Diff of the two buildlogs: -- --- b1/build.log 2025-10-17 02:13:34.616152768 +0000 +++ b2/build.log 2025-10-17 02:20:20.548552176 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Oct 16 14:04:56 -12 2025 -I: pbuilder-time-stamp: 1760666696 +I: Current time: Thu Nov 19 22:36:35 +14 2026 +I: pbuilder-time-stamp: 1795077395 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying gcc-15.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1845020/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2870230/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 19 08:37 /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/2870230/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2870230/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='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='51f2fbde614447f2af4542f5247de42b' - 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='1845020' - PS1='# ' - PS2='> ' + INVOCATION_ID=1c477f9be87842068ab13708fc56674c + 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=2870230 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.a9RXUbC0/pbuilderrc_vOvJ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.a9RXUbC0/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-5.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.a9RXUbC0/pbuilderrc_HcIo --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.a9RXUbC0/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-5.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) 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/1845020/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2870230/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -257,7 +289,7 @@ Get: 131 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.3-3 [175 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 netcdf-bin amd64 1:4.9.3-1+b1 [261 kB] -Fetched 134 MB in 12s (10.9 MB/s) +Fetched 134 MB in 15s (9157 kB/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 ... 19856 files and directories currently installed.) @@ -815,7 +847,11 @@ 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-5_source.changes +I: user script /srv/workspace/pbuilder/2870230/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2870230/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-5_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -828,7 +864,7 @@ 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' @@ -921,7 +957,7 @@ 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' @@ -954,8 +990,8 @@ CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp -CXX Action_Distance.cpp CXX Action_Dipole.cpp +CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp CXX Action_FilterByData.cpp @@ -965,6 +1001,9 @@ CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp +CXX Action_Image.cpp +CXX Action_InfraredSpectrum.cpp +CXX Action_Jcoupling.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2324: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] @@ -1009,9 +1048,6 @@ 4504 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4511: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4511 | #pragma omp for -CXX Action_Image.cpp -CXX Action_InfraredSpectrum.cpp -CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp @@ -1035,6 +1071,10 @@ 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, @@ -1103,10 +1143,6 @@ Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ -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 @@ -1225,6 +1261,12 @@ CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp CXX DataIO_Peaks.cpp +CXX DataIO_Mdout.cpp +CXX DataIO_NC_Cmatrix.cpp +CXX DataIO_RemLog.cpp +CXX DataIO_Std.cpp +CXX DataIO_VecTraj.cpp +CXX DataIO_Xplor.cpp In file included from /usr/include/c++/15/vector:68, from ArgList.h:3, from Action.h:4, @@ -1255,12 +1297,6 @@ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ -CXX DataIO_Mdout.cpp -CXX DataIO_NC_Cmatrix.cpp -CXX DataIO_RemLog.cpp -CXX DataIO_Std.cpp -CXX DataIO_VecTraj.cpp -CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp @@ -1306,19 +1342,13 @@ CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp -CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp +CXX EnsembleOut.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp -CXX ExclusionArray.cpp -CXX Exec_AddMissingRes.cpp -CXX Exec_Analyze.cpp -CXX Exec_Calc.cpp -CXX Exec_CatCrd.cpp -CXX Exec_Change.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2324: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] @@ -1363,6 +1393,12 @@ 4504 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4511: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4511 | #pragma omp for +CXX ExclusionArray.cpp +CXX Exec_AddMissingRes.cpp +CXX Exec_Analyze.cpp +CXX Exec_Calc.cpp +CXX Exec_CatCrd.cpp +CXX Exec_Change.cpp CXX Exec_ClusterMap.cpp CXX Exec_CombineCoords.cpp CXX Exec_Commands.cpp @@ -1375,6 +1411,10 @@ CXX Exec_DataSetCmd.cpp CXX Exec_Emin.cpp CXX Exec_Flatten.cpp +CXX Exec_GenerateAmberRst.cpp +CXX Exec_Graft.cpp +CXX Exec_Help.cpp +CXX Exec_LoadCrd.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': helpme_standalone.h:3899:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3899 | auto eigenTuple = HtH.diagonalize(); @@ -1516,8 +1556,7 @@ helpme_standalone.h:2209:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2209 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ -CXX Exec_GenerateAmberRst.cpp -CXX Exec_Graft.cpp +CXX Exec_LoadTraj.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:878:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 878 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } @@ -1547,9 +1586,6 @@ helpme_standalone.h:864:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 864 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ -CXX Exec_Help.cpp -CXX Exec_LoadCrd.cpp -CXX Exec_LoadTraj.cpp CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp CXX Exec_ParmSolvent.cpp @@ -1561,8 +1597,8 @@ CXX Exec_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp -CXX Exec_ReadInput.cpp CXX Exec_ReadEnsembleData.cpp +CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp @@ -1581,8 +1617,8 @@ CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp -CXX FileName.cpp CXX FileIO_Std.cpp +CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp @@ -1687,8 +1723,6 @@ CXX Traj_NcEnsemble.cpp CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp -CXX Traj_SQM.cpp -CXX Traj_Tinker.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:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3471 | fftHelperA_ = FFTWWrapper(); @@ -1735,6 +1769,8 @@ helpme_standalone.h:3506:45: note: '' declared here 3506 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ +CXX Traj_SQM.cpp +CXX Traj_Tinker.cpp CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp @@ -1749,7 +1785,6 @@ 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++) @@ -1758,33 +1793,27 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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:5032:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] - 5032 | return energy; - | ^~~~~~ -helpme_standalone.h:5022:14: note: 'energy' was declared here - 5022 | Real energy; - | ^~~~~~ +CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c -cd xdrfile && make all Skipping bundled READLINE build -make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' +cd xdrfile && make all +make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC xdrfile.c +CC xdr_seek.c Skipping bundled ARPACK build -CC xdr_seek.c cd tng && make all 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_io.c CC xdrfile_xtc.c CC tng_compress.c CC coder.c @@ -1802,7 +1831,17 @@ CC lz77.c CC dict.c CC huffman.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:5032:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] + 5032 | return energy; + | ^~~~~~ +helpme_standalone.h:5022:14: note: 'energy' was declared here + 5022 | Real energy; + | ^~~~~~ CC merge_sort.c +/bin/rm -f libxdrfile.a +ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o +make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' tng_io.c: In function 'tng_gen_data_block_add': tng_io.c:12600:9: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); @@ -1810,9 +1849,6 @@ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ -/bin/rm -f libxdrfile.a -ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o -make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' @@ -1823,22 +1859,22 @@ 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/unitTests' 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 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' ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType CPPTRAJ: NameType class unit test. make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' @@ -1847,904 +1883,893 @@ 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 NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.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++ -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 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 184920736 Oct 17 02:11 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 184920736 Nov 19 08:41 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' --rwxr-xr-x 1 pbuilder1 pbuilder1 184920736 Oct 17 02:11 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 184920736 Nov 19 08:41 ../bin/cpptraj ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General - CPPTRAJ: Broken Traj: Running good trajectory. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset + CPPTRAJ: One frame strip command test + CPPTRAJ: General tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj - CPPTRAJ: One frame strip command test ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset + + CPPTRAJ: Trajout Frame Range [Amber Restart] ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj CPPTRAJ: CRD Replica Trajectory Run with offset -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD CPPTRAJ: Normal trajectory read with offsets. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask + CPPTRAJ: Broken Traj: Running good trajectory. - CPPTRAJ: General tests - CPPTRAJ: NetCDF Restart Test - TXT->NetCDF + CPPTRAJ: Secstruct (DSSP) command test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image - CPPTRAJ: Trajout Frame Range [Amber Restart] ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond + CPPTRAJ: Orthorhombic imaged distance test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD + CPPTRAJ: Center command test. + CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask CPPTRAJ: Surface calculation test - CPPTRAJ: Radius of gyration command test + CPPTRAJ: Solute Hbond test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj - +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP - CPPTRAJ: Solute Hbond test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart + CPPTRAJ: Radius of gyration command test CPPTRAJ: Mask single frame test - CPPTRAJ: Per-Residue RMSD Test. -******************************************************************************** + + CPPTRAJ: NetCDF Restart Test - TXT->NetCDF ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling - CPPTRAJ: Orthorhombic imaged distance test. + CPPTRAJ: J-Coupling single frame test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif - +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm - CPPTRAJ: RMSD Test with outtraj. - CPPTRAJ: Secstruct (DSSP) command test. + CPPTRAJ: Diffusion test, no imaging. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj CPPTRAJ: CHARMM PSF/DCD test - CPPTRAJ: Diffusion test, no imaging. - - CPPTRAJ: J-Coupling single frame test + CPPTRAJ: RMSD Test with outtraj. ******************************************************************************** -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_RMSD +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj CPPTRAJ: Rotational diffusion calculation test -******************************************************************************** -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS CPPTRAJ: Convert mdcrd -> NetCDF - - CPPTRAJ: Coordinate Running Average test. - - CPPTRAJ: Basic RMSD tests -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest - - CPPTRAJ: 1D/2D Histogram Analysis test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile - - CPPTRAJ: Closest command test using first solvent atom. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap +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_NAstruct - CPPTRAJ: Average Test. + CPPTRAJ: Basic RMSD tests + CPPTRAJ: 2D RMSD Test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 - CPPTRAJ: NAstruct command test. - CPPTRAJ: Data file output precision test + CPPTRAJ: Gzipped trajectory read with offsets - CPPTRAJ: Radial test, non-orthogonal imaging - CPPTRAJ: AtomMap Test CPPTRAJ: Pucker command test + CPPTRAJ: AtomMap Test - CPPTRAJ: 2D RMSD Test. - - CPPTRAJ: Gzipped trajectory read with offsets -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 - J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. - Skipped test: J-Coupling extended test - -All 1 comparisons passed. -1 comparisons skipped. - + CPPTRAJ: Average Test. + CPPTRAJ: NAstruct command test. - CPPTRAJ: NetCDF Restart Test - NetCDF->TXT + CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Mol2 Parm/Traj Read/Write Test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile - CPPTRAJ: Broken Traj: Running broken trajectory. - - CPPTRAJ: CRD Replica Trajectory Run + CPPTRAJ: Data file output precision test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD + CPPTRAJ: CRD Replica Trajectory Run + CPPTRAJ: Distance RMSD test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist + CPPTRAJ: Cluster command test, in-memory pairwise distances. +******************************************************************************** - CPPTRAJ: Per-Residue RMSD Test with averaging - CPPTRAJ: Center origin command test. + CPPTRAJ: Closest command test using first solvent atom. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial CPPTRAJ: Non-orthorhombic imaged distance test. - CPPTRAJ: CHARMM DCD Write, step 1. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster - - CPPTRAJ: Coordinate Running Average Traj Write + CPPTRAJ: Radial test, non-orthogonal imaging - CPPTRAJ: Cluster command test, in-memory pairwise distances. + CPPTRAJ: 1D/2D Histogram Analysis test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED - CPPTRAJ: Diffusion test, old syntax. - -All 4 comparisons passed. + CPPTRAJ: Trajout Frame Range [Amber Coordinates] + CPPTRAJ: NetCDF Restart Test - NetCDF->TXT -All 2 comparisons passed. + CPPTRAJ: IRED vector/matrix test + CPPTRAJ: Broken Traj: Running broken trajectory. + J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. + Skipped test: J-Coupling extended test - CPPTRAJ: IRED vector/matrix test +All 1 comparisons passed. +1 comparisons skipped. - CPPTRAJ: 2D RMSD Test, mass-weighted. -All 2 comparisons passed. + CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. + CPPTRAJ: Unstrip (Lig/Rec/Complex) command test - CPPTRAJ: Mask longer command test. + CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test + +All 2 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons - CPPTRAJ: Standard -> Grace Data + CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: randomizeions test (original algorithm) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr + + CPPTRAJ: 2D RMSD Test, mass-weighted. + + CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: Bzip2ed trajectory read with offsets CPPTRAJ: Molsurf test - CPPTRAJ: Correlation test + CPPTRAJ: Coordinate Running Average Traj Write - CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. + CPPTRAJ: Center origin command test. - CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF +All 2 comparisons passed. - CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: NetCDF Replica Trajectory Run test - CPPTRAJ: PDB => Mol2 - - CPPTRAJ: Solute Hbond test with disk caching +All 4 comparisons passed. - CPPTRAJ: RMS coordinate rotation/rotation matrices test - -All 2 comparisons passed. +All 6 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr - CPPTRAJ: Orthorhombic coordinate imaging test - CPPTRAJ: Center origin mass command test. + CPPTRAJ: RMS coordinate rotation/rotation matrices test - CPPTRAJ: 2D RMSD Test with reference trajectory + CPPTRAJ: Diffusion test, old syntax. - CPPTRAJ: CHARMM DCD Write, step 2. + CPPTRAJ: Correlation test - CPPTRAJ: AtomMap with 'rmsfit' + CPPTRAJ: Mask longer command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: Structure Check - CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. + CPPTRAJ: AtomMap with 'rmsfit' - CPPTRAJ: Grace -> Standard Data + CPPTRAJ: PDB => Mol2 - CPPTRAJ: Convert NetCDF -> mdcrd + CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. -All 1 comparisons passed. + CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts + CPPTRAJ: Standard -> Grace Data +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr - CPPTRAJ: Per-Residue RMSD Test with residue centering. + CPPTRAJ: Orthorhombic coordinate imaging test - CPPTRAJ: Unstrip (Lig/Rec/Complex) command test -All 6 comparisons passed. + CPPTRAJ: Contacts test. + CPPTRAJ: Secstruct (DSSP) command with changing number of residues. + CPPTRAJ: RmsAvgCorr Reference - CPPTRAJ: Secstruct (DSSP) command with changing number of residues. - CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt + CPPTRAJ: Cluster command test, read pairwise distances. + CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: Start argument offset -All 2 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: 3D histogram test. +All 2 comparisons passed. - CPPTRAJ: Amber Top/Rst => Mol2 CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj - CPPTRAJ: NAstruct command test, single strand -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts - - CPPTRAJ: Cluster command test, read pairwise distances. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr + CPPTRAJ: Per-Residue RMSD Test with residue centering. - CPPTRAJ: Diffusion test, new syntax. + CPPTRAJ: 2D RMSD Test with reference trajectory -All 3 comparisons passed. +All 2 comparisons passed. - CPPTRAJ: Contacts test. + CPPTRAJ: Solute-solvent hbond test - CPPTRAJ: RmsAvgCorr Reference + CPPTRAJ: Center origin mass command test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal CPPTRAJ: Closest command test using all solvent atoms. - CPPTRAJ: Solute-solvent hbond test +All 3 comparisons passed. - CPPTRAJ: 2D DME Test. - CPPTRAJ: Atom map charmm->amber atom order -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal - - CPPTRAJ: CHAMBER topology read/strip test. + CPPTRAJ: Principal Test -All 4 comparisons passed. + CPPTRAJ: NAstruct command test, single strand + CPPTRAJ: Amber Top/Rst => Mol2 +******************************************************************************** +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 7 comparisons passed. + CPPTRAJ: Structure Check with Around and Skip + CPPTRAJ: 3D histogram test. - CPPTRAJ: Principal Test + CPPTRAJ: Basic vector tests - CPPTRAJ: Center reference command test. + CPPTRAJ: Atom map charmm->amber atom order -All 5 comparisons passed. + CPPTRAJ: clusterdihedral test - Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. - Skipped test: Amber Top/Rst => Mol2, SYBYL atom types + CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt All 4 comparisons passed. -1 comparisons skipped. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: RMS fit with no coordinates modification test. - CPPTRAJ: X column format/precision test. +All 5 comparisons passed. - CPPTRAJ: clusterdihedral test -All 11 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix + CPPTRAJ: Matrix Tests + CPPTRAJ: Secstruct (DSSP): SS assign output test - CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector + CPPTRAJ: CHAMBER topology read/strip test. - CPPTRAJ: Matrix Tests + CPPTRAJ: Cluster command test, read NetCDF pairwise distances. - CPPTRAJ: Secstruct (DSSP): SS assign output test + CPPTRAJ: Grace -> Standard Data - CPPTRAJ: Nonorthorhombic coordinate imaging test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct + CPPTRAJ: Convert NetCDF -> mdcrd + + CPPTRAJ: Multi frame strip command test. All 3 comparisons passed. - CPPTRAJ: Structure Check with Around and Skip +All 7 comparisons passed. - CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG + CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj + +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct + CPPTRAJ: RmsAvgCorr First ******************************************************************************** - CPPTRAJ: Basic vector tests TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid -All 2 comparisons passed. - + CPPTRAJ: 2D DME Test. - CPPTRAJ: Read CHARMM restart + CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. - CPPTRAJ: NA test (8OG) + CPPTRAJ: Center reference command test. CPPTRAJ: Dipole test - CPPTRAJ: Cluster command test, read NetCDF pairwise distances. +All 11 comparisons passed. - CPPTRAJ: Compressed broken trajectory test + + CPPTRAJ: Nonorthorhombic coordinate imaging test + 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. + TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project - CPPTRAJ: Data file group by name test + CPPTRAJ: Projection - CPPTRAJ: 2D RMSD with reference mask test. +All 4 comparisons passed. - CPPTRAJ: Atom map charmm->amber atom order, by residue ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap - CPPTRAJ: Projection + CPPTRAJ: Diffusion test, new syntax. - CPPTRAJ: Center point test. + CPPTRAJ: Atom map charmm->amber atom order, by residue CPPTRAJ: Unwrap non-orthogonal test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG CPPTRAJ: Hbond, no intramolecular hydrogen bonds test - CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj +All 3 comparisons passed. - CPPTRAJ: RmsAvgCorr First - CPPTRAJ: Diffusion test, nonorthogonal box + CPPTRAJ: NA test (8OG) - CPPTRAJ: FtuFabI Assignment test + CPPTRAJ: Read CHARMM restart -All 3 comparisons passed. + CPPTRAJ: Strip topology with PDB info +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes + CPPTRAJ: Modes analysis, RMS fluctuations - CPPTRAJ: CHARMM PSF write + CPPTRAJ: 2D RMSD with reference mask test. - CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. + CPPTRAJ: Compressed broken trajectory test - CPPTRAJ: 2D RMSD test, no fitting. + CPPTRAJ: Cluster command test, write ASCII pairwise distances. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell - CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj + CPPTRAJ: Watershell Test, non-orthorhombic imaging. -All 9 comparisons passed. + CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj + CPPTRAJ: X column format/precision test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes - -All 1 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg + CPPTRAJ: FtuFabI Assignment test -All 4 comparisons passed. + CPPTRAJ: Analysis Running Average + CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. - CPPTRAJ: Modes analysis, RMS fluctuations +All 3 comparisons passed. - CPPTRAJ: Multi frame strip command test. All 1 comparisons passed. - CPPTRAJ: Grid test +All 2 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: Test vector center with magnitude -All 3 comparisons passed. +All 9 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap + CPPTRAJ: 2D RMSD test, no fitting. - CPPTRAJ: Analysis Running Average - CPPTRAJ: CRD Replica Trajectory Run with remdout + CPPTRAJ: CHARMM PSF write +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap - CPPTRAJ: Watershell Test, non-orthorhombic imaging. +All 11 comparisons passed. - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar -All 2 comparisons passed. + CPPTRAJ: VMD VolMap Algorithm test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM - - CPPTRAJ: Data file group by aspect test + CPPTRAJ: Center point test. CPPTRAJ: SPAM Test - - CPPTRAJ: VMD VolMap Algorithm test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE - CPPTRAJ: STFC Diffusion Test - - CPPTRAJ: Density along axis tests + CPPTRAJ: Modes analysis, displacements - CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. + CPPTRAJ: LIE test - CPPTRAJ: CHARMM COORdinates test + CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj - CPPTRAJ: Cluster command test, write ASCII pairwise distances. + CPPTRAJ: Cluster command test, read ASCII pairwise distances. - CPPTRAJ: LIE test + CPPTRAJ: Grid test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density - CPPTRAJ: Unwrap orthogonal test - - CPPTRAJ: Hbond, specified solute masks + CPPTRAJ: Lipid Order Parameter Test. - CPPTRAJ: RMS fit to previous test + CPPTRAJ: Density along axis tests - CPPTRAJ: Outtraj Test with maxmin. + CPPTRAJ: Diffusion test, nonorthogonal box - CPPTRAJ: Modes analysis, displacements +All 2 comparisons passed. -All 1 comparisons passed. + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar - CPPTRAJ: Lipid Order Parameter Test. +All 3 comparisons passed. -All 6 comparisons passed. + CPPTRAJ: CHARMM COORdinates test - CPPTRAJ: Strip topology with PDB info -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist +All 2 comparisons passed. - CPPTRAJ: Test vector center with magnitude - CPPTRAJ: PairDist Test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData + CPPTRAJ: Unwrap orthogonal test -All 10 comparisons passed. + CPPTRAJ: Data file group by name test + CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. All 6 comparisons passed. + CPPTRAJ: RMS fit to previous test -All 2 comparisons passed. -All 3 comparisons passed. +All 5 comparisons passed. + + + CPPTRAJ: Momentum/velocity vector test. + CPPTRAJ: Hbond, specified solute masks ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist - CPPTRAJ: Test updating topology with Charmm parameters (single residue) + 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_systemVF + + CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test CPPTRAJ: GIST water-water interaction test - VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. - Skipped test: VMD VolMap Algorithm longer tests +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr -All 2 comparisons passed. -1 comparisons skipped. + CPPTRAJ: Atomic Correlation test + CPPTRAJ: Read vector data test (no origins, origins) -All 2 comparisons passed. + CPPTRAJ: Modes analysis, dipole correlation + CPPTRAJ: CRD Replica Trajectory Run with remdout + +All 10 comparisons passed. All 6 comparisons passed. - CPPTRAJ: Closest command test, using mask center + +All 9 comparisons passed. + + CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. CPPTRAJ: RMS: imaging after unit cell rotation + 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: Cluster command test, read ASCII pairwise distances. - - CPPTRAJ: Modes analysis, dipole correlation +All 2 comparisons passed. +1 comparisons skipped. - CPPTRAJ: STFC Diffusion Test with individual distances +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams - CPPTRAJ: Pairdist test, orthogonal imaging. + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM - CPPTRAJ: Randomize (around, overlap) + CPPTRAJ: Test updating topology with Charmm parameters (single residue) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr -All 8 comparisons passed. + CPPTRAJ: AutoCorr test. + CPPTRAJ: Force vector test. - CPPTRAJ: Read vector data test (no origins, origins) + CPPTRAJ: STFC Diffusion Test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve - CPPTRAJ: Partial Surface calculation test + CPPTRAJ: Cluster, nosieve CPPTRAJ: Hbond, no angle cutoff test All 2 comparisons passed. -All 11 comparisons passed. - - - CPPTRAJ: Structure Check with PBC - - - CPPTRAJ: Momentum/velocity vector test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM + CPPTRAJ: OpenDX Grid read test - CPPTRAJ: Box Test (Add box info) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr - CPPTRAJ: Atomic Correlation test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF + CPPTRAJ: Read vector data set (origins, no origins) + CPPTRAJ: Box Test (Add box info) - CPPTRAJ: AutoCorr test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef + CPPTRAJ: Data file group by aspect test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect - CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test - CPPTRAJ: Selection by atom type test. - CPPTRAJ: Radial test, orthogonal and no imaging +All 1 comparisons passed. - CPPTRAJ: RMSD Test with averaged reference coordinates. - CPPTRAJ: Multi-frame density along axis test + CPPTRAJ: Atomicfluct test with ADP output -All 9 comparisons passed. + CPPTRAJ: Structure Check with PBC +All 12 comparisons passed. -All 4 comparisons passed. + +All 8 comparisons passed. + + +All 1 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef - CPPTRAJ: Atomicfluct test with ADP output + CPPTRAJ: RMSD Test with averaged reference coordinates. - CPPTRAJ: OpenDX Grid read test +All 2 comparisons passed. - CPPTRAJ: SPAM Pure Solvent Test - CPPTRAJ: Read vector data set (origins, no origins) + CPPTRAJ: Read Amber output test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat - CPPTRAJ: COORDS data set creation and CRDFLUCT test. - CPPTRAJ: Crankshaft test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd -All 6 comparisons passed. + CPPTRAJ: Hbond, Bridge nointramol test + + CPPTRAJ: COORDS data set creation and CRDFLUCT test. + CPPTRAJ: Box test (remove box info) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage - CPPTRAJ: STFC Diffusion Test with COM -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve +All 1 comparisons passed. - CPPTRAJ: AutoImage test (split DNA duplex) - CPPTRAJ: Hbond, Bridge nointramol test +All 6 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd - CPPTRAJ: LoadCrd test. +All 15 comparisons passed. - CPPTRAJ: Cluster, nosieve + CPPTRAJ: AutoImage test (split DNA duplex) -All 1 comparisons passed. -All 12 comparisons passed. + CPPTRAJ: LoadCrd test. + CPPTRAJ: STFC Diffusion Test with individual distances + CPPTRAJ: Closest command test, using mask center and solvent mask -All 1 comparisons passed. + CPPTRAJ: Cluster, sieve5 + +All 14 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD All 1 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel - CPPTRAJ: Basic lipid order parameter test + CPPTRAJ: Modes analysis, pseudo trajectory creation test - CPPTRAJ: Force vector test. + CPPTRAJ: Parallel tests. - CPPTRAJ: Read Amber output test + CPPTRAJ: Read CHARMM output test - CPPTRAJ: Closest command test, using mask center and solvent mask + CPPTRAJ: Box test (Modify box length) -All 9 comparisons passed. + CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. + CPPTRAJ: Pairdist test, orthogonal imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT - - CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: Lifetime test. CPPTRAJ: Multivector test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr - CPPTRAJ: FFT test. + CPPTRAJ: Grid with specified center test. + +All 3 comparisons passed. - CPPTRAJ: Box test (remove box info) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr + + CPPTRAJ: Timecorr test. All 6 comparisons passed. - CPPTRAJ: CrossCorr test + CPPTRAJ: COORDS data set creation with velocities test - CPPTRAJ: Timecorr test. + CPPTRAJ: LoadTraj test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT - CPPTRAJ: Modes analysis, pseudo trajectory creation test + CPPTRAJ: FFT test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd -All 3 comparisons passed. - - CPPTRAJ: SymmRmsd - - CPPTRAJ: LoadTraj 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_CrossCorr - CPPTRAJ: STFC Diffusion Test with second mask + CPPTRAJ: CrossCorr test - CPPTRAJ: Grid with specified center test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral + CPPTRAJ: 3D data read/write test - CPPTRAJ: Total system density test +All 6 comparisons passed. - CPPTRAJ: M-REMD sort test. - CPPTRAJ: Generate matrix with trajectory start/stop/offset +All 1 comparisons passed. - CPPTRAJ: Multidihedral test - CPPTRAJ: Box test (Modify box length) + CPPTRAJ: Multi-frame density along axis test -All 15 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Read CHARMM output test + CPPTRAJ: Outtraj Test with maxmin. -All 1 comparisons passed. +All 13 comparisons passed. - CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. + CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test -All 1 comparisons passed. + CPPTRAJ: Parallel test with trajectory offset +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD + CPPTRAJ: Box test (auto orthogonal box, no radii) - CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test + CPPTRAJ: ASP symmetry-corrected RMSD test -All 14 comparisons passed. + CPPTRAJ: STFC Diffusion Test with COM + CPPTRAJ: Basic lipid order parameter test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD - CPPTRAJ: Parallel tests. + CPPTRAJ: Closest command test, solvent mask, water oxygen only ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral - CPPTRAJ: Basic makestructure test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate + CPPTRAJ: Standard 3D data write test - CPPTRAJ: Rotation (and inverse) of coords from matrices + CPPTRAJ: Generate matrix with trajectory start/stop/offset - CPPTRAJ: LCPO test with GAFF atom types + CPPTRAJ: M-REMD sort test. - CPPTRAJ: ASP symmetry-corrected RMSD test + CPPTRAJ: LoadTraj from trajin test. -All 3 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate + CPPTRAJ: Multidihedral test + CPPTRAJ: SPAM Pure Solvent Test - CPPTRAJ: Closest command test, solvent mask, water oxygen only +All 7 comparisons passed. - CPPTRAJ: Integration test. -All 6 comparisons passed. +All 1 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: Partial Surface calculation test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure + CPPTRAJ: Cluster, nosieve savepairdist -All 3 comparisons passed. + CPPTRAJ: Basic makestructure test + CPPTRAJ: Lifetime test with data set caching. -All 7 comparisons passed. + CPPTRAJ: Grid with box center offset test. + CPPTRAJ: GLU symmetry-corrected RMSD test + CPPTRAJ: Box test (auto orthogonal box, VDW radii) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate - CPPTRAJ: Generate matrix with action stop/start/offset - CPPTRAJ: Cluster, sieve5 + CPPTRAJ: Integration test. - CPPTRAJ: LoadTraj from trajin test. - CPPTRAJ: New Lipid Order Parameter Test, DOPC. + CPPTRAJ: Rotation (and inverse) of coords from matrices +All 6 comparisons passed. - CPPTRAJ: Lifetime test with data set caching. - CPPTRAJ: 3D data read/write test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts +All 5 comparisons passed. - CPPTRAJ: Multidihedral Nucleotide CHI test + + CPPTRAJ: STFC Diffusion Test with second mask + + CPPTRAJ: Generate matrix with action stop/start/offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts + + CPPTRAJ: Check chirality test + + CPPTRAJ: Standard 3D data read test CPPTRAJ: NativeContacts test. - CPPTRAJ: Check chirality test + CPPTRAJ: LoadCrd append from multiple files test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy CPPTRAJ: Simple energy tests - CPPTRAJ: Box test (auto orthogonal box, no radii) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit - - CPPTRAJ: Makestructure test with reference. +All 1 comparisons passed. -All 2 comparisons passed. +All 7 comparisons passed. - CPPTRAJ: Grid with box center offset test. - CPPTRAJ: GLU symmetry-corrected RMSD test + CPPTRAJ: TYR symmetry-corrected RMSD test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: LES split/average test -All 7 comparisons passed. - - CPPTRAJ: PermuteDihedrals interval -120, phi psi - - -All 15 comparisons passed. + CPPTRAJ: Multidihedral Nucleotide CHI test +All 4 comparisons passed. -All 13 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals + CPPTRAJ: PermuteDihedrals interval -120, phi psi - CPPTRAJ: Rotate with defined axis +All 15 comparisons passed. - CPPTRAJ: Parallel test with trajectory offset - CPPTRAJ: TRAJ data set creation and CRDFLUCT test. + CPPTRAJ: Radial test, orthogonal and no imaging +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 -All 1 comparisons passed. + CPPTRAJ: Makestructure test with reference. +All 2 comparisons passed. - CPPTRAJ: LoadCrd append from multiple files test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. - CPPTRAJ: Standard 3D data write test +All 4 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage - CPPTRAJ: Data set averaging and averaging over all sets test. +All 1 comparisons passed. - CPPTRAJ: Multidihedral protein dihedrals test - CPPTRAJ: Dihedral Covariance Matrix Test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath + CPPTRAJ: Grid with mask center offset test. - CPPTRAJ: Vector dot/cross product test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit + CPPTRAJ: M-REMD actions test. -All 5 comparisons passed. + CPPTRAJ: Total system density test + CPPTRAJ: Standard 3D data read/append test -All 1 comparisons passed. + CPPTRAJ: Lifetime average and cumulative average test. + CPPTRAJ: Cluster, nosieve loadpairdist - CPPTRAJ: Curve fitting test. + CPPTRAJ: TRAJ data set creation and CRDFLUCT test. - CPPTRAJ: Box test (auto orthogonal box, VDW radii) + CPPTRAJ: Dihedral Covariance Matrix Test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit -All 1 comparisons passed. + CPPTRAJ: Multidihedral protein dihedrals test + CPPTRAJ: Curve fitting test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage - CPPTRAJ: M-REMD actions test. + CPPTRAJ: Data set averaging and averaging over all sets test. - CPPTRAJ: Cluster, nosieve savepairdist + CPPTRAJ: Rotate with defined axis +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath -All 4 comparisons passed. + CPPTRAJ: Vector dot/cross product test +All 7 comparisons passed. - CPPTRAJ: TYR symmetry-corrected RMSD test - CPPTRAJ: PermuteDihedrals, random rotations + CPPTRAJ: Longer symmetry-corrected RMSD test. -All 4 comparisons passed. +All 9 comparisons passed. - CPPTRAJ: TRAJ data set creation with velocities test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline +All 5 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander SANDER energy tests (long) requires SANDER API from AmberTools. @@ -2753,16 +2778,19 @@ SKIP: SANDER energy tests (long) - CPPTRAJ: Temperature test. +All 12 comparisons passed. - CPPTRAJ: Spline test -All 2 comparisons passed. +All 3 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature - CPPTRAJ: KDE test. + + + CPPTRAJ: Temperature test. + CPPTRAJ: TRAJ data set creation with velocities test. + CPPTRAJ: New Lipid Order Parameter Test, DOPC. ******************************************************************************** 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. @@ -2770,724 +2798,730 @@ SKIP: Energy via sander API short tests (GB/PME) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet - - CPPTRAJ: Wavelet analysis test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF - -All 7 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline + CPPTRAJ: KDE test. - CPPTRAJ: Multidihedral cyclic molecule test + CPPTRAJ: PermuteDihedrals, random rotations - CPPTRAJ: Lifetime average and cumulative average test. +All 2 comparisons passed. - CPPTRAJ: Standard 3D data read test - CPPTRAJ: AutoImage test, use anchor mask + CPPTRAJ: Spline test - CPPTRAJ: Grid with mask center offset test. +All 2 comparisons passed. - CPPTRAJ: CIF read test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF -All 2 comparisons passed. + CPPTRAJ: Standard 3D data, sparse +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet + CPPTRAJ: Multidihedral cyclic molecule test - CPPTRAJ: Curve fitting multi-exponential tests. + CPPTRAJ: M-REMD ensemble outtraj test. -All 3 comparisons passed. + CPPTRAJ: Wavelet analysis test +******************************************************************************** +All 8 comparisons passed. -All 2 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align + CPPTRAJ: CIF read test - CPPTRAJ: Temperature with SHAKE on hydrogens. + CPPTRAJ: Align Tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB -All 1 comparisons passed. - - 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. +All 2 comparisons passed. + CPPTRAJ: Velocity autocorrelation test + + CPPTRAJ: Temperature with SHAKE on hydrogens. + + CPPTRAJ: Curve fitting multi-exponential tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral CPPTRAJ: Test combining coordinates, velocities, and forces. - CPPTRAJ: Rotate dihedral to target value. +All 3 comparisons passed. -All 6 comparisons passed. + + CPPTRAJ: Cluster, sieve5 savepairdist + +All 7 comparisons passed. + + + CPPTRAJ: Non-orthogonal grid test. + +All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap - CPPTRAJ: Data Set commands test +All 6 comparisons passed. -All 4 comparisons passed. + CPPTRAJ: Rotate dihedral to target value. - CPPTRAJ: Longer symmetry-corrected RMSD test. + CPPTRAJ: Remap Test - CPPTRAJ: M-REMD ensemble outtraj test. + CPPTRAJ: Data Set commands test - CPPTRAJ: COORDS data set append test + CPPTRAJ: Test using velocities as coordinates. -All 12 comparisons passed. + CPPTRAJ: M-REMD no sort, running average test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap +All 4 comparisons passed. - CPPTRAJ: Remap Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Compare topology test - CPPTRAJ: Standard 3D data read/append test - -All 7 comparisons passed. - + CPPTRAJ: Temperature with SHAKE on all atoms. - CPPTRAJ: Test kinetic energy calculation + CPPTRAJ: Nonorthogonal grid standard write/read tests. -All 16 comparisons passed. +All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter - CPPTRAJ: Temperature with SHAKE on all atoms. - CPPTRAJ: Basic filter test - CPPTRAJ: Non-orthogonal grid test. + CPPTRAJ: COORDS data set append test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd - CPPTRAJ: Rotate dihedral by increment - -All 2 comparisons passed. - - CPPTRAJ: Test using velocities as coordinates. - - - CPPTRAJ: Randomize (around) - - CPPTRAJ: Combine COORDS test. - CPPTRAJ: COORDS test storing frame metadata ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo - CPPTRAJ: Align, unit cell rotation/imaging test. - CPPTRAJ: Topology info print test. - CPPTRAJ: Test total energy calculation - - CPPTRAJ: Cluster, nosieve loadpairdist - -All 3 comparisons passed. + CPPTRAJ: Test writing velocities (MDVEL) +All 1 comparisons passed. - CPPTRAJ: Generate offset traj from PDB - CPPTRAJ: Curve fitting, custom output range. + CPPTRAJ: Temperature calc with extra points. - CPPTRAJ: M-REMD no sort, running average test + CPPTRAJ: Align, unit cell rotation/imaging test. -All 8 comparisons passed. + CPPTRAJ: M-REMD, generate RMS data + CPPTRAJ: Rotate dihedral by increment ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr -All 1 comparisons passed. - - + CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: TRR force/velocity read -> NetCDF write test - CPPTRAJ: Wavelet WAFEX test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald + + CPPTRAJ: Test kinetic energy calculation All 1 comparisons passed. +All 4 comparisons passed. + + CPPTRAJ: Combine COORDS test with box info. - CPPTRAJ: Direct sum test +All 10 comparisons passed. - CPPTRAJ: Rotate dihedral in TRAJ data set - CPPTRAJ: Standard 3D data, sparse +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_TI - CPPTRAJ: TI analysis test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds +All 16 comparisons passed. - CPPTRAJ: Test partial energy calculation - CPPTRAJ: Temperature calc with extra points. + CPPTRAJ: Curve fitting, custom output range. + + CPPTRAJ: Test using forces as coordinates. CPPTRAJ: Fix imaged bonds test (Ortho.) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI -All 10 comparisons passed. + CPPTRAJ: AutoImage test, use anchor mask + CPPTRAJ: TI analysis test. ******************************************************************************** + TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance + CPPTRAJ: M-REMD, meltcurve analysis +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Distance tests - CPPTRAJ: Test writing velocities (MDVEL) - -All 6 comparisons passed. - - - CPPTRAJ: M-REMD, generate RMS data + CPPTRAJ: Direct sum test - CPPTRAJ: Generate offset traj from CIF + CPPTRAJ: Rotate dihedral in TRAJ data set ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume -All 3 comparisons passed. - + CPPTRAJ: Randomize (around, overlap) CPPTRAJ: Volume tests -All 3 comparisons passed. + CPPTRAJ: Wavelet WAFEX test + + CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test + CPPTRAJ: PQR file write with various radii + + CPPTRAJ: Cluster, sieve5 loadpairdist + + CPPTRAJ: LCPO test with GAFF atom types CPPTRAJ: Data filter test. +All 1 comparisons passed. - CPPTRAJ: Cluster, sieve5 savepairdist + CPPTRAJ: KDE with Kullback-Leibler divergence test - CPPTRAJ: PQR file write with various radii +All 17 comparisons passed. - CPPTRAJ: Nonorthogonal grid standard write/read tests. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve - CPPTRAJ: Multicurve test +All 6 comparisons passed. + + + CPPTRAJ: Test writing forces (MDFRC) + + CPPTRAJ: Generate offset traj from PDB + +All 5 comparisons passed. + + + CPPTRAJ: NativeContacts test, orthorhombic imaging. + + CPPTRAJ: Orthogonal imaged distance ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity - - CPPTRAJ: KDE with Kullback-Leibler divergence test CPPTRAJ: Set Velocity test + +All 3 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog + + CPPTRAJ: TRAJ test storing frame metadata + + CPPTRAJ: Test total energy calculation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol CPPTRAJ: Replica log read/analyze test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Area per molecule test - CPPTRAJ: Pairdist test, nonorthogonal imaging. - - CPPTRAJ: Test using forces as coordinates. - - CPPTRAJ: M-REMD, meltcurve analysis - - CPPTRAJ: NativeContacts test, orthorhombic imaging. + CPPTRAJ: Multicurve test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask - CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test + CPPTRAJ: Distance-based atom mask tests (atom, residue) - CPPTRAJ: Orthogonal imaged distance +All 3 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: PDB filter alternate atom location IDs test -All 6 comparisons passed. + CPPTRAJ: Fix imaged bonds test (Non-ortho.) + CPPTRAJ: Generate offset traj from CIF + CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. - CPPTRAJ: TRAJ test storing frame metadata All 2 comparisons passed. - CPPTRAJ: Split coords and recombine test. - CPPTRAJ: Scale velocity test -All 1 comparisons passed. + CPPTRAJ: Split coords and recombine test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc + CPPTRAJ: Filter matrix test. -All 1 comparisons passed. + CPPTRAJ: Non-orthogonal imaged distance + CPPTRAJ: Calc test -All 17 comparisons passed. +All 4 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask - CPPTRAJ: Fix imaged bonds test (Non-ortho.) -******************************************************************************** -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState +All 5 comparisons passed. - CPPTRAJ: Distance-based atom mask tests (atom, residue) - CPPTRAJ: Calcstate test +All 1 comparisons passed. -All 4 comparisons passed. + CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. - CPPTRAJ: Calc test +All 2 comparisons passed. - CPPTRAJ: Test writing forces (MDFRC) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState - CPPTRAJ: TRR force/velocity read -> TRR write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir + CPPTRAJ: Cluster, nosieve pairwisecache none - CPPTRAJ: Structure Check with Around + CPPTRAJ: Test partial energy calculation - CPPTRAJ: Create RREMD NetCDF reservoir test + CPPTRAJ: Calcstate test -All 2 comparisons passed. + CPPTRAJ: Create RREMD NetCDF reservoir test + CPPTRAJ: Grid generation from 'bounds' test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change -All 5 comparisons passed. +All 7 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change - CPPTRAJ: Filter matrix test. +All 1 comparisons passed. CPPTRAJ: Change atom and residue name tests -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve - CPPTRAJ: Out of order molecules test - CPPTRAJ: PDB filter alternate atom location IDs test - - CPPTRAJ: LowestCurve test + CPPTRAJ: Distance-based atom mask tests (molecule) All 3 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve -All 3 comparisons passed. +All 8 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder -All 7 comparisons passed. + CPPTRAJ: LowestCurve test + + CPPTRAJ: Out of order molecules test + CPPTRAJ: TRR force/velocity read -> TRR write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress - CPPTRAJ: Non-orthogonal imaged distance + CPPTRAJ: Linear regression test. + CPPTRAJ: Calc test with data sets +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise - CPPTRAJ: Linear regression test. - CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. CPPTRAJ: Minimum Image test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise + CPPTRAJ: Pairwise tests CPPTRAJ: Generate restraints (rst) test - CPPTRAJ: Calc test with data sets - - CPPTRAJ: Pairwise tests + CPPTRAJ: Adding PDB info to topology All 5 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox - CPPTRAJ: CRD => TRR +All 2 comparisons passed. - CPPTRAJ: Parmbox test - CPPTRAJ: Grid generation from 'bounds' test. +All 3 comparisons passed. -All 8 comparisons passed. + CPPTRAJ: Change chain ID test -All 6 comparisons passed. + CPPTRAJ: Hbond with imaging +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent + CPPTRAJ: Test solvent command with closest +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox + +All 2 comparisons passed. + + + CPPTRAJ: Test math functions All 4 comparisons passed. -All 2 comparisons passed. + CPPTRAJ: Parmbox test +All 3 comparisons passed. - CPPTRAJ: Distance-based atom mask tests (molecule) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent - CPPTRAJ: Change chain ID test + CPPTRAJ: CRD => TRR CPPTRAJ: Translate test - -All 8 comparisons passed. - - - CPPTRAJ: Test solvent command with closest ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK - CPPTRAJ: Topology info with reference coords test - -All 2 comparisons passed. - + CPPTRAJ: Scale dihedral force constant test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell CPPTRAJ: Replicate cell test - CPPTRAJ: Scale dihedral force constant test +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_Control - CPPTRAJ: Phipsi test - -All 3 comparisons passed. + CPPTRAJ: Topology info with reference coords test +All 10 comparisons passed. - CPPTRAJ: Test math functions - CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. + CPPTRAJ: Phipsi test - CPPTRAJ: Loop tests +All 2 comparisons passed. - CPPTRAJ: Hbond with imaging All 1 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec -All 1 comparisons passed. +All 4 comparisons passed. - CPPTRAJ: Infrared spectrum calculation test + CPPTRAJ: Change chain ID of COORDS set test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control + + CPPTRAJ: Loop tests + +All 6 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_InfraredSpec + CPPTRAJ: Pairwise test, partial system - CPPTRAJ: Change chain ID of COORDS set test + CPPTRAJ: Infrared spectrum calculation test All 1 comparisons passed. - CPPTRAJ: Explicit pH REMD ensemble data read / sort - -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine - CPPTRAJ: Command line trajectory args test, part 1 +All 5 comparisons passed. -All 12 comparisons passed. + CPPTRAJ: Hbond, orthogonal imaging CPPTRAJ: Scale dihedral force constant with 'useall' - ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat - CPPTRAJ: Adding PDB info to topology +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine -All 1 comparisons passed. +All 1 comparisons passed. -All 4 comparisons passed. + CPPTRAJ: Command line trajectory args test, part 1 +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats +All 1 comparisons passed. -All 17 comparisons passed. + CPPTRAJ: XYZ format write ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff - CPPTRAJ: XYZ format write - All 1 comparisons passed. + CPPTRAJ: Explicit pH REMD ensemble data read / sort + + CPPTRAJ: Simple Hausdorff distance test. +All 6 comparisons passed. + + +All 13 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd All 1 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm - CPPTRAJ: Concatenate COORDS data set test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time + CPPTRAJ: SplitCoords test CPPTRAJ: XtalSymm Reference -All 13 comparisons passed. +All 3 comparisons passed. - CPPTRAJ: Hbond, orthogonal imaging + CPPTRAJ: Concatenate COORDS data set test - CPPTRAJ: Add time to restart test +All 12 comparisons passed. - CPPTRAJ: Cluster, sieve5 loadpairdist -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords All 3 comparisons passed. - - CPPTRAJ: SplitCoords test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope - - CPPTRAJ: Finite difference test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS -All 3 comparisons passed. - +All 2 comparisons passed. - CPPTRAJ: Pairwise test, partial system CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix - CPPTRAJ: MW covariance matrix thermo analysis test +All 1 comparisons passed. - CPPTRAJ: Command line test trajectory args test, part 2 +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time -All 2 comparisons passed. + CPPTRAJ: Add time to restart test + CPPTRAJ: Structure Check with Around +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope All 8 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix - CPPTRAJ: Ewald test (NaCl crystal) + CPPTRAJ: Finite difference test. + + CPPTRAJ: TRR => CRD + + CPPTRAJ: MW covariance matrix thermo analysis test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin + + CPPTRAJ: Command line test trajectory args test, part 2 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau - CPPTRAJ: Evalulate plateau test CPPTRAJ: Basic energy minimization test. - -All 5 comparisons passed. - - -All 1 comparisons passed. - - -All 10 comparisons passed. - + CPPTRAJ: Evalulate plateau test +******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten -All 2 comparisons passed. + CPPTRAJ: Graft test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random + CPPTRAJ: Flatten test. - CPPTRAJ: Graft test +All 17 comparisons passed. - CPPTRAJ: TRR => CRD -All 1 comparisons passed. + CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten + CPPTRAJ: Test set command + + CPPTRAJ: Cluster, sieve5 pairwisecache none CPPTRAJ: Hausdorff distance of 2D rms output test. - CPPTRAJ: Remove time from restart test + CPPTRAJ: Atom XYZ format read, test 1 + +All 10 comparisons passed. - CPPTRAJ: Flatten test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random All 1 comparisons passed. - CPPTRAJ: Test set command +All 1 comparisons passed. - CPPTRAJ: Atom XYZ format read, test 1 - CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs + CPPTRAJ: Remove time from restart test - CPPTRAJ: Constant pH stats test +All 23 comparisons passed. - CPPTRAJ: Dihedral RMSD test (to previous) All 1 comparisons passed. -All 10 comparisons passed. - + CPPTRAJ: Constant pH stats test -All 23 comparisons passed. +All 1 comparisons passed. All 1 comparisons passed. + CPPTRAJ: PCG32 RNG test. + CPPTRAJ: Command line wildcard test, part 1 - CPPTRAJ: Ewald test (trunc. oct) +All 2 comparisons passed. + All 1 comparisons passed. - CPPTRAJ: Add time to trajectory test - - CPPTRAJ: PCG32 RNG test. + CPPTRAJ: Dihedral RMSD test (to previous) -All 1 comparisons passed. + CPPTRAJ: Energy minimization with angle term test. +All 2 comparisons passed. - CPPTRAJ: Energy minimization with angle term test. - CPPTRAJ: Atom XYZ format read, test 2 + CPPTRAJ: Add time to trajectory test - CPPTRAJ: Cluster, nosieve pairwisecache none + CPPTRAJ: Test Stdlib RNG -All 2 comparisons passed. + CPPTRAJ: Command line wildcard test, part 2 + CPPTRAJ: Atom XYZ format read, test 2 All 1 comparisons passed. - CPPTRAJ: Sorted implicit constant pH stats test - - CPPTRAJ: Command line wildcard test, part 2 + CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: Test reading comma-separated list of strings - CPPTRAJ: Dihedral RMS fluctuation test. - -All 6 comparisons passed. - + CPPTRAJ: Sorted implicit constant pH stats test - CPPTRAJ: Hausdorff distance of 2D rms output test. + CPPTRAJ: CRD(1-5) => TRR - CPPTRAJ: Randomize (overlap) +All 6 comparisons passed. - CPPTRAJ: Test Stdlib RNG - CPPTRAJ: Atom XYZ format read, test 3 + CPPTRAJ: Dihedral RMS fluctuation test. - CPPTRAJ: CRD(1-5) => TRR + CPPTRAJ: Test Mersenne Twister RNG CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. All 2 comparisons passed. + CPPTRAJ: Cluster, random + + CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats + CPPTRAJ: Atom XYZ format read, test 3 All 4 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: Ewald test (trunc. oct) + CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Test nested loops and variables in loops - CPPTRAJ: Test Mersenne Twister RNG - - CPPTRAJ: Energy minimization with nonbond term test. + CPPTRAJ: Modify time info test. - CPPTRAJ: Atom XYZ format read, test 4 +All 5 comparisons passed. - CPPTRAJ: Modify time info test. -All 1 comparisons passed. + CPPTRAJ: Energy minimization with nonbond term test. + CPPTRAJ: Pairdist test, nonorthogonal imaging. - CPPTRAJ: Test loop over data set blocks + CPPTRAJ: Atom XYZ format read, test 4 All 4 comparisons passed. - CPPTRAJ: XtalSymm Reimaging by Atom + CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: Unsorted pH read/write test - CPPTRAJ: Cluster, sieve5 pairwisecache none +All 28 comparisons passed. - CPPTRAJ: CRD(6-10) => TRR -All 4 comparisons passed. + CPPTRAJ: Test loop over data set blocks +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve + CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: Atom XYZ format read, test 5 All 16 comparisons passed. - CPPTRAJ: Test for filename wildcards and oversets +All 8 comparisons passed. - CPPTRAJ: Randomize (no restrictions) - CPPTRAJ: Cluster, random -g++ -o a.out main.o NameType.o CpptrajStdio.o + CPPTRAJ: TRR (appended) => CRD CPPTRAJ: Atom XYZ format read, test 6 - CPPTRAJ: TRR (appended) => CRD + CPPTRAJ: Test for filename wildcards and oversets + +All 6 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). All 13 comparisons passed. -All 6 comparisons passed. +g++ -o a.out main.o NameType.o CpptrajStdio.o - CPPTRAJ: Ewald test (partial system, trunc. oct) +All 3 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: OpenMM basic energy minimization tests (bonds) -All 28 comparisons passed. + CPPTRAJ: GMX: CRD with offset + CPPTRAJ: Randomize (around) - CPPTRAJ: OpenMM basic energy minimization tests (bonds) + CPPTRAJ: OpenMM basic energy minimization tests (angles) - CPPTRAJ: Watershell Test, orthorhombic imaging. +All 4 comparisons passed. + + + CPPTRAJ: Ewald test (partial system, trunc. oct) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet - CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). + CPPTRAJ: Clustering, One DataSet make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' - CPPTRAJ: OpenMM basic energy minimization tests (angles) + CPPTRAJ: XtalSymm Reimaging by Atom + + CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) 'ZN' 'HA2' 'HA' 'HA' 'CT11' Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' @@ -3495,7 +3529,23 @@ Unit test passed. - CPPTRAJ: GMX: CRD with offset + CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) + + CPPTRAJ: Clustering, Two DataSets + +All 4 comparisons passed. + + + CPPTRAJ: GMX: TRR with offset + + CPPTRAJ: Watershell Test, orthorhombic imaging. + + CPPTRAJ: Clustering, dihedral DataSet + +All 1 comparisons passed. + + + CPPTRAJ: Clustering, two dihedral DataSets 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. @@ -3504,117 +3554,103 @@ 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_LibPME - CPPTRAJ: Pairdist test, 2 masks. - CPPTRAJ: Particle mesh Ewald test (NaCl crystal) - CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). + CPPTRAJ: Clustering, dihedral DataSet, K-means - CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) +All 5 comparisons passed. - CPPTRAJ: GMX: TRR with offset +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc - CPPTRAJ: Read specific columns test. + CPPTRAJ: XTC read test CPPTRAJ: Particle mesh Ewald test (trunc. oct) -All 4 comparisons passed. - - - CPPTRAJ: Write non-square matrix - - CPPTRAJ: GIST test, orthogonal cell + CPPTRAJ: Clustering, two dihedral DataSets, K-means -All 4 comparisons passed. +All 8 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN - CPPTRAJ: Clustering, One DataSet + CPPTRAJ: DBSCAN test - CPPTRAJ: Watershell Test, no imaging. + CPPTRAJ: CRD => XTC -All 5 comparisons passed. + CPPTRAJ: Randomize (overlap) + CPPTRAJ: DBSCAN automatic parameter determination test. - CPPTRAJ: Read non-square matrix -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc + CPPTRAJ: Read specific columns test. - CPPTRAJ: XTC read test + CPPTRAJ: XTC => CRD - CPPTRAJ: Clustering, Two DataSets + CPPTRAJ: DBSCAN kdist map test - CPPTRAJ: Read square matrix + CPPTRAJ: Write non-square matrix - CPPTRAJ: Clustering, dihedral DataSet + CPPTRAJ: DBSCAN with sieve -All 15 comparisons passed. + CPPTRAJ: Randomize (no restrictions) + CPPTRAJ: Watershell Test, no imaging. - CPPTRAJ: Clustering, two dihedral DataSets +All 4 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Read non-square matrix - CPPTRAJ: CRD => XTC + CPPTRAJ: Pairdist test, 2 masks. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans - CPPTRAJ: Particle mesh Ewald test (ortho) + CPPTRAJ: Cpptraj Kmeans - CPPTRAJ: Clustering, dihedral DataSet, K-means + CPPTRAJ: Read square matrix -All 5 comparisons passed. +All 4 comparisons passed. - CPPTRAJ: Clustering, two dihedral DataSets, K-means + CPPTRAJ: CRD(1-5) => XTC - CPPTRAJ: XTC => CRD +All 15 comparisons passed. -All 8 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN + CPPTRAJ: Particle mesh Ewald test (ortho) - CPPTRAJ: DBSCAN test + CPPTRAJ: Cpptraj Kmeans random - CPPTRAJ: DBSCAN automatic parameter determination test. + CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) +All 5 comparisons passed. - CPPTRAJ: CRD(1-5) => XTC - CPPTRAJ: Particle mesh Ewald test (ortho, with mask) -g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o - CPPTRAJ: DBSCAN kdist map test + CPPTRAJ: CRD(6-10) => XTC - CPPTRAJ: DBSCAN with sieve +All 6 comparisons passed. - CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD -All 4 comparisons passed. + CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' +All 3 comparisons passed. - CPPTRAJ: PME test (partial system, trunc. oct) - Unit test passed. + CPPTRAJ: XTC (appended) => CRD -make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans -make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' + CPPTRAJ: Particle mesh Ewald test (ortho, with mask) - CPPTRAJ: Cpptraj Kmeans + CPPTRAJ: PME test (partial system, trunc. oct) +All 5 comparisons passed. - CPPTRAJ: XtalSymm Reimaging by Molecule - CPPTRAJ: CRD(6-10) => XTC - CPPTRAJ: Cpptraj Kmeans random + CPPTRAJ: GMX: CRD with offset 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 @@ -3626,27 +3662,22 @@ CPPTRAJ: LJ PME test. -All 5 comparisons passed. - + CPPTRAJ: LJ PME kappa sweep test, 0.25 -All 6 comparisons passed. +All 5 comparisons passed. - CPPTRAJ: XTC (appended) => CRD + CPPTRAJ: GMX: XTC with offset ******************************************************************************** -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: GMX: CRD with offset +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites - CPPTRAJ: GMX: XTC with offset + CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: LJ PME kappa sweep test, 0.35 - CPPTRAJ: LJ PME kappa sweep test, 0.45 + CPPTRAJ: GIST test, orthogonal cell + + CPPTRAJ: XtalSymm Reimaging by Molecule All 4 comparisons passed. @@ -3655,51 +3686,56 @@ CPPTRAJ: TNG read test - CPPTRAJ: LJ PME kappa sweep test, 0.5 + CPPTRAJ: Cluster command test, coordinate writes using info file. -All 5 comparisons passed. + CPPTRAJ: LJ PME kappa sweep test, 0.45 -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites + CPPTRAJ: LJ PME kappa sweep test, 0.5 - CPPTRAJ: Cluster command test, coordinate writes. +All 8 comparisons passed. - CPPTRAJ: LJ with switch function test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks - CPPTRAJ: Cluster command test, coordinate writes using info file. + CPPTRAJ: Density peaks clustering test CPPTRAJ: TNG read test (with offset) + CPPTRAJ: LJ with switch function test + All 3 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps -All 5 comparisons passed. + CPPTRAJ: Clustering with specified # reps +All 5 comparisons passed. -All 9 comparisons passed. +All 2 comparisons passed. - CPPTRAJ: GIST test, nonorthogonal cell All 6 comparisons passed. +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' -All 8 comparisons passed. + Unit test passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks +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: 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 9 comparisons passed. -All 2 comparisons passed. + CPPTRAJ: GIST test, nonorthogonal cell All 11 comparisons passed. @@ -3719,7 +3755,7 @@ 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 184920736 Oct 17 02:11 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 184920736 Nov 19 08:41 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. @@ -3731,14 +3767,14 @@ 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 +Skipping bundled READLINE 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 @@ -3776,12 +3812,14 @@ 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/2870230/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2870230/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/1845020 and its subdirectories -I: Current time: Thu Oct 16 14:13:34 -12 2025 -I: pbuilder-time-stamp: 1760667214 +I: removing directory /srv/workspace/pbuilder/2870230 and its subdirectories +I: Current time: Thu Nov 19 22:43:18 +14 2026 +I: pbuilder-time-stamp: 1795077798