Diff of the two buildlogs: -- --- b1/build.log 2025-09-03 03:20:16.578240614 +0000 +++ b2/build.log 2025-09-03 03:22:56.814435081 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 2 15:14:07 -12 2025 -I: pbuilder-time-stamp: 1756869247 +I: Current time: Tue Oct 6 23:43:18 +14 2026 +I: pbuilder-time-stamp: 1791279798 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ 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/3165505/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4023854/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 6 09:43 /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/4023854/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4023854/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=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3089930acf964a6a9d2b0290f942f8f9' - 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='3165505' - PS1='# ' - PS2='> ' + INVOCATION_ID=85714bcf06404a998f22a526f0c0084c + 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=4023854 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.sxSjaQT3/pbuilderrc_4MBN --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sxSjaQT3/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-4.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - 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.sxSjaQT3/pbuilderrc_FZIF --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sxSjaQT3/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-4.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + 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 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3165505/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4023854/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -255,7 +287,7 @@ Get: 130 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-2 [180 kB] Get: 131 http://deb.debian.org/debian forky/main amd64 libreadline-dev amd64 8.3-2 [162 kB] Get: 132 http://deb.debian.org/debian forky/main amd64 netcdf-bin amd64 1:4.9.3-1+b1 [261 kB] -Fetched 64.5 MB in 1s (46.0 MB/s) +Fetched 64.5 MB in 1s (48.2 MB/s) Preconfiguring packages ... 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 ... 19897 files and directories currently installed.) @@ -809,7 +841,11 @@ 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/4023854/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/4023854/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 @@ -822,7 +858,7 @@ make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean - make -j40 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' @@ -915,7 +951,7 @@ make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_build - make -j40 + 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' @@ -936,13 +972,13 @@ CXX Action_Center.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp -CXX Action_Closest.cpp CXX Action_CheckStructure.cpp +CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp -CXX Action_DNAionTracker.cpp CXX Action_CreateReservoir.cpp +CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp @@ -957,9 +993,10 @@ CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp CXX Action_Grid.cpp -CXX Action_HydrogenBond.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] @@ -1004,7 +1041,6 @@ 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for -CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp @@ -1027,12 +1063,6 @@ 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 In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, @@ -1101,6 +1131,12 @@ Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ +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 @@ -1136,8 +1172,8 @@ CXX Analysis_FFT.cpp CXX Analysis_HausdorffDistance.cpp CXX Analysis_Hist.cpp -CXX Analysis_Integrate.cpp CXX Analysis_IRED.cpp +CXX Analysis_Integrate.cpp CXX Analysis_KDE.cpp CXX Analysis_Lifetime.cpp CXX Analysis_LowestCurve.cpp @@ -1197,8 +1233,8 @@ CXX Constraints.cpp CXX ControlBlock_For.cpp CXX CoordinateInfo.cpp -CXX Cph.cpp CXX Corr.cpp +CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp @@ -1227,6 +1263,10 @@ CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp +CXX DataSetList.cpp +CXX DataSet_1D.cpp +CXX DataSet_3D.cpp +CXX DataSet_Cmatrix.cpp In file included from /usr/include/c++/14/vector:66, from ArgList.h:3, from Action.h:4, @@ -1257,10 +1297,6 @@ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ -CXX DataSetList.cpp -CXX DataSet_1D.cpp -CXX DataSet_3D.cpp -CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp @@ -1296,8 +1332,8 @@ CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp -CXX EnsembleIn_Multi.cpp CXX EnsembleIn.cpp +CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp @@ -1311,6 +1347,8 @@ CXX Exec_AddMissingRes.cpp CXX Exec_Analyze.cpp CXX Exec_Calc.cpp +CXX Exec_CatCrd.cpp +CXX Exec_Change.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] @@ -1351,13 +1389,11 @@ 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) +CXX Exec_ClusterMap.cpp helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for -CXX Exec_CatCrd.cpp -CXX Exec_Change.cpp -CXX Exec_ClusterMap.cpp CXX Exec_CombineCoords.cpp CXX Exec_Commands.cpp CXX Exec_CompareTop.cpp @@ -1373,9 +1409,7 @@ CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp -CXX Exec_ParallelAnalysis.cpp CXX Exec_LoadTraj.cpp -CXX Exec_ParmBox.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(); @@ -1393,6 +1427,7 @@ helpme_standalone.h:1013:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ +CXX Exec_ParallelAnalysis.cpp helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5018:9: 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]' 5018 | sanityChecks(parameterAngMom, parameters, coordinates); @@ -1438,7 +1473,6 @@ 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_ParmSolvent.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); @@ -1449,9 +1483,8 @@ helpme_standalone.h:4004:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ -CXX Exec_ParmStrip.cpp -CXX Exec_ParmWrite.cpp -CXX Exec_PermuteDihedrals.cpp +CXX Exec_ParmBox.cpp +CXX Exec_ParmSolvent.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(); @@ -1469,7 +1502,6 @@ helpme_standalone.h:796:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 796 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ -CXX Exec_Precision.cpp helpme_standalone.h: In instantiation of 'void helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with Real = double]': helpme_standalone.h:1006:42: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1006 | JacobiCyclicDiagonalization(eigenValues[0], unsortedEigenVectors[0], cbegin(), nRows_); @@ -1487,7 +1519,6 @@ helpme_standalone.h:213:20: warning: variable 'cos_2phi' set but not used [-Wunused-but-set-variable] 213 | Real sin_2phi, cos_2phi, cot_2phi; | ^~~~~~~~ -CXX Exec_PrepareForLeap.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]': helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); @@ -1523,7 +1554,7 @@ 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_PrintData.cpp +CXX Exec_ParmStrip.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); } @@ -1553,9 +1584,14 @@ 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_ParmWrite.cpp +CXX Exec_PermuteDihedrals.cpp +CXX Exec_Precision.cpp +CXX Exec_PrepareForLeap.cpp +CXX Exec_PrintData.cpp CXX Exec_Random.cpp -CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp +CXX Exec_ReadData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp @@ -1654,6 +1690,52 @@ CXX StringRoutines.cpp CXX StructureCheck.cpp CXX StructureMapper.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 SymmetricRmsdCalc.cpp CXX TextFormat.cpp CXX Timer.cpp @@ -1687,6 +1769,13 @@ CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp CXX TrajFrameCounter.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 TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp @@ -1696,8 +1785,6 @@ CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp -CXX Action_Esander.cpp -CXX Command.cpp xoshiro128plusplus.cpp: In function 'void jump()': xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) @@ -1706,78 +1793,34 @@ xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CXX Action_Esander.cpp +CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c -cd xdrfile && make all -make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' Skipping bundled READLINE build -CC xdrfile.c +cd xdrfile && make all -CC xdr_seek.c -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(); - | ^~~~~~~~~ +make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' Skipping bundled ARPACK build +CC xdrfile.c cd tng && make all +CC xdr_seek.c make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC md5.c CC tng_io.c -CC xdrfile_trr.c CC tng_compress.c -CC xdrfile_xtc.c CC coder.c +CC xdrfile_trr.c CC warnmalloc.c -CC xtc3.c +CC xdrfile_xtc.c CC fixpoint.c +CC xtc3.c CC bwlzh.c CC xtc2.c CC widemuldiv.c @@ -1790,13 +1833,6 @@ CC dict.c CC huffman.c CC merge_sort.c -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; - | ^~~~~~ 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); @@ -1817,16 +1853,16 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest - make -j40 test "TESTSUITEFLAGS=-j40 --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 cd unitTests && make test.complete summary -make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' - CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src +make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h + CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' ******************************************************************************** @@ -1835,1767 +1871,1729 @@ TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: NameType class unit test. + + CPPTRAJ: ArgList 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 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: ArgList class unit 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 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 +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 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 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 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 --rwxr-xr-x 1 pbuilder1 pbuilder1 186086912 Sep 3 03:18 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 186086912 Oct 6 09:45 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 186086912 Oct 6 09:45 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' --rwxr-xr-x 1 pbuilder1 pbuilder1 186086912 Sep 3 03:18 ../bin/cpptraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj - - CPPTRAJ: One frame strip command test - - CPPTRAJ: Broken Traj: Running good trajectory. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj - - CPPTRAJ: CRD Replica Trajectory Run with offset +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD - - CPPTRAJ: Normal trajectory read with offsets. - - CPPTRAJ: General tests - - CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General - CPPTRAJ: Trajout Frame Range [Amber Restart] + CPPTRAJ: One frame strip command test - CPPTRAJ: Secstruct (DSSP) command test. + CPPTRAJ: Trajout Frame Range [Amber Restart] ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling + + CPPTRAJ: Normal trajectory read with offsets. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart - CPPTRAJ: Center command test. + CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image - - CPPTRAJ: Radius of gyration command test - +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf - CPPTRAJ: NetCDF Restart Test - TXT->NetCDF - CPPTRAJ: Surface calculation test + CPPTRAJ: CRD Replica Trajectory Run with offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask - CPPTRAJ: Orthorhombic imaged distance test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling + CPPTRAJ: Solute Hbond test - CPPTRAJ: J-Coupling single frame test ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj - CPPTRAJ: Mask single frame test -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj + CPPTRAJ: Surface calculation test - CPPTRAJ: Solute Hbond test + CPPTRAJ: General tests + CPPTRAJ: J-Coupling single frame test - CPPTRAJ: Convert mdcrd -> NetCDF + CPPTRAJ: NetCDF Restart Test - TXT->NetCDF ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr ******************************************************************************** ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg -******************************************************************************** -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 - - CPPTRAJ: RMSD Test with outtraj. - - CPPTRAJ: Mol2 Parm/Traj Read/Write Test. - CPPTRAJ: Rotational diffusion calculation test + CPPTRAJ: Mask single frame test ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS - CPPTRAJ: 2D RMSD Test. -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm CPPTRAJ: Coordinate Running Average test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct - - CPPTRAJ: Diffusion test, no imaging. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj + CPPTRAJ: RMSD Test with outtraj. - CPPTRAJ: Basic RMSD tests + CPPTRAJ: Radius of gyration command test CPPTRAJ: CHARMM PSF/DCD test - CPPTRAJ: Pucker command test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile - + CPPTRAJ: Diffusion test, no imaging. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial - CPPTRAJ: NAstruct command test. - CPPTRAJ: Data file output precision test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD + CPPTRAJ: 2D RMSD Test. - CPPTRAJ: Radial test, non-orthogonal imaging -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average + CPPTRAJ: Convert mdcrd -> NetCDF ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct - CPPTRAJ: Average Test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest + CPPTRAJ: Mol2 Parm/Traj Read/Write Test. - CPPTRAJ: AtomMap Test + CPPTRAJ: Basic RMSD tests - CPPTRAJ: Gzipped trajectory read with offsets + CPPTRAJ: NAstruct command test. - CPPTRAJ: NetCDF Restart Test - NetCDF->TXT + CPPTRAJ: CHARMM DCD Write, step 1. - CPPTRAJ: 1D/2D Histogram Analysis test + CPPTRAJ: NAstruct command test, single strand - CPPTRAJ: Closest command test using first solvent atom. +All 11 comparisons passed. - CPPTRAJ: CRD Replica Trajectory Run -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD - CPPTRAJ: Distance RMSD test + CPPTRAJ: Broken Traj: Running good trajectory. + + CPPTRAJ: CHARMM DCD Write, step 2. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif -All 2 comparisons passed. + CPPTRAJ: Rotational diffusion calculation test + CPPTRAJ: Secstruct (DSSP) command test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average - CPPTRAJ: Cluster command test, in-memory pairwise distances. + CPPTRAJ: Center command test. J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG + + CPPTRAJ: Orthorhombic imaged distance test. All 1 comparisons passed. 1 comparisons skipped. - CPPTRAJ: Center origin command test. - - CPPTRAJ: Broken Traj: Running broken trajectory. - - CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test - - CPPTRAJ: PDB => Mol2 - - CPPTRAJ: Non-orthorhombic imaged distance test. - - CPPTRAJ: 2D RMSD Test, mass-weighted. - - CPPTRAJ: Trajout Frame Range [Amber Coordinates] - - CPPTRAJ: Unstrip (Lig/Rec/Complex) command test - - - CPPTRAJ: Coordinate Running Average Traj Write - CPPTRAJ: CHARMM DCD Write, step 1. - - CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. + CPPTRAJ: Average Test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile - CPPTRAJ: Per-Residue RMSD Test with averaging + CPPTRAJ: NA test (8OG) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial - CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist + CPPTRAJ: Data file output precision test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons -All 4 comparisons passed. + CPPTRAJ: AtomMap Test + CPPTRAJ: Closest command test using first solvent atom. +******************************************************************************** - CPPTRAJ: NetCDF Replica Trajectory Run test + CPPTRAJ: Radial test, non-orthogonal imaging ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD + + CPPTRAJ: Pucker command test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED -All 2 comparisons passed. - + CPPTRAJ: 1D/2D Histogram Analysis test CPPTRAJ: randomizeions test (original algorithm) - CPPTRAJ: IRED vector/matrix test - - CPPTRAJ: Bzip2ed trajectory read with offsets -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf - - CPPTRAJ: Molsurf test + CPPTRAJ: Distance RMSD test - CPPTRAJ: Solute Hbond test with disk caching + CPPTRAJ: Cluster command test, in-memory pairwise distances. - CPPTRAJ: Standard -> Grace Data + CPPTRAJ: IRED vector/matrix test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf - CPPTRAJ: Mask longer command test. +All 2 comparisons passed. - CPPTRAJ: Correlation test - CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. CPPTRAJ: Diffusion test, old syntax. + CPPTRAJ: NetCDF Restart Test - NetCDF->TXT - CPPTRAJ: 2D RMSD Test with reference trajectory - - CPPTRAJ: Amber Top/Rst => Mol2 - - CPPTRAJ: AtomMap with 'rmsfit' - - CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj - - CPPTRAJ: Cluster command test, read pairwise distances. - CPPTRAJ: CHARMM DCD Write, step 2. + CPPTRAJ: CRD Replica Trajectory Run + CPPTRAJ: Mask longer command test. - CPPTRAJ: Per-Residue RMSD Test with residue centering. + CPPTRAJ: 2D RMSD Test, mass-weighted. -All 6 comparisons passed. + CPPTRAJ: Molsurf test + CPPTRAJ: Trajout Frame Range [Amber Coordinates] -All 2 comparisons passed. + CPPTRAJ: Gzipped trajectory read with offsets - CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt + CPPTRAJ: Coordinate Running Average Traj Write + CPPTRAJ: PDB => Mol2 +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr - CPPTRAJ: Center origin mass command test. + CPPTRAJ: Correlation test - CPPTRAJ: NAstruct command test, single strand +All 4 comparisons passed. - CPPTRAJ: Secstruct (DSSP) command with changing number of residues. -All 3 comparisons passed. + CPPTRAJ: Broken Traj: Running broken trajectory. +All 2 comparisons passed. - CPPTRAJ: Orthorhombic coordinate imaging test - CPPTRAJ: RMS coordinate rotation/rotation matrices test + CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: Structure Check - CPPTRAJ: Convert NetCDF -> mdcrd +All 6 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr - CPPTRAJ: CHAMBER topology read/strip test. + CPPTRAJ: RmsAvgCorr Reference All 2 comparisons passed. - - CPPTRAJ: 3D histogram test. - - CPPTRAJ: RmsAvgCorr Reference ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts - Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. - Skipped test: Amber Top/Rst => Mol2, SYBYL atom types -All 4 comparisons passed. -1 comparisons skipped. + CPPTRAJ: Contacts test. +All 3 comparisons passed. - CPPTRAJ: Start argument offset - CPPTRAJ: 2D DME Test. +All 5 comparisons passed. - CPPTRAJ: Solute-solvent hbond test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal -All 1 comparisons passed. + CPPTRAJ: Principal Test +All 1 comparisons passed. - CPPTRAJ: Contacts test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector -All 5 comparisons passed. + CPPTRAJ: clusterdihedral test +All 2 comparisons passed. - CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj + CPPTRAJ: Basic vector tests - CPPTRAJ: Grace -> Standard Data +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix -All 11 comparisons passed. + CPPTRAJ: Matrix Tests +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct + CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. - CPPTRAJ: Atom map charmm->amber atom order +All 3 comparisons passed. - CPPTRAJ: Closest command test using all solvent atoms. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal - CPPTRAJ: Principal Test +All 4 comparisons passed. - CPPTRAJ: Cluster command test, read NetCDF pairwise distances. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral - -All 3 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid + CPPTRAJ: Dipole test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap - CPPTRAJ: clusterdihedral test + CPPTRAJ: Unwrap non-orthogonal test - CPPTRAJ: Read CHARMM restart + CPPTRAJ: Compressed broken trajectory test - CPPTRAJ: Matrix Tests -******************************************************************************** - CPPTRAJ: Center reference command test. -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG + CPPTRAJ: Closest command test using all solvent atoms. - CPPTRAJ: NA test (8OG) -All 2 comparisons passed. + CPPTRAJ: Cluster command test, read pairwise distances. + CPPTRAJ: Non-orthorhombic imaged distance test. - CPPTRAJ: Multi frame strip command test. + CPPTRAJ: Standard -> Grace Data -All 7 comparisons passed. + CPPTRAJ: 3D histogram test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector + CPPTRAJ: 2D RMSD Test with reference trajectory + CPPTRAJ: RmsAvgCorr First - CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj + CPPTRAJ: Unstrip (Lig/Rec/Complex) command test - CPPTRAJ: Basic vector tests -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct - CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. + CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. + CPPTRAJ: Bzip2ed trajectory read with offsets - CPPTRAJ: Structure Check with Around and Skip - CPPTRAJ: Diffusion test, new syntax. + CPPTRAJ: Amber Top/Rst => Mol2 + CPPTRAJ: Center origin command test. - CPPTRAJ: Secstruct (DSSP): SS assign output test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap + CPPTRAJ: AtomMap with 'rmsfit' - CPPTRAJ: X column format/precision test. + CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. - CPPTRAJ: Nonorthorhombic coordinate imaging test + CPPTRAJ: RMS coordinate rotation/rotation matrices test - CPPTRAJ: Dipole test + CPPTRAJ: Diffusion test, new syntax. + CPPTRAJ: Per-Residue RMSD Test with averaging - CPPTRAJ: Unwrap non-orthogonal test + CPPTRAJ: Test vector center with magnitude - CPPTRAJ: Compressed broken trajectory test + CPPTRAJ: Structure Check with Around and Skip -All 4 comparisons passed. + CPPTRAJ: Convert NetCDF -> mdcrd + CPPTRAJ: NetCDF Replica Trajectory Run test - CPPTRAJ: Atom map charmm->amber atom order, by residue + CPPTRAJ: Solute Hbond test with disk caching - CPPTRAJ: RmsAvgCorr First - CPPTRAJ: 2D RMSD with reference mask test. + CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. + CPPTRAJ: Grid test - CPPTRAJ: RMS fit with no coordinates modification test. + CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF - CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project +All 7 comparisons passed. - CPPTRAJ: Projection -All 3 comparisons passed. + CPPTRAJ: Outtraj Test with maxmin. + Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. + Skipped test: Amber Top/Rst => Mol2, SYBYL atom types +All 4 comparisons passed. +1 comparisons skipped. - CPPTRAJ: CHARMM PSF write All 3 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project - CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. -All 4 comparisons passed. + CPPTRAJ: Unwrap orthogonal test - CPPTRAJ: Cluster command test, write ASCII pairwise distances. + CPPTRAJ: Atom map charmm->amber atom order + CPPTRAJ: CHAMBER topology read/strip test. - CPPTRAJ: Hbond, no intramolecular hydrogen bonds test + CPPTRAJ: Momentum/velocity vector test. + CPPTRAJ: Projection - CPPTRAJ: Data file group by name test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell + CPPTRAJ: Grace -> Standard Data - CPPTRAJ: Watershell Test, non-orthorhombic imaging. + CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj - CPPTRAJ: FtuFabI Assignment test + CPPTRAJ: Secstruct (DSSP) command with changing number of residues. - CPPTRAJ: Modes analysis, RMS fluctuations +All 3 comparisons passed. -All 9 comparisons passed. + CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes - CPPTRAJ: Strip topology with PDB info +All 2 comparisons passed. - CPPTRAJ: 2D RMSD test, no fitting. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell - CPPTRAJ: CRD Replica Trajectory Run with remdout + CPPTRAJ: Modes analysis, RMS fluctuations -All 3 comparisons passed. + CPPTRAJ: Watershell Test, non-orthorhombic imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg CPPTRAJ: Analysis Running Average - CPPTRAJ: Diffusion test, nonorthogonal box - - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar - -All 1 comparisons passed. + CPPTRAJ: Start argument offset + CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt - CPPTRAJ: Center point test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap + CPPTRAJ: Center origin mass command test. + CPPTRAJ: RMS fit with no coordinates modification test. - CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. + CPPTRAJ: Solute-solvent hbond test - CPPTRAJ: CHARMM COORdinates test - CPPTRAJ: VMD VolMap Algorithm test + CPPTRAJ: 2D DME Test. + CPPTRAJ: Per-Residue RMSD Test with residue centering. -All 2 comparisons passed. + CPPTRAJ: Orthorhombic coordinate imaging test + CPPTRAJ: Cluster command test, read NetCDF pairwise distances. - CPPTRAJ: Grid test + CPPTRAJ: Diffusion test, nonorthogonal box +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap - CPPTRAJ: Cluster command test, read ASCII pairwise distances. + CPPTRAJ: VMD VolMap Algorithm test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE + +All 1 comparisons passed. + CPPTRAJ: SPAM Test - CPPTRAJ: Data file group by aspect test + CPPTRAJ: Read CHARMM restart - CPPTRAJ: LIE test + CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj + + CPPTRAJ: Partial Surface calculation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density - CPPTRAJ: Unwrap orthogonal test - - CPPTRAJ: Density along axis tests + CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. - CPPTRAJ: Modes analysis, displacements +All 4 comparisons passed. -All 6 comparisons passed. + CPPTRAJ: Atom map charmm->amber atom order, by residue All 2 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: Modes analysis, displacements + CPPTRAJ: Density along axis tests +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE -All 11 comparisons passed. +All 1 comparisons passed. -All 1 comparisons passed. + CPPTRAJ: LIE test +All 3 comparisons passed. - CPPTRAJ: Test vector center with magnitude -All 6 comparisons passed. +All 4 comparisons passed. -All 8 comparisons passed. +All 2 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist -******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder - - CPPTRAJ: PairDist Test. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist + CPPTRAJ: Lipid Order Parameter Test. + CPPTRAJ: PairDist Test. +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData CPPTRAJ: GIST water-water interaction test +All 15 comparisons passed. + + CPPTRAJ: Read vector data test (no origins, origins) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF - -All 9 comparisons passed. - ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test - CPPTRAJ: Atomic Correlation test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams - VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. - Skipped test: VMD VolMap Algorithm longer tests -All 2 comparisons passed. -1 comparisons skipped. + CPPTRAJ: STFC Diffusion Test + CPPTRAJ: Force vector test. - CPPTRAJ: RMS fit to previous test - CPPTRAJ: Test updating topology with Charmm parameters (single residue) - - CPPTRAJ: Hbond, specified solute masks + CPPTRAJ: Hbond, no intramolecular hydrogen bonds test + CPPTRAJ: Multi frame strip command test. + CPPTRAJ: Secstruct (DSSP): SS assign output test -All 10 comparisons passed. + CPPTRAJ: X column format/precision test. + CPPTRAJ: CHARMM PSF write - CPPTRAJ: Modes analysis, dipole correlation -All 6 comparisons passed. - CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. + CPPTRAJ: Center reference command test. + CPPTRAJ: 2D RMSD with reference mask test. + CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj + CPPTRAJ: OpenDX Grid read test - CPPTRAJ: STFC Diffusion Test + CPPTRAJ: Closest command test, using mask center ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel - CPPTRAJ: Outtraj Test with maxmin. + CPPTRAJ: Parallel tests. - CPPTRAJ: Cluster, nosieve -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr - CPPTRAJ: Closest command test, using mask center + CPPTRAJ: Atomic Correlation test - CPPTRAJ: AutoCorr test. +All 1 comparisons passed. - CPPTRAJ: RMS: imaging after unit cell rotation +All 2 comparisons passed. - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM CPPTRAJ: Read vector data set (origins, no origins) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect - CPPTRAJ: OpenDX Grid read test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box + CPPTRAJ: Nonorthorhombic coordinate imaging test - CPPTRAJ: Box Test (Add box info) + CPPTRAJ: Modes analysis, dipole correlation + VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. + Skipped test: VMD VolMap Algorithm longer tests - CPPTRAJ: Momentum/velocity vector test. +All 2 comparisons passed. +1 comparisons skipped. - CPPTRAJ: Selection by atom type test. -All 2 comparisons passed. +All 9 comparisons passed. + CPPTRAJ: Randomize (around, overlap) + + + CPPTRAJ: RMS fit to previous test CPPTRAJ: Atomicfluct test with ADP output + + CPPTRAJ: Cluster command test, write ASCII pairwise distances. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr - CPPTRAJ: RMSD Test with averaged reference coordinates. +All 3 comparisons passed. -All 1 comparisons passed. + CPPTRAJ: AutoCorr test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef - CPPTRAJ: Partial Surface calculation test + CPPTRAJ: Selection by atom type test. -All 2 comparisons passed. + CPPTRAJ: Box Test (Add box info) + CPPTRAJ: RMSD Test with averaged reference coordinates. - CPPTRAJ: Read Amber output test + CPPTRAJ: Generate matrix with trajectory start/stop/offset + + CPPTRAJ: CHARMM COORdinates test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat - CPPTRAJ: Pairdist test, orthogonal imaging. - CPPTRAJ: Crankshaft test - CPPTRAJ: STFC Diffusion Test with individual distances - - CPPTRAJ: Hbond, no angle cutoff test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd - All 1 comparisons passed. -All 1 comparisons passed. +All 14 comparisons passed. -All 12 comparisons passed. +All 6 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd - CPPTRAJ: Force vector test. +All 1 comparisons passed. - CPPTRAJ: Cluster, sieve5 CPPTRAJ: COORDS data set creation and CRDFLUCT test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage -All 4 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Read CHARMM output test + CPPTRAJ: AutoImage test (split DNA duplex) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams - CPPTRAJ: Closest command test, using mask center and solvent mask + CPPTRAJ: LoadCrd test. - CPPTRAJ: Box test (remove box info) + CPPTRAJ: Test updating topology with Charmm parameters (single residue) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector -All 6 comparisons passed. - -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd +All 3 comparisons passed. CPPTRAJ: Multivector test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage - CPPTRAJ: Grid with specified center test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime - CPPTRAJ: AutoImage test (split DNA duplex) + CPPTRAJ: Lifetime test. - CPPTRAJ: LoadCrd test. +All 6 comparisons passed. - CPPTRAJ: STFC Diffusion Test with COM - CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime - CPPTRAJ: Multi-frame density along axis test + CPPTRAJ: Parallel test with trajectory offset -All 3 comparisons passed. - CPPTRAJ: Lifetime test. + CPPTRAJ: LoadTraj test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT + CPPTRAJ: Pairdist test, orthogonal imaging. - CPPTRAJ: Hbond, Bridge nointramol test + CPPTRAJ: Structure Check with PBC - CPPTRAJ: FFT test. - CPPTRAJ: 3D data read/write test + CPPTRAJ: Strip topology with PDB info - CPPTRAJ: Modes analysis, pseudo trajectory creation test + CPPTRAJ: LCPO test with GAFF atom types + CPPTRAJ: Cluster command test, read ASCII pairwise distances. - CPPTRAJ: Box test (Modify box length) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr + CPPTRAJ: Data file group by name test + CPPTRAJ: STFC Diffusion Test with individual distances - CPPTRAJ: Structure Check with PBC - CPPTRAJ: Timecorr test. + CPPTRAJ: Center point test. - CPPTRAJ: COORDS data set creation with velocities test -All 3 comparisons passed. + CPPTRAJ: FtuFabI Assignment test + CPPTRAJ: Radial test, orthogonal and no imaging + CPPTRAJ: Closest command test, using mask center and solvent mask + CPPTRAJ: Box test (remove box info) -All 14 comparisons passed. + CPPTRAJ: Hbond, specified solute masks + CPPTRAJ: Grid with specified center test. + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar - CPPTRAJ: LoadTraj test. + CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj - CPPTRAJ: STFC Diffusion Test with second mask -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr + CPPTRAJ: 2D RMSD test, no fitting. - CPPTRAJ: Cluster, nosieve savepairdist - CPPTRAJ: CrossCorr test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd + CPPTRAJ: Multi-frame density along axis test + CPPTRAJ: Read Amber output test - CPPTRAJ: Generate matrix with trajectory start/stop/offset + CPPTRAJ: Modes analysis, pseudo trajectory creation test -All 1 comparisons passed. + CPPTRAJ: RMS: imaging after unit cell rotation + CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. All 1 comparisons passed. - CPPTRAJ: LCPO test with GAFF atom types +All 2 comparisons passed. - CPPTRAJ: SymmRmsd + CPPTRAJ: Generate matrix with action stop/start/offset - CPPTRAJ: Standard 3D data write test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral - CPPTRAJ: Closest command test, solvent mask, water oxygen only +All 1 comparisons passed. - CPPTRAJ: Multidihedral test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure - -All 13 comparisons passed. - +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD -All 15 comparisons passed. + CPPTRAJ: FFT test. + CPPTRAJ: Basic lipid order parameter test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr - CPPTRAJ: Basic makestructure test + CPPTRAJ: Timecorr test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr - CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test + CPPTRAJ: CrossCorr test - CPPTRAJ: M-REMD sort test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate +All 3 comparisons passed. - CPPTRAJ: Rotation (and inverse) of coords from matrices -All 1 comparisons passed. +All 11 comparisons passed. All 5 comparisons passed. +All 6 comparisons passed. -All 1 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel - CPPTRAJ: LoadTraj from trajin test. +All 15 comparisons passed. - CPPTRAJ: Lifetime test with data set caching. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate - CPPTRAJ: Parallel tests. +All 9 comparisons passed. - CPPTRAJ: Integration test. - CPPTRAJ: Generate matrix with action stop/start/offset + CPPTRAJ: COORDS data set creation with velocities test - CPPTRAJ: Standard 3D data read test -All 3 comparisons passed. + CPPTRAJ: CRD Replica Trajectory Run with remdout + CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test + CPPTRAJ: Read CHARMM output test - CPPTRAJ: Box test (auto orthogonal box, no radii) + CPPTRAJ: Lifetime test with data set caching. - CPPTRAJ: ASP symmetry-corrected RMSD test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts + CPPTRAJ: Box test (Modify box length) CPPTRAJ: SPAM Pure Solvent Test - CPPTRAJ: NativeContacts test. +All 12 comparisons passed. + ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy - - CPPTRAJ: Check chirality test - - CPPTRAJ: Grid with box center offset test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve +******************************************************************************** - CPPTRAJ: Simple energy tests +All 13 comparisons passed. -All 7 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate - CPPTRAJ: LES split/average test + CPPTRAJ: LoadTraj from trajin test. + CPPTRAJ: Data file group by aspect test -All 6 comparisons passed. + CPPTRAJ: SymmRmsd - CPPTRAJ: Total system density test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals + CPPTRAJ: Basic makestructure test +All 9 comparisons passed. -All 6 comparisons passed. + CPPTRAJ: Cluster, nosieve - CPPTRAJ: Multidihedral Nucleotide CHI test - CPPTRAJ: LoadCrd append from multiple files test + CPPTRAJ: M-REMD sort test. + CPPTRAJ: Multidihedral test - CPPTRAJ: PermuteDihedrals interval -120, phi psi + CPPTRAJ: Rotation (and inverse) of coords from matrices ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate - CPPTRAJ: Basic lipid order parameter test + CPPTRAJ: STFC Diffusion Test with COM - CPPTRAJ: Makestructure test with reference. +All 1 comparisons passed. - CPPTRAJ: Box test (auto orthogonal box, VDW radii) -All 15 comparisons passed. -******************************************************************************** + CPPTRAJ: Hbond, no angle cutoff test -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 + CPPTRAJ: NativeContacts test. - CPPTRAJ: Parallel test with trajectory offset + CPPTRAJ: 3D data read/write test -All 2 comparisons passed. + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM + CPPTRAJ: Integration test. - CPPTRAJ: CCP4 read/write and DX conversion test. +All 1 comparisons passed. - CPPTRAJ: GLU symmetry-corrected RMSD test - CPPTRAJ: Cluster, nosieve loadpairdist + CPPTRAJ: Closest command test, solvent mask, water oxygen only -All 1 comparisons passed. +All 6 comparisons passed. - CPPTRAJ: Rotate with defined axis ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral + CPPTRAJ: ASP symmetry-corrected RMSD test -All 4 comparisons passed. + CPPTRAJ: Randomize (around) + CPPTRAJ: Box test (auto orthogonal box, no radii) - CPPTRAJ: Dihedral Covariance Matrix Test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit + CPPTRAJ: New Lipid Order Parameter Test, DOPC. - CPPTRAJ: Standard 3D data read/append test + CPPTRAJ: LoadCrd append from multiple files test - CPPTRAJ: Curve fitting test. + CPPTRAJ: Check chirality test + +All 6 comparisons passed. - CPPTRAJ: TRAJ data set creation and CRDFLUCT test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy + +All 5 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit - CPPTRAJ: Radial test, orthogonal and no imaging - CPPTRAJ: Grid with mask center offset test. + CPPTRAJ: Simple energy tests - CPPTRAJ: Data set averaging and averaging over all sets test. + CPPTRAJ: LES split/average test - CPPTRAJ: Multidihedral protein dihedrals test +All 8 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals All 7 comparisons passed. - CPPTRAJ: M-REMD actions test. + CPPTRAJ: PermuteDihedrals interval -120, phi psi + +All 10 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar + + CPPTRAJ: CCP4 read/write and DX conversion test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit + + CPPTRAJ: Dihedral Covariance Matrix Test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage + + CPPTRAJ: Curve fitting test. All 7 comparisons passed. - CPPTRAJ: Lifetime average and cumulative average test. + CPPTRAJ: Data set averaging and averaging over all sets test. -All 5 comparisons passed. +All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test - CPPTRAJ: TYR symmetry-corrected RMSD test +All 4 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander + +All 1 comparisons passed. SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. + SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) - - CPPTRAJ: Curve fitting multi-exponential tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature - CPPTRAJ: PermuteDihedrals, random rotations -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline - CPPTRAJ: Temperature test. - CPPTRAJ: TRAJ data set creation with velocities test. - CPPTRAJ: Spline test -All 3 comparisons passed. - CPPTRAJ: Multidihedral cyclic molecule test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short - Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. - Cpptraj was compiled without SANDER API from AmberTools support. - SKIP: Energy via sander API short tests (GB/PME) + CPPTRAJ: Total system density test + CPPTRAJ: Rotate with defined axis + CPPTRAJ: Grid with box center offset test. + CPPTRAJ: STFC Diffusion Test with second mask - CPPTRAJ: Standard 3D data, sparse + CPPTRAJ: GLU symmetry-corrected RMSD test + CPPTRAJ: Lifetime average and cumulative average test. + CPPTRAJ: AutoImage test, use anchor mask -All 2 comparisons passed. + CPPTRAJ: Multidihedral Nucleotide CHI test -All 2 comparisons passed. + CPPTRAJ: Hbond, Bridge nointramol test + CPPTRAJ: Standard 3D data write test + + CPPTRAJ: Box test (auto orthogonal box, VDW radii) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE +******************************************************************************** + CPPTRAJ: Makestructure test with reference. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline -All 2 comparisons passed. - + CPPTRAJ: Cluster, sieve5 CPPTRAJ: KDE test. - CPPTRAJ: Longer symmetry-corrected RMSD test. + CPPTRAJ: Spline test + + + +All 1 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: Wavelet analysis test - CPPTRAJ: Non-orthogonal grid test. + CPPTRAJ: CIF read test - CPPTRAJ: Cluster, sieve5 savepairdist +All 2 comparisons passed. -All 9 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short + Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. + Cpptraj was compiled without SANDER API from AmberTools support. + SKIP: Energy via sander API short tests (GB/PME) +g++ -o a.out main.o NameType.o CpptrajStdio.o - CPPTRAJ: M-REMD ensemble outtraj test. +All 6 comparisons passed. -All 7 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF +All 4 comparisons passed. - CPPTRAJ: PDB format read/write test All 12 comparisons passed. - CPPTRAJ: CIF read test +All 2 comparisons passed. -All 1 comparisons passed. + +All 2 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB All 3 comparisons passed. - CPPTRAJ: Temperature with SHAKE on hydrogens. - - CPPTRAJ: New Lipid Order Parameter Test, DOPC. + CPPTRAJ: PDB format read/write test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align CPPTRAJ: Align Tests. - CPPTRAJ: Velocity autocorrelation test - -All 6 comparisons passed. +All 3 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc - -All 1 comparisons passed. - - -All 8 comparisons passed. - ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd - CPPTRAJ: Nonorthogonal grid standard write/read tests. + + CPPTRAJ: Rotate dihedral to target value. + CPPTRAJ: Velocity autocorrelation test + CPPTRAJ: Test combining coordinates, velocities, and forces. +All 7 comparisons passed. - CPPTRAJ: Test kinetic energy calculation +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap CPPTRAJ: Data Set commands test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop -All 4 comparisons passed. + CPPTRAJ: Remap Test + CPPTRAJ: Compare topology test - CPPTRAJ: Randomize (around, overlap) +All 7 comparisons passed. -All 16 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter + CPPTRAJ: Basic filter test - CPPTRAJ: Rotate dihedral to target value. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap - CPPTRAJ: Remap Test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter +All 2 comparisons passed. + +All 5 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop - - CPPTRAJ: Basic filter test -******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Combine COORDS test. - CPPTRAJ: Compare topology test + CPPTRAJ: Topology info print test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr - - CPPTRAJ: Topology info print test. - - CPPTRAJ: M-REMD no sort, running average test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: TRR force/velocity read -> NetCDF write test - CPPTRAJ: Curve fitting, custom output range. +All 1 comparisons passed. - CPPTRAJ: COORDS data set append test - CPPTRAJ: Temperature with SHAKE on all atoms. - - CPPTRAJ: Test using velocities as coordinates. + CPPTRAJ: Direct sum test All 1 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI - CPPTRAJ: Test total energy calculation + CPPTRAJ: TI analysis test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds - CPPTRAJ: Align, unit cell rotation/imaging test. + CPPTRAJ: Fix imaged bonds test (Ortho.) - CPPTRAJ: Combine COORDS test with box info. +All 10 comparisons passed. - CPPTRAJ: Rotate dihedral by increment +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance -All 1 comparisons passed. + CPPTRAJ: Distance tests +All 3 comparisons passed. - CPPTRAJ: NativeContacts test, save non-native contacts, residue time series ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume - CPPTRAJ: Direct sum test + CPPTRAJ: Volume tests - CPPTRAJ: AutoImage test, use anchor mask -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI +All 5 comparisons passed. - CPPTRAJ: COORDS test storing frame metadata +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity -All 6 comparisons passed. + CPPTRAJ: Set Velocity test +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' +Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' + Unit test passed. - CPPTRAJ: M-REMD, generate RMS data - CPPTRAJ: TI analysis test. +All 16 comparisons passed. - CPPTRAJ: Test partial energy calculation ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog - CPPTRAJ: Multicurve test + CPPTRAJ: Replica log read/analyze test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol - CPPTRAJ: Pairdist test, nonorthogonal imaging. + CPPTRAJ: Area per molecule test - CPPTRAJ: M-REMD, meltcurve analysis +All 2 comparisons passed. -All 10 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask + CPPTRAJ: Distance-based atom mask tests (atom, residue) -All 5 comparisons passed. +All 7 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc - CPPTRAJ: Generate offset traj from PDB + CPPTRAJ: Calc test - CPPTRAJ: Data filter test. -All 6 comparisons passed. + CPPTRAJ: Curve fitting multi-exponential tests. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance + CPPTRAJ: Standard 3D data read test -All 1 comparisons passed. - CPPTRAJ: Distance tests + CPPTRAJ: NativeContacts test, save non-native contacts, residue time series -All 2 comparisons passed. + CPPTRAJ: Grid with mask center offset test. - CPPTRAJ: KDE with Kullback-Leibler divergence test + CPPTRAJ: Structure Check with Around + CPPTRAJ: PermuteDihedrals, random rotations + CPPTRAJ: Wavelet WAFEX test - CPPTRAJ: Test writing velocities (MDVEL) + CPPTRAJ: Cluster, nosieve savepairdist + CPPTRAJ: M-REMD actions test. - CPPTRAJ: Generate offset traj from CIF + CPPTRAJ: Randomize (overlap) - CPPTRAJ: Temperature calc with extra points. + CPPTRAJ: Data filter test. -All 4 comparisons passed. + CPPTRAJ: TRR force/velocity read -> TRR write test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity + CPPTRAJ: Multidihedral protein dihedrals test - CPPTRAJ: Cluster, sieve5 loadpairdist + CPPTRAJ: Pairdist test, nonorthogonal imaging. - CPPTRAJ: Replica log read/analyze test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume + CPPTRAJ: Rotate dihedral by increment -All 17 comparisons passed. + CPPTRAJ: Align, unit cell rotation/imaging test. + CPPTRAJ: Test using velocities as coordinates. - CPPTRAJ: Volume tests + CPPTRAJ: PQR file write with various radii - CPPTRAJ: Set Velocity test + CPPTRAJ: Fix imaged bonds test (Non-ortho.) - CPPTRAJ: Wavelet WAFEX test + CPPTRAJ: Test kinetic energy calculation - CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test + CPPTRAJ: Combine COORDS test with box info. CPPTRAJ: Orthogonal imaged distance - CPPTRAJ: PQR file write with various radii + CPPTRAJ: Scale velocity test - CPPTRAJ: Split coords and recombine test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask + CPPTRAJ: Watershell Test, orthorhombic imaging. - CPPTRAJ: TRAJ test storing frame metadata -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol + CPPTRAJ: Temperature with SHAKE on hydrogens. - CPPTRAJ: Fix imaged bonds test (Ortho.) - CPPTRAJ: Area per molecule test + CPPTRAJ: Generate offset traj from PDB + CPPTRAJ: Topology info with reference coords test + CPPTRAJ: TYR symmetry-corrected RMSD test - CPPTRAJ: Test using forces as coordinates. + CPPTRAJ: TRAJ data set creation and CRDFLUCT test. - CPPTRAJ: Structure Check with Around + CPPTRAJ: KDE with Kullback-Leibler divergence test - CPPTRAJ: Distance-based atom mask tests (atom, residue) +All 1 comparisons passed. -All 2 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState + CPPTRAJ: Calcstate test -All 4 comparisons passed. + CPPTRAJ: Distance-based atom mask tests (molecule) + CPPTRAJ: Calc test with data sets - CPPTRAJ: Rotate dihedral in TRAJ data set -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc - CPPTRAJ: Calc test +All 3 comparisons passed. +All 6 comparisons passed. - CPPTRAJ: Non-orthogonal imaged distance - CPPTRAJ: Fix imaged bonds test (Non-ortho.) -All 3 comparisons passed. +All 12 comparisons passed. -All 5 comparisons passed. +All 4 comparisons passed. - CPPTRAJ: Calc test with data sets ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change -All 2 comparisons passed. +All 4 comparisons passed. + CPPTRAJ: Change atom and residue name tests +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir -All 1 comparisons passed. - CPPTRAJ: Calcstate test + CPPTRAJ: Multidihedral cyclic molecule test + CPPTRAJ: Temperature with SHAKE on all atoms. - CPPTRAJ: Test writing forces (MDFRC) - CPPTRAJ: Grid generation from 'bounds' test. + CPPTRAJ: CRD => TRR + CPPTRAJ: Test total energy calculation + CPPTRAJ: Longer symmetry-corrected RMSD test. - CPPTRAJ: Filter matrix test. + CPPTRAJ: Test writing velocities (MDVEL) - CPPTRAJ: TRR force/velocity read -> TRR write test -All 8 comparisons passed. + CPPTRAJ: Non-orthogonal imaged distance + CPPTRAJ: Standard 3D data read/append test - CPPTRAJ: Topology info with reference coords test + CPPTRAJ: Filter matrix test. + CPPTRAJ: Rotate dihedral in TRAJ data set - CPPTRAJ: Scale velocity test + CPPTRAJ: Generate offset traj from CIF All 8 comparisons passed. - - CPPTRAJ: PDB filter alternate atom location IDs test ******************************************************************************** + + CPPTRAJ: Create RREMD NetCDF reservoir test TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage + CPPTRAJ: Non-orthogonal grid test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve - CPPTRAJ: Hbond with imaging -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change + CPPTRAJ: Out of order molecules test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir - - CPPTRAJ: Minimum Image test. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage - CPPTRAJ: Change atom and residue name tests + CPPTRAJ: LowestCurve test + CPPTRAJ: Minimum Image test. +All 2 comparisons passed. - CPPTRAJ: LowestCurve test - CPPTRAJ: Out of order molecules test +All 2 comparisons passed. - CPPTRAJ: Create RREMD NetCDF reservoir test - CPPTRAJ: Distance-based atom mask tests (molecule) +All 3 comparisons passed. -All 7 comparisons passed. - CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. +All 3 comparisons passed. - CPPTRAJ: Cluster, nosieve pairwisecache none ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress - CPPTRAJ: Test math functions - -All 4 comparisons passed. - -All 12 comparisons passed. - - -All 5 comparisons passed. +All 8 comparisons passed. CPPTRAJ: Linear regression test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst +All 6 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise - CPPTRAJ: NativeContacts test, orthorhombic imaging. - CPPTRAJ: Pairwise tests - -All 2 comparisons passed. - - - CPPTRAJ: Generate restraints (rst) test - - CPPTRAJ: CRD => TRR ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox - - CPPTRAJ: Parmbox test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate - - CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. - -All 3 comparisons passed. - - -All 3 comparisons passed. - +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent - CPPTRAJ: Translate test +All 5 comparisons passed. - CPPTRAJ: Change chain ID test + CPPTRAJ: Parmbox test + + + CPPTRAJ: Generate restraints (rst) test CPPTRAJ: Test solvent command with closest All 4 comparisons passed. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell -All 6 comparisons passed. +All 1 comparisons passed. + + CPPTRAJ: Translate test -******************************************************************************** CPPTRAJ: Replicate cell test -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK All 2 comparisons passed. - - CPPTRAJ: Hbond, orthogonal imaging +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control CPPTRAJ: Scale dihedral force constant test - -All 1 comparisons passed. - - -All 3 comparisons passed. - ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi + + CPPTRAJ: Loop tests All 1 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi -******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec +All 8 comparisons passed. + + CPPTRAJ: Phipsi test CPPTRAJ: Infrared spectrum calculation test - CPPTRAJ: Loop tests -******************************************************************************** +All 1 comparisons passed. -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats -All 3 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Change chain ID of COORDS set test All 1 comparisons passed. + +All 1 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine -All 13 comparisons passed. +All 1 comparisons passed. CPPTRAJ: Explicit pH REMD ensemble data read / sort - - CPPTRAJ: Command line trajectory args test, part 1 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat - CPPTRAJ: Ewald test (NaCl crystal) + CPPTRAJ: Command line trajectory args test, part 1 CPPTRAJ: XYZ format write ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd + +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff +All 3 comparisons passed. + + + CPPTRAJ: Concatenate COORDS data set test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm - - CPPTRAJ: Simple Hausdorff distance test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time - CPPTRAJ: Add time to restart test + CPPTRAJ: Simple Hausdorff distance test. CPPTRAJ: XtalSymm Reference -All 5 comparisons passed. - -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd + CPPTRAJ: Add time to restart test All 1 comparisons passed. - CPPTRAJ: Concatenate COORDS data set test +All 3 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords -All 3 comparisons passed. -All 1 comparisons passed. + CPPTRAJ: SplitCoords test + CPPTRAJ: M-REMD ensemble outtraj test. + CPPTRAJ: NativeContacts test, orthorhombic imaging. - CPPTRAJ: Pairwise test, partial system + CPPTRAJ: Watershell Test, no imaging. - CPPTRAJ: Command line test trajectory args test, part 2 -All 3 comparisons passed. -All 1 comparisons passed. + CPPTRAJ: Test using forces as coordinates. + CPPTRAJ: Test math functions + CPPTRAJ: TRAJ data set creation with velocities test. + CPPTRAJ: PDB filter alternate atom location IDs test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords + CPPTRAJ: Randomize (no restrictions) - CPPTRAJ: Scale dihedral force constant with 'useall' + CPPTRAJ: Hbond with imaging - CPPTRAJ: SplitCoords test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix + CPPTRAJ: TRR => CRD - CPPTRAJ: Remove time from restart test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin + CPPTRAJ: Temperature calc with extra points. - CPPTRAJ: MW covariance matrix thermo analysis test + CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test - CPPTRAJ: Basic energy minimization test. + CPPTRAJ: Curve fitting, custom output range. -All 1 comparisons passed. + CPPTRAJ: Test partial energy calculation + CPPTRAJ: Split coords and recombine test. - CPPTRAJ: Adding PDB info to topology + CPPTRAJ: Ewald test (NaCl crystal) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau - CPPTRAJ: Hausdorff distance of 2D rms output test. + CPPTRAJ: Change chain ID test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope - CPPTRAJ: Evalulate plateau test + CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) + +All 6 comparisons passed. + CPPTRAJ: Finite difference test. - CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) + CPPTRAJ: Scale dihedral force constant with 'useall' -All 23 comparisons passed. +All 1 comparisons passed. -All 8 comparisons passed. + CPPTRAJ: Command line test trajectory args test, part 2 + +All 1 comparisons passed. + +All 2 comparisons passed. + ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix -All 1 comparisons passed. + CPPTRAJ: MW covariance matrix thermo analysis test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin + CPPTRAJ: Basic energy minimization test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau - CPPTRAJ: Ewald test (trunc. oct) +All 4 comparisons passed. - CPPTRAJ: Graft test - CPPTRAJ: TRR => CRD + CPPTRAJ: Evalulate plateau test -All 1 comparisons passed. +All 6 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft -All 2 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Constant pH stats test + CPPTRAJ: Graft test -All 4 comparisons passed. +All 2 comparisons passed. All 1 comparisons passed. - - CPPTRAJ: Energy minimization with angle term test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten - CPPTRAJ: Atom XYZ format read, test 1 - CPPTRAJ: Flatten test. + + CPPTRAJ: Multicurve test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random +All 6 comparisons passed. + + CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs - CPPTRAJ: Test set command +All 1 comparisons passed. -All 2 comparisons passed. + CPPTRAJ: Remove time from restart test - CPPTRAJ: Command line wildcard test, part 1 - CPPTRAJ: Add time to trajectory test -All 10 comparisons passed. + CPPTRAJ: Energy minimization with angle term test. + CPPTRAJ: Test writing forces (MDFRC) -All 2 comparisons passed. + CPPTRAJ: Pairwise test, partial system + CPPTRAJ: Constant pH stats test + CPPTRAJ: Ewald test (trunc. oct) + CPPTRAJ: Test set command -All 1 comparisons passed. + CPPTRAJ: Dihedral RMSD test (to previous) + CPPTRAJ: Grid generation from 'bounds' test. - CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. + CPPTRAJ: Atom XYZ format read, test 1 -All 1 comparisons passed. + CPPTRAJ: Hbond, orthogonal imaging + CPPTRAJ: M-REMD no sort, running average test -All 1 comparisons passed. + CPPTRAJ: Standard 3D data, sparse + CPPTRAJ: Change chain ID of COORDS set test - CPPTRAJ: Dihedral RMSD test (to previous) + CPPTRAJ: Hausdorff distance of 2D rms output test. All 1 comparisons passed. - CPPTRAJ: Sorted implicit constant pH stats test + +All 2 comparisons passed. All 1 comparisons passed. - CPPTRAJ: Atom XYZ format read, test 2 +All 1 comparisons passed. -All 6 comparisons passed. +All 5 comparisons passed. -All 10 comparisons passed. +All 3 comparisons passed. - CPPTRAJ: Test reading comma-separated list of strings - CPPTRAJ: Command line wildcard test, part 2 +All 23 comparisons passed. - CPPTRAJ: PCG32 RNG test. - CPPTRAJ: Cluster, sieve5 pairwisecache none +All 5 comparisons passed. - CPPTRAJ: Energy minimization with nonbond term test. - CPPTRAJ: Watershell Test, orthorhombic imaging. +All 13 comparisons passed. - CPPTRAJ: Dihedral RMS fluctuation test. - CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats +All 17 comparisons passed. - CPPTRAJ: Atom XYZ format read, test 3 -All 2 comparisons passed. +All 4 comparisons passed. - CPPTRAJ: Hausdorff distance of 2D rms output test. +All 10 comparisons passed. - CPPTRAJ: Test Stdlib RNG - CPPTRAJ: Modify time info test. + CPPTRAJ: Command line wildcard test, part 1 - CPPTRAJ: Test nested loops and variables in loops + CPPTRAJ: Adding PDB info to topology -All 17 comparisons passed. + CPPTRAJ: Add time to trajectory test + CPPTRAJ: Dihedral RMS fluctuation test. - CPPTRAJ: Atom XYZ format read, test 4 + CPPTRAJ: Test reading comma-separated list of strings -All 5 comparisons passed. + CPPTRAJ: COORDS data set append test + CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. - CPPTRAJ: Test Mersenne Twister RNG + CPPTRAJ: Atom XYZ format read, test 2 - CPPTRAJ: Randomize (around) + CPPTRAJ: CRD(1-5) => TRR - CPPTRAJ: Read specific columns test. + CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. - CPPTRAJ: Unsorted pH read/write test + CPPTRAJ: Nonorthogonal grid standard write/read tests. - CPPTRAJ: Test loop over data set blocks + CPPTRAJ: PCG32 RNG test. -All 4 comparisons passed. + CPPTRAJ: Sorted implicit constant pH stats test + CPPTRAJ: Hausdorff distance of 2D rms output test. -All 4 comparisons passed. + CPPTRAJ: M-REMD, generate RMS data +All 10 comparisons passed. - CPPTRAJ: Atom XYZ format read, test 5 - CPPTRAJ: Cluster, random +All 5 comparisons passed. -All 16 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: CRD(1-5) => TRR - CPPTRAJ: Write non-square matrix + CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. - CPPTRAJ: Ewald test (partial system, trunc. oct) + CPPTRAJ: Test Stdlib RNG - CPPTRAJ: Atom XYZ format read, test 6 + CPPTRAJ: Energy minimization with nonbond term test. - CPPTRAJ: Test for filename wildcards and oversets + CPPTRAJ: Command line wildcard test, part 2 All 3 comparisons passed. -All 28 comparisons passed. -All 6 comparisons passed. + CPPTRAJ: Test nested loops and variables in loops + CPPTRAJ: GIST test, orthogonal cell + CPPTRAJ: COORDS test storing frame metadata - CPPTRAJ: Read non-square matrix -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve + CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats + CPPTRAJ: Atom XYZ format read, test 3 - CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). + CPPTRAJ: M-REMD, meltcurve analysis - CPPTRAJ: Watershell Test, no imaging. +All 2 comparisons passed. -All 13 comparisons passed. + CPPTRAJ: Test Mersenne Twister RNG - CPPTRAJ: OpenMM basic energy minimization tests (bonds) +All 17 comparisons passed. - CPPTRAJ: CRD(6-10) => TRR - CPPTRAJ: Read square matrix +All 3 comparisons passed. - CPPTRAJ: OpenMM basic energy minimization tests (angles) - Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. - Skipped test: Ewald test (trunc. oct), 10 frames - Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. - Skipped test: Ewald test (ortho), 10 frames -All 4 comparisons passed. -2 comparisons skipped. +All 5 comparisons passed. - CPPTRAJ: Pairdist test, 2 masks. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME +All 4 comparisons passed. - CPPTRAJ: Particle mesh Ewald test (NaCl crystal) -All 15 comparisons passed. + CPPTRAJ: Test loop over data set blocks + CPPTRAJ: CRD(6-10) => TRR - CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) -All 1 comparisons passed. + CPPTRAJ: XtalSymm Reimaging by Atom + CPPTRAJ: TRAJ test storing frame metadata - CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). + CPPTRAJ: Unsorted pH read/write test + CPPTRAJ: Atom XYZ format read, test 4 - CPPTRAJ: TRR (appended) => CRD + CPPTRAJ: Modify time info test. - CPPTRAJ: Particle mesh Ewald test (trunc. oct) + CPPTRAJ: Pairdist test, 2 masks. All 4 comparisons passed. - CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) - - CPPTRAJ: XtalSymm Reimaging by Atom +All 16 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: OpenMM basic energy minimization tests (bonds) - CPPTRAJ: Randomize (overlap) -g++ -o a.out main.o NameType.o CpptrajStdio.o + CPPTRAJ: Atom XYZ format read, test 5 All 4 comparisons passed. - CPPTRAJ: GMX: CRD with offset -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet +All 8 comparisons passed. - CPPTRAJ: Clustering, One DataSet - CPPTRAJ: Clustering, Two DataSets - CPPTRAJ: GMX: TRR with offset -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' - CPPTRAJ: Randomize (no restrictions) - 'ZN' 'HA2' 'HA' 'HA' 'CT11' -Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' -Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' + CPPTRAJ: Atom XYZ format read, test 6 + CPPTRAJ: Test for filename wildcards and oversets - Unit test passed. + CPPTRAJ: Cluster, nosieve loadpairdist + CPPTRAJ: TRR (appended) => CRD + CPPTRAJ: OpenMM basic energy minimization tests (angles) - CPPTRAJ: Clustering, dihedral DataSet + CPPTRAJ: Ewald test (partial system, trunc. oct) +g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o - CPPTRAJ: Clustering, two dihedral DataSets +All 13 comparisons passed. - CPPTRAJ: Particle mesh Ewald test (ortho) -All 5 comparisons passed. +All 6 comparisons passed. + + Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. + Skipped test: Ewald test (trunc. oct), 10 frames + Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. + Skipped test: Ewald test (ortho), 10 frames +All 4 comparisons passed. +2 comparisons skipped. + + + CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME - CPPTRAJ: XTC read test + CPPTRAJ: Particle mesh Ewald test (NaCl crystal) +make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' - CPPTRAJ: Clustering, dihedral DataSet, K-means + Unit test passed. - CPPTRAJ: Clustering, two dihedral DataSets, K-means +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' -All 5 comparisons passed. + CPPTRAJ: Read specific columns test. + CPPTRAJ: Particle mesh Ewald test (trunc. oct) -All 8 comparisons passed. + CPPTRAJ: Cluster, sieve5 savepairdist -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN + CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) - CPPTRAJ: DBSCAN test +All 5 comparisons passed. - CPPTRAJ: CRD => XTC - CPPTRAJ: DBSCAN automatic parameter determination test. + CPPTRAJ: Write non-square matrix + + CPPTRAJ: GMX: CRD with offset All 5 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) - CPPTRAJ: DBSCAN kdist map test + CPPTRAJ: Particle mesh Ewald test (ortho) - CPPTRAJ: DBSCAN with sieve + CPPTRAJ: GMX: TRR with offset + + CPPTRAJ: Read non-square matrix + +All 5 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc + + CPPTRAJ: XTC read test + + + CPPTRAJ: CRD => XTC CPPTRAJ: Particle mesh Ewald test (ortho, with mask) - CPPTRAJ: XTC => CRD + CPPTRAJ: XtalSymm Reimaging by Molecule -All 4 comparisons passed. + CPPTRAJ: Read square matrix -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans +All 15 comparisons passed. - CPPTRAJ: Cpptraj Kmeans + + CPPTRAJ: XTC => CRD CPPTRAJ: PME test (partial system, trunc. oct) - CPPTRAJ: Cpptraj Kmeans random + CPPTRAJ: Cluster, sieve5 loadpairdist - CPPTRAJ: CRD(1-5) => XTC + CPPTRAJ: GIST test, nonorthogonal cell + + CPPTRAJ: Cluster, nosieve pairwisecache none PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: PME test (trunc. oct), 10 frames @@ -3607,93 +3605,131 @@ CPPTRAJ: LJ PME test. + CPPTRAJ: CRD(1-5) => XTC -All 6 comparisons passed. - CPPTRAJ: LJ PME kappa sweep test, 0.25 +All 9 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD - CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) + CPPTRAJ: LJ PME kappa sweep test, 0.25 CPPTRAJ: CRD(6-10) => XTC - CPPTRAJ: GIST test, orthogonal cell + CPPTRAJ: Cluster, sieve5 pairwisecache none CPPTRAJ: LJ PME kappa sweep test, 0.35 - CPPTRAJ: XtalSymm Reimaging by Molecule - CPPTRAJ: XTC (appended) => CRD + CPPTRAJ: Cluster, random + CPPTRAJ: LJ PME kappa sweep test, 0.45 -All 5 comparisons passed. +All 28 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve - CPPTRAJ: Cluster command test, coordinate writes. + CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: GMX: CRD with offset CPPTRAJ: LJ PME kappa sweep test, 0.5 - CPPTRAJ: Cluster command test, coordinate writes using info file. + CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). CPPTRAJ: GMX: XTC with offset - CPPTRAJ: LJ with switch function test +All 4 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: LJ with switch function test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet + + CPPTRAJ: Clustering, One DataSet All 5 comparisons passed. + CPPTRAJ: Clustering, Two DataSets + All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG -All 8 comparisons passed. + CPPTRAJ: TNG read test + CPPTRAJ: Clustering, dihedral DataSet - CPPTRAJ: TNG read test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks + CPPTRAJ: Clustering, two dihedral DataSets + + CPPTRAJ: Clustering, dihedral DataSet, K-means + + CPPTRAJ: Clustering, two dihedral DataSets, K-means + +All 8 comparisons passed. - CPPTRAJ: Density peaks clustering test All 3 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN - CPPTRAJ: Clustering with specified # reps + CPPTRAJ: DBSCAN test CPPTRAJ: TNG read test (with offset) -All 2 comparisons passed. + CPPTRAJ: DBSCAN automatic parameter determination test. -g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' + CPPTRAJ: DBSCAN kdist map test - Unit test passed. + CPPTRAJ: DBSCAN with sieve -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' +All 4 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans + + CPPTRAJ: Cpptraj Kmeans + + CPPTRAJ: Cpptraj Kmeans random All 6 comparisons passed. -All 9 comparisons passed. +All 6 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD + + CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) + +All 5 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites + + CPPTRAJ: Cluster command test, coordinate writes. + + CPPTRAJ: Cluster command test, coordinate writes using info file. +All 8 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks + + CPPTRAJ: Density peaks clustering test All 3 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps + + CPPTRAJ: Clustering with specified # reps + +All 2 comparisons passed. - CPPTRAJ: GIST test, nonorthogonal cell All 11 comparisons passed. @@ -3713,7 +3749,7 @@ 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 186086912 Sep 3 03:18 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 186086912 Oct 6 09:45 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. @@ -3725,16 +3761,16 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/cpptraj/ - make -j40 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' Skipping bundled READLINE build - Skipping bundled ARPACK build + g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro mv cpptraj "/build/reproducible-path/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' @@ -3770,12 +3806,14 @@ 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/4023854/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4023854/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/3165505 and its subdirectories -I: Current time: Tue Sep 2 15:20:16 -12 2025 -I: pbuilder-time-stamp: 1756869616 +I: removing directory /srv/workspace/pbuilder/4023854 and its subdirectories +I: Current time: Tue Oct 6 23:45:55 +14 2026 +I: pbuilder-time-stamp: 1791279955