Diff of the two buildlogs: -- --- b1/build.log 2025-03-08 14:49:57.412684261 +0000 +++ b2/build.log 2025-03-08 14:52:48.017033263 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 10 09:09:00 -12 2026 -I: pbuilder-time-stamp: 1775855340 +I: Current time: Sun Mar 9 04:50:00 +14 2025 +I: pbuilder-time-stamp: 1741445400 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,51 +25,83 @@ dpkg-source: info: applying skip-failing-test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1237090/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/120576/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 Mar 8 14:50 /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/120576/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/120576/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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='b9c7e291f29d4deba20342961b970655' - 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='1237090' - PS1='# ' - PS2='> ' + INVOCATION_ID=d352701befd147be92532c4f13d18ebf + 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=120576 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.bEZqnmUs/pbuilderrc_Lf7P --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.bEZqnmUs/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-4.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.bEZqnmUs/pbuilderrc_SfiF --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.bEZqnmUs/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-4.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1237090/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/120576/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -255,7 +287,7 @@ Get: 132 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.2-6 [153 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 netcdf-bin amd64 1:4.9.3-1 [260 kB] -Fetched 83.9 MB in 1s (124 MB/s) +Fetched 83.9 MB in 1s (60.0 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19783 files and directories currently installed.) @@ -817,7 +849,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/120576/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/120576/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -1019,9 +1055,6 @@ CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp -CXX Action_Matrix.cpp -CXX Action_MinImage.cpp -CXX Action_Molsurf.cpp In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, @@ -1090,6 +1123,9 @@ Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ +CXX Action_Matrix.cpp +CXX Action_MinImage.cpp +CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp @@ -1149,8 +1185,6 @@ CXX Analysis_KDE.cpp CXX Analysis_Lifetime.cpp CXX Analysis_LowestCurve.cpp -CXX Analysis_Matrix.cpp -CXX Analysis_MeltCurve.cpp In file included from /usr/include/c++/14/vector:66, from ArgList.h:3, from Action.h:4, @@ -1181,6 +1215,8 @@ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ +CXX Analysis_Matrix.cpp +CXX Analysis_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp @@ -1356,9 +1392,9 @@ 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) +CXX Ewald_Regular.cpp helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for -CXX Ewald_Regular.cpp CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': @@ -1404,7 +1440,6 @@ helpme_standalone.h:3761:61: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3761 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ -CXX Exec_Analyze.cpp helpme_standalone.h:3750:25: warning: unused variable 'gridIteratorC' [-Wunused-variable] 3750 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ @@ -1434,6 +1469,7 @@ helpme_standalone.h:4004:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ +CXX Exec_Analyze.cpp helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1000:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1000 | assertSymmetric(); @@ -1552,7 +1588,6 @@ CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp CXX Exec_LoadTraj.cpp -CXX Exec_ParallelAnalysis.cpp helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3470:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3470 | fftHelperA_ = FFTWWrapper(); @@ -1599,11 +1634,8 @@ helpme_standalone.h:3505:45: note: '' declared here 3505 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ +CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp -CXX Exec_ParmSolvent.cpp -CXX Exec_ParmStrip.cpp -CXX Exec_ParmWrite.cpp -CXX Exec_PermuteDihedrals.cpp helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:5031:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] 5031 | return energy; @@ -1611,6 +1643,10 @@ helpme_standalone.h:5021:14: note: 'energy' was declared here 5021 | Real energy; | ^~~~~~ +CXX Exec_ParmSolvent.cpp +CXX Exec_ParmStrip.cpp +CXX Exec_ParmWrite.cpp +CXX Exec_PermuteDihedrals.cpp CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp CXX Exec_PrintData.cpp @@ -1778,34 +1814,24 @@ 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 cd tng && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC md5.c -CC xdrfile_trr.c CC tng_io.c -CC xdrfile_xtc.c +CC xdr_seek.c +CC xdrfile_trr.c CC tng_compress.c CC coder.c +CC xdrfile_xtc.c CC warnmalloc.c CC fixpoint.c CC xtc3.c CC bwlzh.c CC xtc2.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' CC widemuldiv.c -CC huffmem.c -CC vals16.c -CC bwt.c -CC mtf.c -CC rle.c -CC lz77.c -CC dict.c 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); @@ -1813,6 +1839,16 @@ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ +CC huffmem.c +/bin/rm -f libxdrfile.a +CC vals16.c +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' +CC bwt.c +CC mtf.c +CC rle.c +CC lz77.c +CC dict.c CC huffman.c CC merge_sort.c /bin/rm -f libtng_io.a @@ -1830,8 +1866,8 @@ 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 @@ -1847,711 +1883,707 @@ CPPTRAJ: ArgList class unit test. make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp 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 NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/ArgList.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp --rwxr-xr-x 1 pbuilder1 pbuilder1 186114960 Apr 10 21:12 ../bin/cpptraj --rwxr-xr-x 1 pbuilder1 pbuilder1 186114960 Apr 10 21:12 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 186114960 Mar 8 14:52 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 186114960 Mar 8 14:52 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' ******************************************************************************** -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_BrokenTraj - - CPPTRAJ: General tests CPPTRAJ: One frame strip command test - - CPPTRAJ: Broken Traj: Running good trajectory. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset - CPPTRAJ: Normal trajectory read with offsets. + CPPTRAJ: General tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj + CPPTRAJ: Normal trajectory read with offsets. + CPPTRAJ: CRD Replica Trajectory Run with offset ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj + + CPPTRAJ: Broken Traj: Running good trajectory. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange CPPTRAJ: Trajout Frame Range [Amber Restart] - CPPTRAJ: Per-Residue RMSD Test. - - CPPTRAJ: Broken Traj: Running broken trajectory. - CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: CRD Replica Trajectory Run - CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: Unstrip (Lig/Rec/Complex) command test + CPPTRAJ: Broken Traj: Running broken trajectory. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD + + CPPTRAJ: Per-Residue RMSD Test. CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: Bzip2ed trajectory read with offsets - CPPTRAJ: NetCDF Replica Trajectory Run test - - CPPTRAJ: Per-Residue RMSD Test with residue centering. - All 6 comparisons passed. - - CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj - - CPPTRAJ: Start argument offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. - CPPTRAJ: Compressed broken trajectory test + CPPTRAJ: Per-Residue RMSD Test with averaging + + CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: Multi frame strip command test. - CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj + CPPTRAJ: Start argument offset -All 4 comparisons passed. + CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. + CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj -All 3 comparisons passed. + CPPTRAJ: Strip topology with PDB info +All 4 comparisons passed. + + + CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj ******************************************************************************** -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center +All 11 comparisons passed. + + CPPTRAJ: Center command test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond CPPTRAJ: Solute Hbond test CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj - CPPTRAJ: Strip topology with PDB info + CPPTRAJ: Compressed broken trajectory test + + CPPTRAJ: Center origin command test. + + CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj + + CPPTRAJ: Per-Residue RMSD Test with residue centering. + + CPPTRAJ: Secstruct (DSSP) command with changing number of residues. All 2 comparisons passed. - CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj + CPPTRAJ: Solute Hbond test with disk caching - CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. +All 15 comparisons passed. + + + CPPTRAJ: CRD Replica Trajectory Run with remdout ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel - CPPTRAJ: Center origin command test. + CPPTRAJ: Parallel tests. + + CPPTRAJ: Center origin mass command test. + +All 3 comparisons passed. -All 11 comparisons passed. + CPPTRAJ: Secstruct (DSSP): SS assign output test + + CPPTRAJ: NetCDF Restart Test - NetCDF->TXT ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image - CPPTRAJ: CRD Replica Trajectory Run with remdout - CPPTRAJ: Orthorhombic imaged distance test. - CPPTRAJ: NetCDF Restart Test - NetCDF->TXT + CPPTRAJ: Solute-solvent hbond test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Surface calculation test - CPPTRAJ: Center origin mass command test. +All 8 comparisons passed. - CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF - CPPTRAJ: Secstruct (DSSP) command with changing number of residues. + CPPTRAJ: Parallel test with trajectory offset - CPPTRAJ: Non-orthorhombic imaged distance test. + CPPTRAJ: Center reference command test. - CPPTRAJ: Solute Hbond test with disk caching + CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr CPPTRAJ: Radius of gyration command test -All 8 comparisons passed. - - - CPPTRAJ: Orthorhombic coordinate imaging test - - CPPTRAJ: Center reference command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask - - CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt + CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: Mask single frame test -All 2 comparisons passed. - -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling - - CPPTRAJ: Solute-solvent hbond test - - CPPTRAJ: J-Coupling single frame test + CPPTRAJ: Hbond, no intramolecular hydrogen bonds test - CPPTRAJ: Secstruct (DSSP): SS assign output test + CPPTRAJ: FtuFabI Assignment test CPPTRAJ: Center point test. - CPPTRAJ: Nonorthorhombic coordinate imaging test +All 2 comparisons passed. -All 15 comparisons passed. + CPPTRAJ: Orthorhombic coordinate imaging test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling -All 2 comparisons passed. - J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. - Skipped test: J-Coupling extended test + CPPTRAJ: J-Coupling single frame test + CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt -All 1 comparisons passed. -1 comparisons skipped. + CPPTRAJ: Mask longer command test. +All 5 comparisons passed. - CPPTRAJ: FtuFabI Assignment test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj CPPTRAJ: Diffusion test, no imaging. +All 7 comparisons passed. - CPPTRAJ: RMSD Test with outtraj. - CPPTRAJ: Parallel tests. - -All 5 comparisons passed. + CPPTRAJ: Hbond, specified solute masks ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm - - CPPTRAJ: Mask longer command test. - - CPPTRAJ: CHARMM PSF/DCD test - - CPPTRAJ: Hbond, no intramolecular hydrogen bonds test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar + CPPTRAJ: RMSD Test with outtraj. - CPPTRAJ: CHARMM DCD Write, step 1. + CPPTRAJ: Nonorthorhombic coordinate imaging test All 10 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif + J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. + Skipped test: J-Coupling extended test - CPPTRAJ: Diffusion test, old syntax. +All 1 comparisons passed. +1 comparisons skipped. - CPPTRAJ: CHARMM DCD Write, step 2. - CPPTRAJ: Rotational diffusion calculation test +All 2 comparisons passed. - CPPTRAJ: Parallel test with trajectory offset +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm All 5 comparisons passed. - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM + CPPTRAJ: CHARMM PSF/DCD test - CPPTRAJ: Hbond, specified solute masks + CPPTRAJ: Diffusion test, old syntax. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj - - CPPTRAJ: Convert mdcrd -> NetCDF +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif - CPPTRAJ: CHAMBER topology read/strip test. - CPPTRAJ: Partial Surface calculation test -g++ -o a.out main.o NameType.o CpptrajStdio.o + CPPTRAJ: Hbond, no angle cutoff test + CPPTRAJ: Rotational diffusion calculation test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj -All 4 comparisons passed. + CPPTRAJ: Convert mdcrd -> NetCDF + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar - CPPTRAJ: Diffusion test, new syntax. + CPPTRAJ: CHARMM DCD Write, step 1. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. - CPPTRAJ: Hbond, no angle cutoff test + CPPTRAJ: Hbond, Bridge nointramol test - CPPTRAJ: Read CHARMM restart + CPPTRAJ: Diffusion test, new syntax. -All 6 comparisons passed. + CPPTRAJ: CHARMM DCD Write, step 2. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD + CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: Convert NetCDF -> mdcrd - CPPTRAJ: Basic RMSD tests - - CPPTRAJ: Coordinate Running Average Traj Write + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM - CPPTRAJ: CHARMM PSF write +All 2 comparisons passed. - CPPTRAJ: Hbond, Bridge nointramol test -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' - 'ZN' 'HA2' 'HA' 'HA' 'CT11' -Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' -Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' +All 4 comparisons passed. - Unit test passed. CPPTRAJ: Diffusion test, nonorthogonal box ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD + + CPPTRAJ: Basic RMSD tests +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS CPPTRAJ: 2D RMSD Test. - - CPPTRAJ: Outtraj Test with maxmin. -All 7 comparisons passed. - - -All 2 comparisons passed. +All 6 comparisons passed. - CPPTRAJ: CHARMM COORdinates test + CPPTRAJ: STFC Diffusion Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: Mol2 Parm/Traj Read/Write Test. + + CPPTRAJ: 2D RMSD Test, mass-weighted. + +All 1 comparisons passed. + + + CPPTRAJ: RMS coordinate rotation/rotation matrices test + + CPPTRAJ: Outtraj Test with maxmin. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct CPPTRAJ: NAstruct command test. - CPPTRAJ: STFC Diffusion Test + CPPTRAJ: STFC Diffusion Test with individual distances - CPPTRAJ: RMS coordinate rotation/rotation matrices test + CPPTRAJ: PDB => Mol2 - CPPTRAJ: 2D RMSD Test, mass-weighted. + CPPTRAJ: Amber Top/Rst => Mol2 + CPPTRAJ: RMS fit with no coordinates modification test. -All 1 comparisons passed. -All 6 comparisons passed. + CPPTRAJ: STFC Diffusion Test with COM +All 4 comparisons passed. - CPPTRAJ: PDB => Mol2 + CPPTRAJ: CHAMBER topology read/strip test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average CPPTRAJ: 2D RMSD Test with reference trajectory + Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. + Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 4 comparisons passed. +1 comparisons skipped. CPPTRAJ: Average Test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams - CPPTRAJ: Test updating topology with Charmm parameters (single residue) + CPPTRAJ: NAstruct command test, single strand - CPPTRAJ: LCPO test with GAFF atom types + CPPTRAJ: STFC Diffusion Test with second mask - CPPTRAJ: STFC Diffusion Test with individual distances + CPPTRAJ: Partial Surface calculation test - CPPTRAJ: RMS fit with no coordinates modification test. + CPPTRAJ: Read CHARMM restart + +All 2 comparisons passed. ******************************************************************************** + TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker CPPTRAJ: Pucker command test + + CPPTRAJ: RMS fit to previous test CPPTRAJ: 2D DME Test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap - CPPTRAJ: Amber Top/Rst => Mol2 + CPPTRAJ: AtomMap Test -All 2 comparisons passed. +All 11 comparisons passed. + +g++ -o a.out main.o NameType.o CpptrajStdio.o + CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test -All 2 comparisons passed. + CPPTRAJ: CHARMM PSF write -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile + CPPTRAJ: Hbond with imaging - CPPTRAJ: Data file output precision test + CPPTRAJ: 2D RMSD with reference mask test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap - - CPPTRAJ: AtomMap Test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG - CPPTRAJ: NAstruct command test, single strand + CPPTRAJ: NA test (8OG) -All 3 comparisons passed. + CPPTRAJ: RMS: imaging after unit cell rotation - Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. - Skipped test: Amber Top/Rst => Mol2, SYBYL atom types + CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. -All 4 comparisons passed. -1 comparisons skipped. + CPPTRAJ: AtomMap with 'rmsfit' + CPPTRAJ: Hbond, orthogonal imaging - CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test +All 3 comparisons passed. - CPPTRAJ: 2D RMSD with reference mask test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile - CPPTRAJ: Radial test, non-orthogonal imaging -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist + CPPTRAJ: CHARMM COORdinates test - CPPTRAJ: STFC Diffusion Test with COM + CPPTRAJ: Data file output precision test - CPPTRAJ: 1D/2D Histogram Analysis test + CPPTRAJ: 2D RMSD test, no fitting. -All 11 comparisons passed. +All 12 comparisons passed. +make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' - CPPTRAJ: Standard -> Grace Data +All 3 comparisons passed. - CPPTRAJ: RMS fit to previous test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial - CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. + CPPTRAJ: Atom map charmm->amber atom order + + CPPTRAJ: Radial test, non-orthogonal imaging ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist - CPPTRAJ: NA test (8OG) + CPPTRAJ: 1D/2D Histogram Analysis test - CPPTRAJ: 2D RMSD test, no fitting. +All 6 comparisons passed. - CPPTRAJ: Grace -> Standard Data + 'ZN' 'HA2' 'HA' 'HA' 'CT11' +Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' +Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' - CPPTRAJ: STFC Diffusion Test with second mask + Unit test passed. - CPPTRAJ: AtomMap with 'rmsfit' All 6 comparisons passed. - CPPTRAJ: RMS: imaging after unit cell rotation +All 16 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Standard -> Grace Data - CPPTRAJ: Hbond with imaging +All 23 comparisons passed. - CPPTRAJ: 3D histogram test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest + + CPPTRAJ: Test updating topology with Charmm parameters (single residue) + + CPPTRAJ: Closest command test using first solvent atom. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD CPPTRAJ: Distance RMSD test - - CPPTRAJ: X column format/precision test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED - CPPTRAJ: Closest command test using first solvent atom. + CPPTRAJ: IRED vector/matrix test - CPPTRAJ: Atom map charmm->amber atom order + CPPTRAJ: Grace -> Standard Data +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster -All 7 comparisons passed. + CPPTRAJ: Atom map charmm->amber atom order, by residue + CPPTRAJ: Cluster command test, in-memory pairwise distances. -All 12 comparisons passed. +All 2 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: X column format/precision test. + +All 9 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons - CPPTRAJ: Cluster command test, in-memory pairwise distances. + CPPTRAJ: Closest command test using all solvent atoms. - CPPTRAJ: Hbond, orthogonal imaging -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED + CPPTRAJ: randomizeions test (original algorithm) - CPPTRAJ: IRED vector/matrix test + CPPTRAJ: 3D histogram test. + + CPPTRAJ: Cluster command test, read pairwise distances. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons All 1 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr - CPPTRAJ: randomizeions test (original algorithm) + CPPTRAJ: LCPO test with GAFF atom types + + CPPTRAJ: Correlation test + + CPPTRAJ: Data file group by name test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: Molsurf test -All 16 comparisons passed. +All 7 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr -All 23 comparisons passed. +All 3 comparisons passed. - CPPTRAJ: Correlation test +All 2 comparisons passed. + + + CPPTRAJ: Data file group by aspect test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: Structure Check + + CPPTRAJ: Cluster command test, read NetCDF pairwise distances. + + CPPTRAJ: Closest command test, using mask center ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr - CPPTRAJ: RmsAvgCorr Reference +All 6 comparisons passed. -All 2 comparisons passed. + CPPTRAJ: RmsAvgCorr Reference ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts CPPTRAJ: Contacts test. + CPPTRAJ: Cluster command test, write ASCII pairwise distances. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal - CPPTRAJ: Radial test, orthogonal and no imaging - CPPTRAJ: Data file group by name test - + CPPTRAJ: Principal Test CPPTRAJ: Structure Check with Around and Skip - CPPTRAJ: Cluster command test, read pairwise distances. - CPPTRAJ: Closest command test using all solvent atoms. + CPPTRAJ: Cluster command test, read ASCII pairwise distances. - CPPTRAJ: Atom map charmm->amber atom order, by residue + CPPTRAJ: Closest command test, using mask center and solvent mask CPPTRAJ: RmsAvgCorr First -All 3 comparisons passed. - -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal - - CPPTRAJ: Principal Test - - CPPTRAJ: Cluster command test, read NetCDF pairwise distances. - All 9 comparisons passed. - CPPTRAJ: Data file group by aspect test - All 3 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral - -All 9 comparisons passed. +All 3 comparisons passed. - CPPTRAJ: clusterdihedral test - -All 6 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve + CPPTRAJ: Cluster, nosieve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector CPPTRAJ: Basic vector tests + + CPPTRAJ: Closest command test, solvent mask, water oxygen only + + CPPTRAJ: Radial test, orthogonal and no imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: Matrix Tests - ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct - CPPTRAJ: Closest command test, using mask center +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral - CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. + CPPTRAJ: clusterdihedral test - CPPTRAJ: Cluster command test, write ASCII pairwise distances. + CPPTRAJ: Cluster, sieve5 + + CPPTRAJ: Structure Check with PBC - CPPTRAJ: Randomize (around, overlap) All 4 comparisons passed. +All 3 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct + + CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. + +All 9 comparisons passed. - CPPTRAJ: Structure Check with PBC ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid CPPTRAJ: Dipole test -All 1 comparisons passed. + CPPTRAJ: Cluster, nosieve savepairdist + CPPTRAJ: Test vector center with magnitude - CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. + CPPTRAJ: Randomize (around, overlap) - CPPTRAJ: Cluster command test, read ASCII pairwise distances. + CPPTRAJ: Grid test + + CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap CPPTRAJ: Unwrap non-orthogonal test - CPPTRAJ: Closest command test, using mask center and solvent mask +All 1 comparisons passed. - CPPTRAJ: Grid test - CPPTRAJ: Test vector center with magnitude + CPPTRAJ: Cluster, nosieve loadpairdist - CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. + CPPTRAJ: Generate matrix with trajectory start/stop/offset -All 9 comparisons passed. - CPPTRAJ: Unwrap orthogonal test + CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve - - CPPTRAJ: Cluster, nosieve - -All 3 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes + CPPTRAJ: Modes analysis, RMS fluctuations - CPPTRAJ: Closest command test, solvent mask, water oxygen only + CPPTRAJ: Momentum/velocity vector test. CPPTRAJ: OpenDX Grid read test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project - CPPTRAJ: Projection + CPPTRAJ: Generate matrix with action stop/start/offset CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. + CPPTRAJ: Modes analysis, displacements + CPPTRAJ: Unwrap orthogonal test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project - CPPTRAJ: Momentum/velocity vector test. +All 15 comparisons passed. -All 2 comparisons passed. + CPPTRAJ: Cluster, sieve5 savepairdist -All 1 comparisons passed. + CPPTRAJ: Modes analysis, dipole correlation +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell + CPPTRAJ: Force vector test. - CPPTRAJ: Generate matrix with trajectory start/stop/offset + CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Grid with specified center test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes CPPTRAJ: Atomicfluct test with ADP output - CPPTRAJ: Modes analysis, RMS fluctuations + CPPTRAJ: Projection + +All 2 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg CPPTRAJ: Analysis Running Average -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell - CPPTRAJ: Watershell Test, non-orthorhombic imaging. +All 8 comparisons passed. - CPPTRAJ: Cluster, sieve5 - CPPTRAJ: Force vector test. - - CPPTRAJ: Generate matrix with action stop/start/offset +All 1 comparisons passed. - CPPTRAJ: Modes analysis, displacements -g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o -All 2 comparisons passed. + CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. + CPPTRAJ: Grid with box center offset test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap - CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. +All 14 comparisons passed. - CPPTRAJ: VMD VolMap Algorithm test -All 14 comparisons passed. + CPPTRAJ: VMD VolMap Algorithm test +All 2 comparisons passed. - CPPTRAJ: Grid with box center offset test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM - CPPTRAJ: Modes analysis, dipole correlation - - CPPTRAJ: Cluster, nosieve savepairdist - CPPTRAJ: SPAM Test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density - CPPTRAJ: Randomize (around) + CPPTRAJ: Density along axis tests +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE -All 15 comparisons passed. + CPPTRAJ: LIE test + CPPTRAJ: Grid with mask center offset test. All 13 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density 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: LIE test - - - CPPTRAJ: Density along axis tests All 2 comparisons passed. 1 comparisons skipped. - - CPPTRAJ: Grid with mask center offset test. -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder - Unit test passed. - -make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' - CPPTRAJ: Lipid Order Parameter Test. -make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist CPPTRAJ: PairDist Test. - CPPTRAJ: Cluster, nosieve loadpairdist + CPPTRAJ: Cluster, sieve5 loadpairdist - CPPTRAJ: Non-orthogonal grid test. + CPPTRAJ: Modes analysis, pseudo trajectory creation test -All 8 comparisons passed. + CPPTRAJ: Multi-frame density along axis test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData + CPPTRAJ: Randomize (around) + CPPTRAJ: Non-orthogonal grid test. - CPPTRAJ: Read vector data test (no origins, origins) - CPPTRAJ: Structure Check with Around + CPPTRAJ: Cluster, nosieve pairwisecache none - CPPTRAJ: Modes analysis, pseudo trajectory creation test + CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test - CPPTRAJ: Multi-frame density along axis test + CPPTRAJ: Total system density test + + CPPTRAJ: Pairdist test, orthogonal imaging. CPPTRAJ: SPAM Pure Solvent Test - CPPTRAJ: Read vector data set (origins, no origins) + CPPTRAJ: Structure Check with Around CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test - CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test - - CPPTRAJ: Cluster, sieve5 savepairdist +All 7 comparisons passed. - CPPTRAJ: Read Amber output test All 6 comparisons passed. @@ -2559,332 +2591,384 @@ All 6 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST -******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData + CPPTRAJ: Read vector data test (no origins, origins) +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD - CPPTRAJ: GIST water-water interaction test - - CPPTRAJ: Pairdist test, orthogonal imaging. CPPTRAJ: Basic lipid order parameter test - CPPTRAJ: Randomize (overlap) + CPPTRAJ: Grid generation from 'bounds' test. - CPPTRAJ: Read CHARMM output test + CPPTRAJ: Read vector data set (origins, no origins) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST - CPPTRAJ: Total system density test + CPPTRAJ: GIST water-water interaction test +g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o - CPPTRAJ: Grid generation from 'bounds' test. + CPPTRAJ: Read Amber output test -All 1 comparisons passed. +All 13 comparisons passed. -All 8 comparisons passed. +All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr + + CPPTRAJ: Read CHARMM output test CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test CPPTRAJ: New Lipid Order Parameter Test, DOPC. - - CPPTRAJ: 3D data read/write test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test - CPPTRAJ: Randomize (no restrictions) +All 8 comparisons passed. -All 13 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr + CPPTRAJ: AutoCorr test. -All 7 comparisons passed. + CPPTRAJ: 3D data read/write test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr + CPPTRAJ: Cluster, sieve5 pairwisecache none +make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' CPPTRAJ: Standard 3D data write test - CPPTRAJ: AutoCorr test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box - - CPPTRAJ: Box Test (Add box info) + Unit test passed. - CPPTRAJ: Standard 3D data read test +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 1 comparisons passed. + + CPPTRAJ: Randomize (overlap) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect - CPPTRAJ: Box test (remove box info) +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect + CPPTRAJ: Box Test (Add box info) CPPTRAJ: Selection by atom type test. -All 5 comparisons passed. +All 4 comparisons passed. -All 4 comparisons passed. + CPPTRAJ: Cluster, random + CPPTRAJ: Standard 3D data read test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat - - CPPTRAJ: Standard 3D data read/append test CPPTRAJ: RMSD Test with averaged reference coordinates. - CPPTRAJ: Crankshaft test +All 1 comparisons passed. - CPPTRAJ: Box test (Modify box length) - - CPPTRAJ: Cluster, sieve5 loadpairdist All 1 comparisons passed. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat + + CPPTRAJ: Crankshaft test +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd - CPPTRAJ: Standard 3D data, sparse + CPPTRAJ: Standard 3D data read/append test CPPTRAJ: COORDS data set creation and CRDFLUCT test. All 1 comparisons passed. - CPPTRAJ: Watershell Test, orthorhombic imaging. + CPPTRAJ: Box test (remove box info) + + CPPTRAJ: Randomize (no restrictions) + +All 28 comparisons passed. + All 3 comparisons passed. + + CPPTRAJ: COORDS data set creation with velocities test + + CPPTRAJ: Box test (Modify box length) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd + + CPPTRAJ: LoadCrd test. + + CPPTRAJ: Standard 3D data, sparse +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve + + CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) -All 1 comparisons passed. + CPPTRAJ: Nonorthogonal grid standard write/read tests. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd + CPPTRAJ: Box test (auto orthogonal box, no radii) + +All 5 comparisons passed. - CPPTRAJ: LoadCrd test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector CPPTRAJ: Multivector test + CPPTRAJ: LoadTraj test. + + CPPTRAJ: Pairdist test, nonorthogonal imaging. + + CPPTRAJ: TRAJ data set creation and CRDFLUCT test. + All 1 comparisons passed. + + CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime + CPPTRAJ: LoadTraj from trajin test. + CPPTRAJ: Lifetime test. - CPPTRAJ: LoadTraj test. + CPPTRAJ: Box test (auto orthogonal box, VDW radii) + CPPTRAJ: TRAJ data set creation with velocities test. - CPPTRAJ: Nonorthogonal grid standard write/read tests. - CPPTRAJ: Box test (auto orthogonal box, no radii) +All 7 comparisons passed. - CPPTRAJ: AutoImage test, use anchor mask +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT - CPPTRAJ: COORDS data set creation with velocities test + CPPTRAJ: FFT test. + CPPTRAJ: LoadCrd append from multiple files test CPPTRAJ: Lifetime test with data set caching. - CPPTRAJ: Box test (auto orthogonal box, VDW radii) - CPPTRAJ: Watershell Test, no imaging. + CPPTRAJ: AutoImage test, use anchor mask + +All 4 comparisons passed. -All 7 comparisons passed. + CPPTRAJ: COORDS data set append test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet + +All 4 comparisons passed. + + + CPPTRAJ: Clustering, One DataSet + + CPPTRAJ: Watershell Test, orthorhombic imaging. All 2 comparisons passed. - CPPTRAJ: FFT test. +All 5 comparisons passed. + + + CPPTRAJ: Lifetime average and cumulative average test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr CPPTRAJ: Timecorr test. -All 5 comparisons passed. - -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr + CPPTRAJ: COORDS test storing frame metadata - CPPTRAJ: CrossCorr test + CPPTRAJ: Clustering, Two DataSets -All 7 comparisons passed. +All 12 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd CPPTRAJ: SymmRmsd - -All 1 comparisons passed. - - -All 3 comparisons passed. - +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral + CPPTRAJ: CrossCorr test + CPPTRAJ: Multidihedral test + CPPTRAJ: Clustering, dihedral DataSet + CPPTRAJ: ASP symmetry-corrected RMSD test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD - CPPTRAJ: M-REMD sort test. + CPPTRAJ: Multidihedral Nucleotide CHI test +All 1 comparisons passed. - CPPTRAJ: LoadTraj from trajin test. - CPPTRAJ: Cluster, nosieve pairwisecache none - CPPTRAJ: TRAJ data set creation and CRDFLUCT test. +All 7 comparisons passed. - CPPTRAJ: Lifetime average and cumulative average test. - CPPTRAJ: GLU symmetry-corrected RMSD test + CPPTRAJ: TRAJ test storing frame metadata + CPPTRAJ: Clustering, two dihedral DataSets +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure - CPPTRAJ: Multidihedral Nucleotide CHI test - CPPTRAJ: Pairdist test, nonorthogonal imaging. + CPPTRAJ: Read specific columns test. -All 12 comparisons passed. + CPPTRAJ: Basic makestructure test + CPPTRAJ: GLU symmetry-corrected RMSD test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD - CPPTRAJ: Basic makestructure test + CPPTRAJ: Clustering, dihedral DataSet, K-means -All 1 comparisons passed. + CPPTRAJ: Multidihedral protein dihedrals test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate + CPPTRAJ: M-REMD sort test. - CPPTRAJ: Rotation (and inverse) of coords from matrices + CPPTRAJ: Write non-square matrix - CPPTRAJ: Rotate with defined axis + CPPTRAJ: Makestructure test with reference. - CPPTRAJ: TYR symmetry-corrected RMSD test + CPPTRAJ: Clustering, two dihedral DataSets, K-means - CPPTRAJ: M-REMD actions test. + CPPTRAJ: Watershell Test, no imaging. - CPPTRAJ: Read specific columns test. + CPPTRAJ: Multidihedral cyclic molecule test - CPPTRAJ: Multidihedral protein dihedrals test +All 8 comparisons passed. - CPPTRAJ: Makestructure test with reference. -All 5 comparisons passed. + CPPTRAJ: Read non-square matrix + CPPTRAJ: TYR symmetry-corrected RMSD test -All 3 comparisons passed. +All 5 comparisons passed. ******************************************************************************** -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: Integration test. + CPPTRAJ: Rotation (and inverse) of coords from matrices ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate - CPPTRAJ: NativeContacts test. + CPPTRAJ: Integration test. -All 2 comparisons passed. +All 8 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral - - CPPTRAJ: Check chirality test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN - CPPTRAJ: LoadCrd append from multiple files test +All 6 comparisons passed. - CPPTRAJ: GIST test, orthogonal cell - CPPTRAJ: Write non-square matrix CPPTRAJ: Longer symmetry-corrected RMSD test. + CPPTRAJ: DBSCAN test - CPPTRAJ: TRAJ data set creation with velocities test. + CPPTRAJ: Read square matrix - CPPTRAJ: Multidihedral cyclic molecule test +All 1 comparisons passed. - CPPTRAJ: M-REMD ensemble outtraj test. -All 6 comparisons passed. +All 2 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral + CPPTRAJ: Check chirality test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy + + CPPTRAJ: M-REMD actions test. + + CPPTRAJ: Simple energy tests -All 4 comparisons passed. All 8 comparisons passed. +All 15 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts + CPPTRAJ: Rotate with defined axis All 1 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy -******************************************************************************** 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: Simple energy tests -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 - CPPTRAJ: PermuteDihedrals interval -120, phi psi CPPTRAJ: LES split/average test - CPPTRAJ: CCP4 read/write and DX conversion test. + CPPTRAJ: NativeContacts test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 - CPPTRAJ: M-REMD no sort, running average test + CPPTRAJ: CCP4 read/write and DX conversion test. - CPPTRAJ: COORDS data set append test + CPPTRAJ: DBSCAN automatic parameter determination test. - CPPTRAJ: Read non-square matrix +All 3 comparisons passed. -All 2 comparisons passed. + CPPTRAJ: PermuteDihedrals, random rotations ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar - CPPTRAJ: Dihedral Covariance Matrix Test All 3 comparisons passed. +All 2 comparisons passed. + + CPPTRAJ: Dihedral Covariance Matrix Test + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit +******************************************************************************** - CPPTRAJ: Curve fitting test. - -All 2 comparisons passed. -******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage + CPPTRAJ: Curve fitting test. + CPPTRAJ: DBSCAN kdist map test + + CPPTRAJ: M-REMD ensemble outtraj test. CPPTRAJ: Data set averaging and averaging over all sets test. -All 2 comparisons passed. + CPPTRAJ: Test kinetic energy calculation -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath +All 4 comparisons passed. - CPPTRAJ: Vector dot/cross product test All 2 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: Curve fitting multi-exponential tests. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath + CPPTRAJ: Vector dot/cross product test + + CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander SANDER energy tests (long) requires SANDER API from AmberTools. @@ -2892,368 +2976,398 @@ SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature - CPPTRAJ: Temperature test. +All 3 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SKIP: Energy via sander API short tests (GB/PME) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline - CPPTRAJ: Spline test + CPPTRAJ: Pairdist test, 2 masks. -All 1 comparisons passed. + CPPTRAJ: Test total energy calculation + CPPTRAJ: DBSCAN with sieve ******************************************************************************** -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. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline + CPPTRAJ: Spline test - CPPTRAJ: Cluster, sieve5 pairwisecache none - CPPTRAJ: COORDS test storing frame metadata +All 2 comparisons passed. - CPPTRAJ: Test kinetic energy calculation - CPPTRAJ: M-REMD, generate RMS data +All 2 comparisons passed. - CPPTRAJ: Read square matrix +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet - CPPTRAJ: Pairdist test, 2 masks. + CPPTRAJ: KDE test. - CPPTRAJ: NativeContacts test, save non-native contacts, residue time series + CPPTRAJ: Wavelet analysis test - CPPTRAJ: PermuteDihedrals, random rotations +All 1 comparisons passed. - CPPTRAJ: Curve fitting multi-exponential tests. CPPTRAJ: Temperature with SHAKE on hydrogens. -All 15 comparisons passed. - - All 4 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet - CPPTRAJ: Wavelet analysis test + CPPTRAJ: M-REMD, generate RMS data All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF + CPPTRAJ: Test partial energy calculation + CPPTRAJ: CIF read test + + CPPTRAJ: Curve fitting, custom output range. + + CPPTRAJ: GIST test, orthogonal cell ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB CPPTRAJ: PDB format read/write test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans CPPTRAJ: Temperature with SHAKE on all atoms. - CPPTRAJ: M-REMD, meltcurve analysis - CPPTRAJ: KDE with Kullback-Leibler divergence test - CPPTRAJ: Test total energy calculation +All 6 comparisons passed. - CPPTRAJ: Curve fitting, custom output range. - CPPTRAJ: NativeContacts test, orthorhombic imaging. + CPPTRAJ: Cpptraj Kmeans CPPTRAJ: Wavelet WAFEX test - CPPTRAJ: Generate offset traj from PDB - - CPPTRAJ: TRAJ test storing frame metadata - -All 17 comparisons passed. - - All 6 comparisons passed. -All 4 comparisons passed. + CPPTRAJ: NativeContacts test, save non-native contacts, residue time series + + CPPTRAJ: Temperature calc with extra points. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align - - - CPPTRAJ: Align Tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve - CPPTRAJ: Multicurve test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr - - CPPTRAJ: Velocity autocorrelation test + CPPTRAJ: Align Tests. -All 1 comparisons passed. +All 17 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Multicurve test + CPPTRAJ: PQR file write with various radii ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr - CPPTRAJ: Test combining coordinates, velocities, and forces. + CPPTRAJ: Velocity autocorrelation test - CPPTRAJ: Rotate dihedral to target value. + CPPTRAJ: KDE with Kullback-Leibler divergence test -All 8 comparisons passed. + CPPTRAJ: Generate offset traj from PDB + CPPTRAJ: Cpptraj Kmeans random -All 17 comparisons passed. + CPPTRAJ: Align, unit cell rotation/imaging test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd +All 1 comparisons passed. - CPPTRAJ: PQR file write with various radii - CPPTRAJ: Temperature calc with extra points. +All 5 comparisons passed. - CPPTRAJ: Test partial energy calculation - CPPTRAJ: Remap Test + CPPTRAJ: PDB filter alternate atom location IDs test - CPPTRAJ: Align, unit cell rotation/imaging test. + CPPTRAJ: Generate offset traj from CIF - CPPTRAJ: Data Set commands test + CPPTRAJ: NativeContacts test, orthorhombic imaging. - CPPTRAJ: Generate offset traj from CIF +All 4 comparisons passed. - CPPTRAJ: Test using velocities as coordinates. -All 1 comparisons passed. +All 3 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc - CPPTRAJ: Rotate dihedral by increment + CPPTRAJ: Rotate dihedral to target value. + + CPPTRAJ: Test combining coordinates, velocities, and forces. All 3 comparisons passed. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap + + CPPTRAJ: Remap Test +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Compare topology test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd -All 5 comparisons passed. - + CPPTRAJ: Data Set commands test -All 6 comparisons passed. + CPPTRAJ: Test using velocities as coordinates. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter + CPPTRAJ: Rotate dihedral by increment - CPPTRAJ: Basic filter test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd + CPPTRAJ: Adding PDB info to topology - CPPTRAJ: Combine COORDS test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo +All 6 comparisons passed. - CPPTRAJ: Topology info print test. All 2 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Cluster, random - CPPTRAJ: PDB filter alternate atom location IDs test +All 1 comparisons passed. -All 10 comparisons passed. CPPTRAJ: Test writing velocities (MDVEL) +All 10 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter +******************************************************************************** + CPPTRAJ: Rotate dihedral in TRAJ data set +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD +******************************************************************************** -All 1 comparisons passed. + CPPTRAJ: Basic filter test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd + + CPPTRAJ: Combine COORDS test. + CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr -******************************************************************************** CPPTRAJ: TRR force/velocity read -> NetCDF write test -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald + +All 17 comparisons passed. + ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo - CPPTRAJ: TI analysis test. + CPPTRAJ: Test using forces as coordinates. - CPPTRAJ: Direct sum test + CPPTRAJ: Topology info print test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Combine COORDS test with box info. + CPPTRAJ: Direct sum test - CPPTRAJ: Test using forces as coordinates. All 3 comparisons passed. CPPTRAJ: Data filter test. -All 28 comparisons passed. + CPPTRAJ: Test writing forces (MDFRC) +All 10 comparisons passed. - CPPTRAJ: Adding PDB info to topology ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI - CPPTRAJ: Fix imaged bonds test (Ortho.) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve + CPPTRAJ: TI analysis test. - CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). + CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. - CPPTRAJ: Test writing forces (MDFRC) + CPPTRAJ: Split coords and recombine test. -All 10 comparisons passed. + CPPTRAJ: Filter matrix test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds + CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. -All 5 comparisons passed. + CPPTRAJ: Fix imaged bonds test (Ortho.) +All 5 comparisons passed. - CPPTRAJ: Split coords and recombine test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Distance tests + +All 5 comparisons passed. + + + CPPTRAJ: TRR force/velocity read -> TRR write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: Volume tests - CPPTRAJ: Fix imaged bonds test (Non-ortho.) + CPPTRAJ: Orthogonal imaged distance - CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. +All 1 comparisons passed. - CPPTRAJ: Filter matrix test. - CPPTRAJ: Topology info with reference coords test - CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. + CPPTRAJ: CRD => TRR +All 5 comparisons passed. - CPPTRAJ: Orthogonal imaged distance - CPPTRAJ: TRR force/velocity read -> TRR write test + CPPTRAJ: Topology info with reference coords test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity + CPPTRAJ: Set Velocity test -All 12 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: Fix imaged bonds test (Non-ortho.) +All 5 comparisons passed. - CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). +All 12 comparisons passed. -All 2 comparisons passed. + CPPTRAJ: Non-orthogonal imaged distance ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity - - CPPTRAJ: Set Velocity test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog -All 1 comparisons passed. - + CPPTRAJ: Scale velocity test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol CPPTRAJ: Replica log read/analyze test. + CPPTRAJ: Cluster command test, coordinate writes. + CPPTRAJ: Area per molecule test -All 4 comparisons passed. + CPPTRAJ: TRR => CRD + + +All 3 comparisons passed. + +All 3 comparisons passed. + + +All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask CPPTRAJ: Distance-based atom mask tests (atom, residue) - - CPPTRAJ: CRD => TRR - - CPPTRAJ: Non-orthogonal imaged distance ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc + CPPTRAJ: Calc test + CPPTRAJ: Cluster command test, coordinate writes using info file. - CPPTRAJ: Scale velocity test +All 4 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Distance-based atom mask tests (molecule) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState -All 5 comparisons passed. + CPPTRAJ: Calcstate test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change + CPPTRAJ: Change atom and residue name tests -All 3 comparisons passed. + CPPTRAJ: Calc test with data sets + +All 7 comparisons passed. All 6 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState - CPPTRAJ: Change atom and residue name tests + CPPTRAJ: CRD(1-5) => TRR - CPPTRAJ: Calcstate test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir + CPPTRAJ: Ewald test (NaCl crystal) - CPPTRAJ: Create RREMD NetCDF reservoir test + CPPTRAJ: Change chain ID test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder -All 7 comparisons passed. + CPPTRAJ: Out of order molecules test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir + CPPTRAJ: Test math functions - CPPTRAJ: Out of order molecules test - CPPTRAJ: TRR => CRD + CPPTRAJ: Ewald test (trunc. oct) + CPPTRAJ: Create RREMD NetCDF reservoir test - CPPTRAJ: Ewald test (NaCl crystal) +All 4 comparisons passed. + + + CPPTRAJ: Change chain ID of COORDS set test + +All 2 comparisons passed. - CPPTRAJ: Calc test with data sets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve + + CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: LowestCurve test - CPPTRAJ: Distance-based atom mask tests (molecule) +All 6 comparisons passed. + All 4 comparisons passed. -All 2 comparisons passed. +All 3 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_Cluster_DataSet - -All 4 comparisons passed. - - - CPPTRAJ: Clustering, One DataSet CPPTRAJ: Minimum Image test. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst + + CPPTRAJ: Generate restraints (rst) test +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress CPPTRAJ: Linear regression test. + CPPTRAJ: TRR (appended) => CRD + +All 8 comparisons passed. + + +All 1 comparisons passed. + + All 1 comparisons passed. @@ -3264,337 +3378,313 @@ CPPTRAJ: Pairwise tests ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst - - CPPTRAJ: Generate restraints (rst) test - -All 6 comparisons passed. - +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox CPPTRAJ: Parmbox test -All 1 comparisons passed. - - -All 3 comparisons passed. - - - CPPTRAJ: Ewald test (trunc. oct) - - CPPTRAJ: Test math functions -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent + CPPTRAJ: Density peaks clustering test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate - - CPPTRAJ: Change chain ID test - - CPPTRAJ: Clustering, Two DataSets +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent CPPTRAJ: Test solvent command with closest - CPPTRAJ: CRD(1-5) => TRR - CPPTRAJ: Translate test All 1 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell All 1 comparisons passed. - CPPTRAJ: Replicate cell test +All 3 comparisons passed. -All 4 comparisons passed. + CPPTRAJ: GMX: CRD with offset All 1 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell + + CPPTRAJ: Replicate cell test All 1 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK CPPTRAJ: Scale dihedral force constant test - CPPTRAJ: Phipsi test + CPPTRAJ: Pairwise test, partial system + + CPPTRAJ: Scale dihedral force constant with 'useall' + +All 3 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control +All 5 comparisons passed. + + CPPTRAJ: Loop tests + + CPPTRAJ: GMX: TRR with offset + + CPPTRAJ: Ewald test (partial system, trunc. oct) + +All 1 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi + +All 2 comparisons passed. + CPPTRAJ: Infrared spectrum calculation test -All 1 comparisons passed. +All 10 comparisons passed. -All 1 comparisons passed. + CPPTRAJ: Phipsi test + +All 5 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_Cluster_Nreps CPPTRAJ: Explicit pH REMD ensemble data read / sort + + CPPTRAJ: Clustering with specified # reps + Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. + Skipped test: Ewald test (trunc. oct), 10 frames + Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. + Skipped test: Ewald test (ortho), 10 frames + +All 4 comparisons passed. +2 comparisons skipped. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: Command line trajectory args test, part 1 -All 2 comparisons passed. - - All 5 comparisons passed. - CPPTRAJ: Change chain ID of COORDS set test - - - CPPTRAJ: CRD(6-10) => TRR - CPPTRAJ: Scale dihedral force constant with 'useall' - - CPPTRAJ: Pairwise test, partial system +All 1 comparisons passed. - CPPTRAJ: Clustering, dihedral DataSet ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: XYZ format write -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff CPPTRAJ: Command line test trajectory args test, part 2 - CPPTRAJ: Simple Hausdorff distance test. - -All 3 comparisons passed. - + CPPTRAJ: Concatenate COORDS data set test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff All 2 comparisons passed. - CPPTRAJ: GIST test, nonorthogonal cell + CPPTRAJ: Simple Hausdorff distance test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc - CPPTRAJ: Test set command + CPPTRAJ: Particle mesh Ewald test (NaCl crystal) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time - CPPTRAJ: Concatenate COORDS data set test + CPPTRAJ: Add time to restart test - CPPTRAJ: TRR (appended) => CRD + CPPTRAJ: XTC read test - CPPTRAJ: Constant pH stats test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm +All 1 comparisons passed. - CPPTRAJ: XtalSymm Reference - CPPTRAJ: Ewald test (partial system, trunc. oct) - CPPTRAJ: Hausdorff distance of 2D rms output test. + CPPTRAJ: Test set command + CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Atom XYZ format read, test 1 +All 2 comparisons passed. - CPPTRAJ: Clustering, two dihedral DataSets - CPPTRAJ: Command line wildcard test, part 1 -All 10 comparisons passed. + CPPTRAJ: Constant pH stats test + CPPTRAJ: Particle mesh Ewald test (trunc. oct) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm - CPPTRAJ: Add time to restart test + CPPTRAJ: XtalSymm Reference +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS + CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) - CPPTRAJ: Command line wildcard test, part 2 + CPPTRAJ: CRD => XTC - CPPTRAJ: Sorted implicit constant pH stats test - CPPTRAJ: Atom XYZ format read, test 2 + CPPTRAJ: SplitCoords test -All 1 comparisons passed. + CPPTRAJ: Remove time from restart test + CPPTRAJ: Hausdorff distance of 2D rms output test. - CPPTRAJ: Clustering, dihedral DataSet, K-means - Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. - Skipped test: Ewald test (trunc. oct), 10 frames - Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. - Skipped test: Ewald test (ortho), 10 frames + CPPTRAJ: Atom XYZ format read, test 2 -All 4 comparisons passed. -2 comparisons skipped. + CPPTRAJ: Sorted implicit constant pH stats test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords + CPPTRAJ: Command line wildcard test, part 2 - CPPTRAJ: SplitCoords test + CPPTRAJ: Test reading comma-separated list of strings - CPPTRAJ: Remove time from restart test + CPPTRAJ: Add time to trajectory test -******************************************************************************** - CPPTRAJ: Test reading comma-separated list of strings -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME + CPPTRAJ: XTC => CRD - CPPTRAJ: Particle mesh Ewald test (NaCl crystal) +All 1 comparisons passed. -All 2 comparisons passed. +All 2 comparisons passed. - CPPTRAJ: XtalSymm Reimaging by Atom - CPPTRAJ: Particle mesh Ewald test (trunc. oct) + CPPTRAJ: Atom XYZ format read, test 3 - CPPTRAJ: Hausdorff distance of 2D rms output test. + CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats -All 1 comparisons passed. + CPPTRAJ: Dihedral RMSD test (to previous) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS + CPPTRAJ: Test nested loops and variables in loops - CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) + CPPTRAJ: Hausdorff distance of 2D rms output test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope CPPTRAJ: Finite difference test. - -All 1 comparisons passed. - ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix + CPPTRAJ: Dihedral RMS fluctuation test. + CPPTRAJ: MW covariance matrix thermo analysis test -All 3 comparisons passed. + CPPTRAJ: Test loop over data set blocks -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin + CPPTRAJ: Particle mesh Ewald test (ortho) - CPPTRAJ: Basic energy minimization test. + CPPTRAJ: CRD(1-5) => XTC -All 1 comparisons passed. + CPPTRAJ: Atom XYZ format read, test 4 -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau +All 1 comparisons passed. - CPPTRAJ: Evalulate plateau test -All 2 comparisons passed. +All 5 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft - CPPTRAJ: Graft test + CPPTRAJ: XtalSymm Reimaging by Atom All 1 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten - CPPTRAJ: Flatten test. + CPPTRAJ: Modify time info test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau -All 1 comparisons passed. + CPPTRAJ: Evalulate plateau test + CPPTRAJ: CRD(6-10) => XTC ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin - CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs + CPPTRAJ: Basic energy minimization test. + CPPTRAJ: Atom XYZ format read, test 5 - CPPTRAJ: GMX: CRD with offset + CPPTRAJ: Test for filename wildcards and oversets +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft - CPPTRAJ: Atom XYZ format read, test 3 + CPPTRAJ: Graft test - CPPTRAJ: Test nested loops and variables in loops - CPPTRAJ: Add time to trajectory test +All 2 comparisons passed. - CPPTRAJ: Dihedral RMSD test (to previous) - CPPTRAJ: PCG32 RNG test. +All 4 comparisons passed. - CPPTRAJ: Clustering, two dihedral DataSets, K-means - CPPTRAJ: Particle mesh Ewald test (ortho) + CPPTRAJ: Unsorted pH read/write test - CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats + CPPTRAJ: XTC (appended) => CRD CPPTRAJ: Energy minimization with angle term test. - CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. - - CPPTRAJ: Dihedral RMS fluctuation test. - - - CPPTRAJ: Test Stdlib RNG - CPPTRAJ: Atom XYZ format read, test 4 - - CPPTRAJ: Test loop over data set blocks +All 1 comparisons passed. - CPPTRAJ: Modify time info test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random - CPPTRAJ: Unsorted pH read/write test + CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs - CPPTRAJ: GMX: TRR with offset + CPPTRAJ: Particle mesh Ewald test (ortho, with mask) -All 8 comparisons passed. +All 13 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN - - CPPTRAJ: DBSCAN test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten -All 4 comparisons passed. +All 3 comparisons passed. All 16 comparisons passed. -All 5 comparisons passed. - - -All 5 comparisons passed. - + CPPTRAJ: Flatten test. - CPPTRAJ: DBSCAN automatic parameter determination test. + CPPTRAJ: Atom XYZ format read, test 6 - CPPTRAJ: Test Mersenne Twister RNG + CPPTRAJ: PCG32 RNG test. - CPPTRAJ: Particle mesh Ewald test (ortho, with mask) + CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. CPPTRAJ: Energy minimization with nonbond term test. - CPPTRAJ: Test for filename wildcards and oversets - - CPPTRAJ: Atom XYZ format read, test 5 -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc - - CPPTRAJ: XTC read test + CPPTRAJ: Test Stdlib RNG -All 4 comparisons passed. +All 6 comparisons passed. -All 13 comparisons passed. + CPPTRAJ: PME test (partial system, trunc. oct) + CPPTRAJ: GIST test, nonorthogonal cell - CPPTRAJ: DBSCAN kdist map test + CPPTRAJ: Test Mersenne Twister RNG - CPPTRAJ: Atom XYZ format read, test 6 - CPPTRAJ: PME test (partial system, trunc. oct) +All 1 comparisons passed. + CPPTRAJ: GMX: CRD with offset - CPPTRAJ: XtalSymm Reimaging by Molecule - CPPTRAJ: CRD => XTC +All 4 comparisons passed. -All 6 comparisons passed. + CPPTRAJ: GMX: XTC 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 @@ -3604,96 +3694,47 @@ CPPTRAJ: OpenMM basic energy minimization tests (bonds) - CPPTRAJ: XTC => CRD +All 4 comparisons passed. - CPPTRAJ: DBSCAN with sieve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LJ_PME - CPPTRAJ: LJ PME test. - -All 4 comparisons passed. - ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans - - CPPTRAJ: Cpptraj Kmeans - +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: OpenMM basic energy minimization tests (angles) - CPPTRAJ: LJ PME kappa sweep test, 0.25 - - - CPPTRAJ: Cpptraj Kmeans random - CPPTRAJ: CRD(1-5) => XTC - -All 6 comparisons passed. - -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD - - CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) + CPPTRAJ: LJ PME test. - CPPTRAJ: LJ PME kappa sweep test, 0.35 + CPPTRAJ: TNG read test CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) - CPPTRAJ: CRD(6-10) => XTC + CPPTRAJ: LJ PME kappa sweep test, 0.25 -All 5 comparisons passed. + CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites + CPPTRAJ: LJ PME kappa sweep test, 0.35 - CPPTRAJ: Cluster command test, coordinate writes. + CPPTRAJ: TNG read test (with offset) CPPTRAJ: LJ PME kappa sweep test, 0.45 - CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) - - CPPTRAJ: Cluster command test, coordinate writes using info file. - - CPPTRAJ: XTC (appended) => CRD + CPPTRAJ: XtalSymm Reimaging by Molecule CPPTRAJ: LJ PME kappa sweep test, 0.5 -All 8 comparisons passed. - -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks - - CPPTRAJ: Density peaks clustering test - -All 3 comparisons passed. - - - CPPTRAJ: LJ with switch function test - CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) - CPPTRAJ: GMX: CRD with offset - -All 3 comparisons passed. +All 6 comparisons passed. All 5 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps - - CPPTRAJ: Clustering with specified # reps - - CPPTRAJ: GMX: XTC with offset - -All 2 comparisons passed. + CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) -All 4 comparisons passed. +All 3 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG - - CPPTRAJ: TNG read test All 11 comparisons passed. @@ -3702,8 +3743,6 @@ CPPTRAJ: TIP3P water cluster test - CPPTRAJ: TNG read test (with offset) - CPPTRAJ: TIP4P water cluster test CPPTRAJ: TIP5P water cluster test @@ -3711,9 +3750,6 @@ All 4 comparisons passed. -All 6 comparisons passed. - - All 9 comparisons passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' @@ -3721,7 +3757,7 @@ 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 186114960 Apr 10 21:12 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 186114960 Mar 8 14:52 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. @@ -3778,12 +3814,14 @@ 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/120576/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/120576/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/1237090 and its subdirectories -I: Current time: Fri Apr 10 09:12:56 -12 2026 -I: pbuilder-time-stamp: 1775855576 +I: removing directory /srv/workspace/pbuilder/120576 and its subdirectories +I: Current time: Sun Mar 9 04:52:47 +14 2025 +I: pbuilder-time-stamp: 1741445567