simulateCodonsJumps.h treeIt.h likelihoodComputationGL.h tree.h bblEMProportionalEB.h fromCountTableComponentToDistancePropEB.h likeDistPropEB.h bblLSProportionalEB.h phylipFormat.h maseFormat.h clustalFormat.h fastaFormat.h phylipSequentialFormat.h molphyFormat.h getRandomWeights.h nexusFormat.h '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' @@ -483,8 +527,8 @@ Making install in src/rate4site make[2]: Entering directory '/build/rate4site-3.0.0/src/rate4site' make[3]: Entering directory '/build/rate4site-3.0.0/src/rate4site' - /bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/bin' - /bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/share/man/man1' + /usr/bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/bin' + /usr/bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/share/man/man1' /usr/bin/install -c rate4site rate4site_doublerep '/build/rate4site-3.0.0/debian/rate4site/usr/bin' /usr/bin/install -c -m 644 rate4site.1 '/build/rate4site-3.0.0/debian/rate4site/usr/share/man/man1' make[3]: Leaving directory '/build/rate4site-3.0.0/src/rate4site' @@ -520,12 +564,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/2376/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2376/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/26806 and its subdirectories -I: Current time: Wed Jun 12 05:40:38 -12 2019 -I: pbuilder-time-stamp: 1560361238 +I: removing directory /srv/workspace/pbuilder/2376 and its subdirectories +I: Current time: Wed Jul 15 14:04:29 +14 2020 +I: pbuilder-time-stamp: 1594771469