Diff of the two buildlogs: -- --- b1/build.log 2024-09-08 08:22:52.145729062 +0000 +++ b2/build.log 2024-09-08 08:26:28.092570891 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Sep 7 20:16:46 -12 2024 -I: pbuilder-time-stamp: 1725783406 +I: Current time: Sun Oct 12 04:45:55 +14 2025 +I: pbuilder-time-stamp: 1760193955 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying skip-failing-test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/966547/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/369190/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 11 14:46 /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/369190/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/369190/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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(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='6a1907e3d3a04c328c59f5e65f039929' - 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='966547' - PS1='# ' - PS2='> ' + INVOCATION_ID=0698ad1ed1d94fc794626c625b7cd39b + 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=369190 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.j9lgVDvp/pbuilderrc_Vbxv --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.j9lgVDvp/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-4.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.j9lgVDvp/pbuilderrc_4rER --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.j9lgVDvp/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-4.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 ionos11-amd64 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.10.6+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.6-1~bpo12+1 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/966547/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/369190/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -247,7 +279,7 @@ Get: 119 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.2-5 [153 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 netcdf-bin amd64 1:4.9.2-7 [252 kB] -Fetched 79.1 MB in 1s (54.0 MB/s) +Fetched 79.1 MB in 2s (45.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (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 ... 19770 files and directories currently installed.) @@ -757,7 +789,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && 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 > ../cpptraj_5.1.0+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/369190/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/369190/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && 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 > ../cpptraj_5.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -770,7 +806,7 @@ make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean - make -j20 clean + make -j42 clean make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' @@ -865,7 +901,7 @@ make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_build - make -j20 + make -j42 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' @@ -903,6 +939,14 @@ CXX Action_DistRmsd.cpp CXX Action_Energy.cpp CXX Action_FilterByData.cpp +CXX Action_FixAtomOrder.cpp +CXX Action_FixImagedBonds.cpp +CXX Action_Grid.cpp +CXX Action_GIST.cpp +CXX Action_GridFreeEnergy.cpp +CXX Action_HydrogenBond.cpp +CXX Action_Image.cpp +CXX Action_InfraredSpectrum.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] @@ -947,14 +991,6 @@ 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for -CXX Action_FixAtomOrder.cpp -CXX Action_FixImagedBonds.cpp -CXX Action_GIST.cpp -CXX Action_Grid.cpp -CXX Action_GridFreeEnergy.cpp -CXX Action_HydrogenBond.cpp -CXX Action_Image.cpp -CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp @@ -965,6 +1001,27 @@ CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp +CXX Action_MultiVector.cpp +CXX Action_NAstruct.cpp +CXX Action_NativeContacts.cpp +CXX Action_NMRrst.cpp +CXX Action_OrderParameter.cpp +CXX Action_Outtraj.cpp +CXX Action_PairDist.cpp +CXX Action_Pairwise.cpp +CXX Action_Principal.cpp +CXX Action_Projection.cpp +CXX Action_Pucker.cpp +CXX Action_Radgyr.cpp +CXX Action_Radial.cpp +CXX Action_RandomizeIons.cpp +CXX Action_Remap.cpp +CXX Action_ReplicateCell.cpp +CXX Action_Rmsd.cpp +CXX Action_Rotate.cpp +CXX Action_RunningAvg.cpp +CXX Action_STFC_Diffusion.cpp +CXX Action_Scale.cpp In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, @@ -1033,27 +1090,6 @@ Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ -CXX Action_MultiVector.cpp -CXX Action_NAstruct.cpp -CXX Action_NativeContacts.cpp -CXX Action_NMRrst.cpp -CXX Action_OrderParameter.cpp -CXX Action_Outtraj.cpp -CXX Action_PairDist.cpp -CXX Action_Pairwise.cpp -CXX Action_Principal.cpp -CXX Action_Projection.cpp -CXX Action_Pucker.cpp -CXX Action_Radgyr.cpp -CXX Action_Radial.cpp -CXX Action_RandomizeIons.cpp -CXX Action_Remap.cpp -CXX Action_ReplicateCell.cpp -CXX Action_Rmsd.cpp -CXX Action_Rotate.cpp -CXX Action_RunningAvg.cpp -CXX Action_STFC_Diffusion.cpp -CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp @@ -1109,36 +1145,6 @@ CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp -In file included from /usr/include/c++/14/vector:66, - from ArgList.h:3, - from Action.h:4, - from Action_XtalSymm.h:3, - from Action_XtalSymm.cpp:1: -In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', - inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:57:12: -/usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] - 809 | { _M_fill_assign(__n, __val); } - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72: -/usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': -/usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here - 270 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -Action_XtalSymm.cpp:57:33: note: '' declared here - 57 | T_.assign( nCopyTotal, Vec3()); - | ^ -In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', - inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:58:15: -/usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] - 809 | { _M_fill_assign(__n, __val); } - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': -/usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here - 270 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -Action_XtalSymm.cpp:58:33: note: '' declared here - 58 | RefT_.assign(nCopyTotal, Vec3()); - | ^ CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp @@ -1206,6 +1212,36 @@ CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp +In file included from /usr/include/c++/14/vector:66, + from ArgList.h:3, + from Action.h:4, + from Action_XtalSymm.h:3, + from Action_XtalSymm.cpp:1: +In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', + inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:57:12: +/usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] + 809 | { _M_fill_assign(__n, __val); } + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72: +/usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': +/usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here + 270 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +Action_XtalSymm.cpp:57:33: note: '' declared here + 57 | T_.assign( nCopyTotal, Vec3()); + | ^ +In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', + inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:58:15: +/usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] + 809 | { _M_fill_assign(__n, __val); } + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': +/usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here + 270 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +Action_XtalSymm.cpp:58:33: note: '' declared here + 58 | RefT_.assign(nCopyTotal, Vec3()); + | ^ CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp @@ -1258,6 +1294,12 @@ CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp CXX ExclusionArray.cpp +CXX Exec_AddMissingRes.cpp +CXX Exec_Analyze.cpp +CXX Exec_Calc.cpp +CXX Exec_CatCrd.cpp +CXX Exec_Change.cpp +CXX Exec_ClusterMap.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] @@ -1280,6 +1322,7 @@ 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) +CXX Exec_CombineCoords.cpp helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] @@ -1302,14 +1345,21 @@ 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for -CXX Exec_AddMissingRes.cpp -CXX Exec_Analyze.cpp -CXX Exec_Calc.cpp -CXX Exec_CatCrd.cpp -CXX Exec_Change.cpp -CXX Exec_ClusterMap.cpp -CXX Exec_CombineCoords.cpp CXX Exec_Commands.cpp +CXX Exec_CompareTop.cpp +CXX Exec_CrdAction.cpp +CXX Exec_CrdOut.cpp +CXX Exec_CreateSet.cpp +CXX Exec_DataFile.cpp +CXX Exec_DataFilter.cpp +CXX Exec_DataSetCmd.cpp +CXX Exec_Emin.cpp +CXX Exec_Flatten.cpp +CXX Exec_GenerateAmberRst.cpp +CXX Exec_Graft.cpp +CXX Exec_Help.cpp +CXX Exec_LoadCrd.cpp +CXX Exec_LoadTraj.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); @@ -1372,6 +1422,7 @@ helpme_standalone.h:3708:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3708 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ +CXX Exec_ParallelAnalysis.cpp helpme_standalone.h: In instantiation of 'helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]': helpme_standalone.h:5023:32: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5023 | auto gridAddress = forwardTransform(realGrid); @@ -1382,8 +1433,7 @@ helpme_standalone.h:4004:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ -CXX Exec_CompareTop.cpp -CXX Exec_CrdAction.cpp +CXX Exec_ParmBox.cpp helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1000:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1000 | assertSymmetric(); @@ -1435,7 +1485,6 @@ helpme_standalone.h:824:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 824 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ -CXX Exec_CrdOut.cpp helpme_standalone.h: In instantiation of 'void helpme::BSpline::update(short int, Real, short int, short int) [with Real = double]': helpme_standalone.h:3829:47: required from 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 3829 | atomSplines.aSpline.update(aStartingGridPoint, gridDimensionA_ * aCoord - aStartingGridPoint, @@ -1454,7 +1503,7 @@ helpme_standalone.h:2208:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ -CXX Exec_CreateSet.cpp +CXX Exec_ParmSolvent.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:877:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 877 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } @@ -1484,19 +1533,6 @@ helpme_standalone.h:863:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ -CXX Exec_DataFile.cpp -CXX Exec_DataFilter.cpp -CXX Exec_DataSetCmd.cpp -CXX Exec_Emin.cpp -CXX Exec_Flatten.cpp -CXX Exec_GenerateAmberRst.cpp -CXX Exec_Graft.cpp -CXX Exec_Help.cpp -CXX Exec_LoadCrd.cpp -CXX Exec_LoadTraj.cpp -CXX Exec_ParallelAnalysis.cpp -CXX Exec_ParmBox.cpp -CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp @@ -1524,59 +1560,13 @@ CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp -helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:3470:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] - 3470 | fftHelperA_ = FFTWWrapper(); - | ^~~~~~~~~~~ -helpme_standalone.h:3470:31: note: '' declared here - 3470 | fftHelperA_ = FFTWWrapper(); - | ^~~~~~~~~~~~~~~~~~~ -helpme_standalone.h:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] - 3471 | fftHelperB_ = FFTWWrapper(); - | ^~~~~~~~~~~ -helpme_standalone.h:3471:31: note: '' declared here - 3471 | fftHelperB_ = FFTWWrapper(); - | ^~~~~~~~~~~~~~~~~~~ -helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] - 3472 | fftHelperC_ = FFTWWrapper(); - | ^~~~~~~~~~~ -helpme_standalone.h:3472:31: note: '' declared here - 3472 | fftHelperC_ = FFTWWrapper(); - | ^~~~~~~~~~~~~~~~~~~ -In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', - inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3503:43: -helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] - 519 | class Matrix { - | ^~~~~~ -helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:3503:45: note: '' declared here - 3503 | compressionCoefficientsA_ = RealMat(); - | ^~~~~~~~~ -In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', - inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3504:43: -helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] - 519 | class Matrix { - | ^~~~~~ -helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:3504:45: note: '' declared here - 3504 | compressionCoefficientsB_ = RealMat(); - | ^~~~~~~~~ -In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', - inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3505:43: -helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] - 519 | class Matrix { - | ^~~~~~ -helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:3505:45: note: '' declared here - 3505 | compressionCoefficientsC_ = RealMat(); - | ^~~~~~~~~ CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp -CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp +CXX ForLoop.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp @@ -1587,13 +1577,6 @@ CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp -helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:5031:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] - 5031 | return energy; - | ^~~~~~ -helpme_standalone.h:5021:14: note: 'energy' was declared here - 5021 | Real energy; - | ^~~~~~ CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp @@ -1685,6 +1668,52 @@ CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp CXX Traj_SQM.cpp +helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:3470:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] + 3470 | fftHelperA_ = FFTWWrapper(); + | ^~~~~~~~~~~ +helpme_standalone.h:3470:31: note: '' declared here + 3470 | fftHelperA_ = FFTWWrapper(); + | ^~~~~~~~~~~~~~~~~~~ +helpme_standalone.h:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] + 3471 | fftHelperB_ = FFTWWrapper(); + | ^~~~~~~~~~~ +helpme_standalone.h:3471:31: note: '' declared here + 3471 | fftHelperB_ = FFTWWrapper(); + | ^~~~~~~~~~~~~~~~~~~ +helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] + 3472 | fftHelperC_ = FFTWWrapper(); + | ^~~~~~~~~~~ +helpme_standalone.h:3472:31: note: '' declared here + 3472 | fftHelperC_ = FFTWWrapper(); + | ^~~~~~~~~~~~~~~~~~~ +In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', + inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3503:43: +helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] + 519 | class Matrix { + | ^~~~~~ +helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:3503:45: note: '' declared here + 3503 | compressionCoefficientsA_ = RealMat(); + | ^~~~~~~~~ +In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', + inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3504:43: +helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] + 519 | class Matrix { + | ^~~~~~ +helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:3504:45: note: '' declared here + 3504 | compressionCoefficientsB_ = RealMat(); + | ^~~~~~~~~ +In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', + inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3505:43: +helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] + 519 | class Matrix { + | ^~~~~~ +helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:3505:45: note: '' declared here + 3505 | compressionCoefficientsC_ = RealMat(); + | ^~~~~~~~~ CXX Traj_Tinker.cpp CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp @@ -1712,6 +1741,13 @@ CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp +helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:5031:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] + 5031 | return energy; + | ^~~~~~ +helpme_standalone.h:5021:14: note: 'energy' was declared here + 5021 | Real energy; + | ^~~~~~ CXX main.cpp CC molsurf.c @@ -1722,15 +1758,15 @@ CC xdrfile.c Skipping bundled ARPACK build - cd tng && make all + +CC xdr_seek.c +CC xdrfile_trr.c make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC md5.c +CC xdrfile_xtc.c CC tng_io.c -CC xdr_seek.c -CC xdrfile_trr.c CC tng_compress.c -CC xdrfile_xtc.c CC coder.c CC warnmalloc.c CC fixpoint.c @@ -1739,17 +1775,17 @@ CC xtc2.c CC widemuldiv.c CC huffmem.c -/bin/rm -f libxdrfile.a -ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o CC vals16.c CC bwt.c CC mtf.c -make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c +/bin/rm -f libxdrfile.a +ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o +make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' tng_io.c: In function 'tng_gen_data_block_add': tng_io.c:12600:9: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); @@ -1767,7 +1803,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest - make -j20 test "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 check unittest + make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary @@ -1786,8 +1822,8 @@ CPPTRAJ: NameType class unit test. make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp --rwxr-xr-x 1 pbuilder1 pbuilder1 185962984 Sep 8 08:20 ../bin/cpptraj --rwxr-xr-x 1 pbuilder1 pbuilder1 185962984 Sep 8 08:20 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 185962984 Oct 11 14:47 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 185962984 Oct 11 14:47 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. ******************************************************************************** @@ -1812,7 +1848,6 @@ CPPTRAJ: One frame strip command test CPPTRAJ: Unstrip (Lig/Rec/Complex) command test -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp CPPTRAJ: Multi frame strip command test. @@ -1824,6 +1859,7 @@ TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp CPPTRAJ: Broken Traj: Running broken trajectory. @@ -1837,12 +1873,11 @@ CPPTRAJ: Normal trajectory read with offsets. CPPTRAJ: Gzipped trajectory read with offsets -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp CPPTRAJ: Bzip2ed trajectory read with offsets CPPTRAJ: Start argument offset -g++ -o a.out main.o NameType.o CpptrajStdio.o +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp All 4 comparisons passed. @@ -1852,10 +1887,13 @@ CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: CRD Replica Trajectory Run +g++ -o a.out main.o NameType.o CpptrajStdio.o CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj + + CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' 'ZN' 'HA2' 'HA' 'HA' 'CT11' Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' @@ -1870,8 +1908,6 @@ make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp - CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj - CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj @@ -1898,7 +1934,6 @@ CPPTRAJ: Per-Residue RMSD Test with residue centering. -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/ArgList.cpp All 3 comparisons passed. ******************************************************************************** @@ -1907,6 +1942,7 @@ CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/ArgList.cpp CPPTRAJ: Secstruct (DSSP) command with changing number of residues. @@ -1979,19 +2015,19 @@ CPPTRAJ: Nonorthorhombic coordinate imaging test CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM All 6 comparisons passed. -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Surface calculation test +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp CPPTRAJ: Partial Surface calculation test +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp CPPTRAJ: LCPO test with GAFF atom types @@ -2041,7 +2077,6 @@ CPPTRAJ: STFC Diffusion Test with COM CPPTRAJ: STFC Diffusion Test with second mask -g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o All 16 comparisons passed. @@ -2049,17 +2084,12 @@ TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' - - Unit test passed. - -make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' -make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ: Outtraj Test with maxmin. All 4 comparisons passed. +g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm @@ -2072,6 +2102,12 @@ CPPTRAJ: CHAMBER topology read/strip test. CPPTRAJ: Read CHARMM restart +make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' + + Unit test passed. + +make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' +make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ: CHARMM PSF write @@ -3665,7 +3701,7 @@ make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' /usr/bin/make -C test summary make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' --rwxr-xr-x 1 pbuilder1 pbuilder1 185962984 Sep 8 08:20 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 185962984 Oct 11 14:47 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. @@ -3677,7 +3713,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/cpptraj/ - make -j20 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no + make -j42 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' @@ -3722,12 +3758,14 @@ 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/369190/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/369190/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/966547 and its subdirectories -I: Current time: Sat Sep 7 20:22:51 -12 2024 -I: pbuilder-time-stamp: 1725783771 +I: removing directory /srv/workspace/pbuilder/369190 and its subdirectories +I: Current time: Sun Oct 12 04:49:27 +14 2025 +I: pbuilder-time-stamp: 1760194167