Diff of the two buildlogs: -- --- b1/build.log 2025-10-19 09:24:38.047791574 +0000 +++ b2/build.log 2025-10-19 09:32:08.116348662 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Oct 18 21:11:56 -12 2025 -I: pbuilder-time-stamp: 1760865116 +I: Current time: Sun Nov 22 05:47:40 +14 2026 +I: pbuilder-time-stamp: 1795276060 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying gcc-15.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/754418/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1551618/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 21 15:49 /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/1551618/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1551618/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='9b2d069b64c04b0aadc9b5c413cf6cda' - 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='754418' - PS1='# ' - PS2='> ' + INVOCATION_ID=73fde13f928748858a7fc091bb8bf507 + 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=1551618 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.HnwPopW0/pbuilderrc_Aycg --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HnwPopW0/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-5.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HnwPopW0/pbuilderrc_MEtB --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HnwPopW0/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-5.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/754418/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1551618/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -257,7 +289,7 @@ Get: 131 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 132 http://deb.debian.org/debian forky/main amd64 libreadline-dev amd64 8.3-3 [175 kB] Get: 133 http://deb.debian.org/debian forky/main amd64 netcdf-bin amd64 1:4.9.3-1+b1 [261 kB] -Fetched 134 MB in 9s (14.9 MB/s) +Fetched 134 MB in 28s (4741 kB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) @@ -815,7 +847,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/1551618/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1551618/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-5_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -828,7 +864,7 @@ make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean - make -j40 clean + make -j42 clean make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' @@ -921,7 +957,7 @@ make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_build - make -j40 + make -j42 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' @@ -956,8 +992,8 @@ CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp -CXX Action_Energy.cpp CXX Action_DistRmsd.cpp +CXX Action_Energy.cpp CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp @@ -965,6 +1001,9 @@ CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp +CXX Action_Image.cpp +CXX Action_InfraredSpectrum.cpp +CXX Action_Jcoupling.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2324: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] @@ -1009,9 +1048,6 @@ 4504 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4511: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4511 | #pragma omp for -CXX Action_Image.cpp -CXX Action_InfraredSpectrum.cpp -CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp @@ -1040,7 +1076,6 @@ CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp -CXX Action_STFC_Diffusion.cpp In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, @@ -1109,6 +1144,7 @@ Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ +CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp @@ -1130,8 +1166,8 @@ CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp -CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp +CXX Analysis_Clustering.cpp CXX Analysis_ConstantPHStats.cpp CXX Analysis_CrankShaft.cpp CXX Analysis_CrdFluct.cpp @@ -1218,6 +1254,17 @@ CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp +CXX DataIO_Cmatrix.cpp +CXX DataIO_Cpout.cpp +CXX DataIO_Evecs.cpp +CXX DataIO_Gnuplot.cpp +CXX DataIO_Grace.cpp +CXX DataIO_OpenDx.cpp +CXX DataIO_Peaks.cpp +CXX DataIO_Mdout.cpp +CXX DataIO_NC_Cmatrix.cpp +CXX DataIO_RemLog.cpp +CXX DataIO_Std.cpp In file included from /usr/include/c++/15/vector:68, from ArgList.h:3, from Action.h:4, @@ -1248,17 +1295,6 @@ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ -CXX DataIO_Cmatrix.cpp -CXX DataIO_Cpout.cpp -CXX DataIO_Evecs.cpp -CXX DataIO_Gnuplot.cpp -CXX DataIO_Grace.cpp -CXX DataIO_OpenDx.cpp -CXX DataIO_Peaks.cpp -CXX DataIO_Mdout.cpp -CXX DataIO_NC_Cmatrix.cpp -CXX DataIO_RemLog.cpp -CXX DataIO_Std.cpp CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp @@ -1317,6 +1353,12 @@ CXX Exec_AddMissingRes.cpp CXX Exec_Analyze.cpp CXX Exec_Calc.cpp +CXX Exec_CatCrd.cpp +CXX Exec_Change.cpp +CXX Exec_ClusterMap.cpp +CXX Exec_CombineCoords.cpp +CXX Exec_Commands.cpp +CXX Exec_CompareTop.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2324: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] @@ -1325,7 +1367,6 @@ 2344 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3015: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3015 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) -CXX Exec_CatCrd.cpp helpme_standalone.h:3121: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3121 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3248: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] @@ -1362,11 +1403,6 @@ 4504 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4511: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4511 | #pragma omp for -CXX Exec_Change.cpp -CXX Exec_ClusterMap.cpp -CXX Exec_CombineCoords.cpp -CXX Exec_Commands.cpp -CXX Exec_CompareTop.cpp CXX Exec_CrdAction.cpp CXX Exec_CrdOut.cpp CXX Exec_CreateSet.cpp @@ -1458,6 +1494,9 @@ 4005 | Real *__restrict__ realCBA; | ^~~~~~~ CXX Exec_PermuteDihedrals.cpp +CXX Exec_Precision.cpp +CXX Exec_PrepareForLeap.cpp +CXX Exec_PrintData.cpp helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1001:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1001 | assertSymmetric(); @@ -1527,8 +1566,11 @@ helpme_standalone.h:2209:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2209 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ -CXX Exec_Precision.cpp -CXX Exec_PrepareForLeap.cpp +CXX Exec_Random.cpp +CXX Exec_ReadData.cpp +CXX Exec_ReadEnsembleData.cpp +CXX Exec_ReadInput.cpp +CXX Exec_RotateDihedral.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:878:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 878 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } @@ -1558,12 +1600,6 @@ helpme_standalone.h:864:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 864 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ -CXX Exec_PrintData.cpp -CXX Exec_Random.cpp -CXX Exec_ReadData.cpp -CXX Exec_ReadEnsembleData.cpp -CXX Exec_ReadInput.cpp -CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp @@ -1643,8 +1679,8 @@ CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp -CXX RNG_Marsaglia.cpp CXX RNG.cpp +CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp @@ -1685,6 +1721,52 @@ CXX Traj_Gro.cpp CXX Traj_Mol2File.cpp CXX Traj_NcEnsemble.cpp +helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] + 3471 | fftHelperA_ = FFTWWrapper(); + | ^~~~~~~~~~~ +helpme_standalone.h:3471:31: note: '' declared here + 3471 | fftHelperA_ = FFTWWrapper(); + | ^~~~~~~~~~~~~~~~~~~ +helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] + 3472 | fftHelperB_ = FFTWWrapper(); + | ^~~~~~~~~~~ +helpme_standalone.h:3472:31: note: '' declared here + 3472 | fftHelperB_ = FFTWWrapper(); + | ^~~~~~~~~~~~~~~~~~~ +helpme_standalone.h:3473:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] + 3473 | fftHelperC_ = FFTWWrapper(); + | ^~~~~~~~~~~ +helpme_standalone.h:3473:31: note: '' declared here + 3473 | fftHelperC_ = FFTWWrapper(); + | ^~~~~~~~~~~~~~~~~~~ +In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', + inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3504:43: +helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] + 520 | class Matrix { + | ^~~~~~ +helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:3504:45: note: '' declared here + 3504 | compressionCoefficientsA_ = RealMat(); + | ^~~~~~~~~ +In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', + inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3505:43: +helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] + 520 | class Matrix { + | ^~~~~~ +helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:3505:45: note: '' declared here + 3505 | compressionCoefficientsB_ = RealMat(); + | ^~~~~~~~~ +In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', + inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3506:43: +helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] + 520 | class Matrix { + | ^~~~~~ +helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:3506:45: note: '' declared here + 3506 | compressionCoefficientsC_ = RealMat(); + | ^~~~~~~~~ CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp CXX Traj_SQM.cpp @@ -1710,6 +1792,13 @@ xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': +helpme_standalone.h:5032:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] + 5032 | return energy; + | ^~~~~~ +helpme_standalone.h:5022:14: note: 'energy' was declared here + 5022 | Real energy; + | ^~~~~~ CXX Action_Esander.cpp CXX Command.cpp CXX Cpptraj.cpp @@ -1719,16 +1808,16 @@ CC molsurf.c cd xdrfile && make all -Skipping bundled ARPACK build make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' - - CC xdrfile.c Skipping bundled READLINE build CC xdr_seek.c CC xdrfile_trr.c + +Skipping bundled ARPACK build CC xdrfile_xtc.c + cd tng && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC md5.c @@ -1739,8 +1828,8 @@ CC fixpoint.c CC xtc3.c CC bwlzh.c -CC xtc2.c CC widemuldiv.c +CC xtc2.c CC huffmem.c CC vals16.c CC bwt.c @@ -1750,55 +1839,6 @@ CC dict.c CC huffman.c CC merge_sort.c -/bin/rm -f libxdrfile.a -ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o -make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' -helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] - 3471 | fftHelperA_ = FFTWWrapper(); - | ^~~~~~~~~~~ -helpme_standalone.h:3471:31: note: '' declared here - 3471 | fftHelperA_ = FFTWWrapper(); - | ^~~~~~~~~~~~~~~~~~~ -helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] - 3472 | fftHelperB_ = FFTWWrapper(); - | ^~~~~~~~~~~ -helpme_standalone.h:3472:31: note: '' declared here - 3472 | fftHelperB_ = FFTWWrapper(); - | ^~~~~~~~~~~~~~~~~~~ -helpme_standalone.h:3473:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] - 3473 | fftHelperC_ = FFTWWrapper(); - | ^~~~~~~~~~~ -helpme_standalone.h:3473:31: note: '' declared here - 3473 | fftHelperC_ = FFTWWrapper(); - | ^~~~~~~~~~~~~~~~~~~ -In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', - inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3504:43: -helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] - 520 | class Matrix { - | ^~~~~~ -helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:3504:45: note: '' declared here - 3504 | compressionCoefficientsA_ = RealMat(); - | ^~~~~~~~~ -In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', - inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3505:43: -helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] - 520 | class Matrix { - | ^~~~~~ -helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:3505:45: note: '' declared here - 3505 | compressionCoefficientsB_ = RealMat(); - | ^~~~~~~~~ -In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', - inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3506:43: -helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] - 520 | class Matrix { - | ^~~~~~ -helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:3506:45: note: '' declared here - 3506 | compressionCoefficientsC_ = RealMat(); - | ^~~~~~~~~ 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); @@ -1806,13 +1846,9 @@ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ -helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': -helpme_standalone.h:5032:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] - 5032 | return energy; - | ^~~~~~ -helpme_standalone.h:5022:14: note: 'energy' was declared here - 5022 | Real energy; - | ^~~~~~ +/bin/rm -f libxdrfile.a +ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o +make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' @@ -1823,13 +1859,13 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest - make -j40 test TESTSUITEFLAGS="-j40 --verbose" VERBOSE=1 check unittest + make -j42 test TESTSUITEFLAGS="-j42 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary cd unitTests && make test.complete summary -make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' +make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src @@ -1841,661 +1877,649 @@ TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: NameType class unit test. -make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' -g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp CPPTRAJ: ArgList class unit test. -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp +make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/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 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 184920736 Oct 19 09:20 ../bin/cpptraj --rwxr-xr-x 1 pbuilder1 pbuilder1 184920736 Oct 19 09:20 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 184920736 Nov 21 15:54 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 184920736 Nov 21 15:54 ../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_RemdTraj +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip - - CPPTRAJ: One frame strip command test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset - - CPPTRAJ: Normal trajectory read with offsets. - - CPPTRAJ: General tests ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP CPPTRAJ: Broken Traj: Running good trajectory. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip CPPTRAJ: CRD Replica Trajectory Run with offset ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Trajout Frame Range [Amber Restart] - - CPPTRAJ: Per-Residue RMSD Test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond - CPPTRAJ: NetCDF Restart Test - TXT->NetCDF - CPPTRAJ: Center command test. + + CPPTRAJ: One frame strip command test + + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image + CPPTRAJ: Secstruct (DSSP) command test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP - - CPPTRAJ: Solute Hbond test - - CPPTRAJ: Orthorhombic imaged distance test. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf - - CPPTRAJ: Secstruct (DSSP) command test. - - CPPTRAJ: Convert mdcrd -> NetCDF +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion - CPPTRAJ: Surface calculation test + CPPTRAJ: General tests ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling + CPPTRAJ: Normal trajectory read with offsets. -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj - CPPTRAJ: Mask single frame test -******************************************************************************** + CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling - CPPTRAJ: J-Coupling single frame test + CPPTRAJ: Orthorhombic imaged distance test. - CPPTRAJ: Radius of gyration command test + CPPTRAJ: Solute Hbond test - CPPTRAJ: RMSD Test with outtraj. + CPPTRAJ: CHARMM PSF/DCD test ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj + + CPPTRAJ: NetCDF Restart Test - TXT->NetCDF ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion - CPPTRAJ: Coordinate Running Average test. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg + CPPTRAJ: J-Coupling single frame test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 - CPPTRAJ: Rotational diffusion calculation test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm CPPTRAJ: Diffusion test, no imaging. -******************************************************************************** + CPPTRAJ: Mask single frame test TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD - CPPTRAJ: CHARMM PSF/DCD test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct + CPPTRAJ: Surface calculation test ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile - - CPPTRAJ: Average Test. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct +******************************************************************************** - CPPTRAJ: Data file output precision test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj + CPPTRAJ: Radius of gyration command test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial - CPPTRAJ: 2D RMSD Test. + CPPTRAJ: RMSD Test with outtraj. - CPPTRAJ: Mol2 Parm/Traj Read/Write Test. + CPPTRAJ: 2D RMSD Test. CPPTRAJ: Basic RMSD tests ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile + + CPPTRAJ: Average Test. + + CPPTRAJ: Rotational diffusion calculation test -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap CPPTRAJ: NAstruct command test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker - CPPTRAJ: Pucker command test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest -******************************************************************************** + CPPTRAJ: Convert mdcrd -> NetCDF - CPPTRAJ: AtomMap Test + CPPTRAJ: Coordinate Running Average test. - CPPTRAJ: 1D/2D Histogram Analysis test -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial + CPPTRAJ: AtomMap Test CPPTRAJ: Radial test, non-orthogonal imaging - CPPTRAJ: Closest command test using first solvent atom. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest + CPPTRAJ: Pucker command test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist - CPPTRAJ: Distance RMSD test + CPPTRAJ: Mol2 Parm/Traj Read/Write Test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD - CPPTRAJ: NetCDF Restart Test - NetCDF->TXT + CPPTRAJ: Data file output precision test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons - CPPTRAJ: Gzipped trajectory read with offsets + CPPTRAJ: Distance RMSD test - CPPTRAJ: Coordinate Running Average Traj Write + CPPTRAJ: 1D/2D Histogram Analysis test - CPPTRAJ: CRD Replica Trajectory Run + CPPTRAJ: Closest command test using first solvent atom. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster - CPPTRAJ: Non-orthorhombic imaged distance test. + CPPTRAJ: randomizeions test (original algorithm) CPPTRAJ: Cluster command test, in-memory pairwise distances. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED + + CPPTRAJ: IRED vector/matrix test + + CPPTRAJ: CRD Replica Trajectory Run + + CPPTRAJ: NetCDF Restart Test - NetCDF->TXT + + CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: Broken Traj: Running broken trajectory. CPPTRAJ: 2D RMSD Test, mass-weighted. - CPPTRAJ: Standard -> Grace Data + CPPTRAJ: Coordinate Running Average Traj Write J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test + CPPTRAJ: CHARMM DCD Write, step 1. + All 1 comparisons passed. 1 comparisons skipped. - CPPTRAJ: Per-Residue RMSD Test with averaging - - CPPTRAJ: CHARMM DCD Write, step 1. + CPPTRAJ: Non-orthorhombic imaged distance test. - CPPTRAJ: Center origin command test. + CPPTRAJ: PDB => Mol2 CPPTRAJ: Trajout Frame Range [Amber Coordinates] - CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test - - CPPTRAJ: PDB => Mol2 - - CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF + CPPTRAJ: Center origin command test. All 2 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED - - CPPTRAJ: IRED vector/matrix test CPPTRAJ: Mask longer command test. - CPPTRAJ: Solute Hbond test with disk caching - - CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. - - CPPTRAJ: NetCDF Replica Trajectory Run test - -All 2 comparisons passed. - All 2 comparisons passed. - CPPTRAJ: Unstrip (Lig/Rec/Complex) command test - -All 4 comparisons passed. + CPPTRAJ: Diffusion test, old syntax. + CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test + CPPTRAJ: Per-Residue RMSD Test with averaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf - CPPTRAJ: Grace -> Standard Data - CPPTRAJ: Molsurf test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons - CPPTRAJ: Orthorhombic coordinate imaging test + CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. - CPPTRAJ: 2D RMSD Test with reference trajectory +All 4 comparisons passed. - CPPTRAJ: Bzip2ed trajectory read with offsets - CPPTRAJ: randomizeions test (original algorithm) + CPPTRAJ: NetCDF Replica Trajectory Run test - CPPTRAJ: Diffusion test, old syntax. + CPPTRAJ: Standard -> Grace Data + + CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF + + CPPTRAJ: Unstrip (Lig/Rec/Complex) command test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr CPPTRAJ: CHARMM DCD Write, step 2. - - CPPTRAJ: NAstruct command test, single strand - -All 6 comparisons passed. - - - CPPTRAJ: Correlation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure - CPPTRAJ: Structure Check + CPPTRAJ: Bzip2ed trajectory read with offsets - CPPTRAJ: AtomMap with 'rmsfit' +All 1 comparisons passed. + + CPPTRAJ: Correlation test - CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: Amber Top/Rst => Mol2 - CPPTRAJ: Center origin mass command test. + CPPTRAJ: AtomMap with 'rmsfit' + + CPPTRAJ: RMS coordinate rotation/rotation matrices test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr - CPPTRAJ: RmsAvgCorr Reference - CPPTRAJ: Per-Residue RMSD Test with residue centering. + CPPTRAJ: Structure Check + CPPTRAJ: Cluster command test, read pairwise distances. - CPPTRAJ: Solute-solvent hbond test + CPPTRAJ: RmsAvgCorr Reference - CPPTRAJ: 3D histogram test. +All 6 comparisons passed. - CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. -All 5 comparisons passed. + CPPTRAJ: Solute Hbond test with disk caching +All 2 comparisons passed. - CPPTRAJ: Cluster command test, read pairwise distances. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts - CPPTRAJ: 2D DME Test. + CPPTRAJ: Contacts test. - CPPTRAJ: RMS coordinate rotation/rotation matrices test + CPPTRAJ: 3D histogram test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal - CPPTRAJ: Convert NetCDF -> mdcrd + CPPTRAJ: 2D RMSD Test with reference trajectory - CPPTRAJ: CHAMBER topology read/strip test. + CPPTRAJ: Principal Test - CPPTRAJ: Secstruct (DSSP) command with changing number of residues. + CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. -All 1 comparisons passed. + CPPTRAJ: NAstruct command test, single strand + CPPTRAJ: Convert NetCDF -> mdcrd - CPPTRAJ: X column format/precision test. + CPPTRAJ: Orthorhombic coordinate imaging test -All 11 comparisons passed. + CPPTRAJ: Center origin mass command test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts + CPPTRAJ: Secstruct (DSSP) command with changing number of residues. - CPPTRAJ: Contacts test. + CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj - CPPTRAJ: Atom map charmm->amber atom order +All 5 comparisons passed. -All 2 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral + CPPTRAJ: clusterdihedral test - CPPTRAJ: Structure Check with Around and Skip + CPPTRAJ: Per-Residue RMSD Test with residue centering. - CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj + CPPTRAJ: Grace -> Standard Data Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 4 comparisons passed. 1 comparisons skipped. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal - - CPPTRAJ: Closest command test using all solvent atoms. CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt - CPPTRAJ: Principal Test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG + CPPTRAJ: Closest command test using all solvent atoms. - CPPTRAJ: Nonorthorhombic coordinate imaging test +All 2 comparisons passed. - CPPTRAJ: Start argument offset + CPPTRAJ: Structure Check with Around and Skip - CPPTRAJ: NA test (8OG) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector -All 7 comparisons passed. + CPPTRAJ: CHAMBER topology read/strip test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral + CPPTRAJ: Atom map charmm->amber atom order - CPPTRAJ: Cluster command test, read NetCDF pairwise distances. + CPPTRAJ: Basic vector tests - CPPTRAJ: clusterdihedral test + CPPTRAJ: Start argument offset All 3 comparisons passed. - CPPTRAJ: 2D RMSD with reference mask test. +All 7 comparisons passed. - CPPTRAJ: Data file group by name test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector -All 3 comparisons passed. + CPPTRAJ: Solute-solvent hbond test + CPPTRAJ: Diffusion test, new syntax. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix - CPPTRAJ: Diffusion test, new syntax. - - CPPTRAJ: Center reference command test. + CPPTRAJ: Matrix Tests - CPPTRAJ: Read CHARMM restart + CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj - CPPTRAJ: Basic vector tests + CPPTRAJ: RmsAvgCorr First - CPPTRAJ: Matrix Tests +All 11 comparisons passed. - CPPTRAJ: Multi frame strip command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct +All 3 comparisons passed. + + CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG - CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj + CPPTRAJ: NA test (8OG) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid - CPPTRAJ: Dipole test - - CPPTRAJ: Atom map charmm->amber atom order, by residue + CPPTRAJ: Projection - CPPTRAJ: RmsAvgCorr First + CPPTRAJ: Dipole test - CPPTRAJ: Hbond, no intramolecular hydrogen bonds test + CPPTRAJ: Multi frame strip command test. -All 2 comparisons passed. + CPPTRAJ: Compressed broken trajectory test + CPPTRAJ: 2D DME Test. - CPPTRAJ: Secstruct (DSSP): SS assign output test + CPPTRAJ: Cluster command test, read NetCDF pairwise distances. All 4 comparisons passed. - CPPTRAJ: 2D RMSD test, no fitting. + CPPTRAJ: Nonorthorhombic coordinate imaging test -All 3 comparisons passed. +All 1 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap CPPTRAJ: RMS fit with no coordinates modification test. - CPPTRAJ: CHARMM PSF write - -All 9 comparisons passed. - + CPPTRAJ: Unwrap non-orthogonal test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes - CPPTRAJ: Diffusion test, nonorthogonal box +All 1 comparisons passed. All 4 comparisons passed. - CPPTRAJ: Cluster command test, write ASCII pairwise distances. - CPPTRAJ: Strip topology with PDB info + CPPTRAJ: Modes analysis, RMS fluctuations - CPPTRAJ: Data file group by aspect test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap + CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. - CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj + CPPTRAJ: Read CHARMM restart - CPPTRAJ: Unwrap non-orthogonal test + CPPTRAJ: Center reference command test. +All 3 comparisons passed. - CPPTRAJ: Projection - CPPTRAJ: Modes analysis, RMS fluctuations + + CPPTRAJ: Atom map charmm->amber atom order, by residue ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell - CPPTRAJ: Watershell Test, non-orthorhombic imaging. +All 3 comparisons passed. - CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. + + CPPTRAJ: Watershell Test, non-orthorhombic imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg - CPPTRAJ: Analysis Running Average - -All 6 comparisons passed. - - - - CPPTRAJ: Closest command test, using mask center -All 1 comparisons passed. + CPPTRAJ: Strip topology with PDB info + CPPTRAJ: Secstruct (DSSP): SS assign output test - CPPTRAJ: FtuFabI Assignment test + CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj - CPPTRAJ: CHARMM COORdinates test + CPPTRAJ: 2D RMSD with reference mask test. -All 3 comparisons passed. + CPPTRAJ: Randomize (around, overlap) + CPPTRAJ: Analysis Running Average ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap - CPPTRAJ: Partial Surface calculation test - CPPTRAJ: VMD VolMap Algorithm test - CPPTRAJ: Cluster command test, read ASCII pairwise distances. +All 2 comparisons passed. - CPPTRAJ: CRD Replica Trajectory Run with remdout -All 1 comparisons passed. + CPPTRAJ: Grid test + CPPTRAJ: Diffusion test, nonorthogonal box ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE -All 3 comparisons passed. +All 2 comparisons passed. CPPTRAJ: SPAM Test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: LIE test - CPPTRAJ: Modes analysis, displacements + CPPTRAJ: Density along axis tests - CPPTRAJ: Grid test +All 3 comparisons passed. -All 6 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density + CPPTRAJ: Hbond, no intramolecular hydrogen bonds test - CPPTRAJ: Density along axis tests + CPPTRAJ: Modes analysis, displacements ******************************************************************************** - - CPPTRAJ: Compressed broken trajectory test TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder - CPPTRAJ: Test vector center with magnitude + + CPPTRAJ: X column format/precision test. + CPPTRAJ: Lipid Order Parameter Test. + +All 11 comparisons passed. + + + CPPTRAJ: Cluster command test, write ASCII pairwise distances. CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. - CPPTRAJ: Lipid Order Parameter Test. + CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist + CPPTRAJ: CHARMM PSF write + CPPTRAJ: PairDist Test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData - CPPTRAJ: Structure Check with PBC + CPPTRAJ: Outtraj Test with maxmin. -All 6 comparisons passed. + CPPTRAJ: Read vector data test (no origins, origins) +All 9 comparisons passed. -All 2 comparisons passed. +All 2 comparisons passed. -All 10 comparisons passed. + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar - CPPTRAJ: Hbond, specified solute masks + CPPTRAJ: FtuFabI Assignment test - CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. + CPPTRAJ: Test vector center with magnitude CPPTRAJ: Center point test. -All 9 comparisons passed. - - -All 8 comparisons passed. + CPPTRAJ: 2D RMSD test, no fitting. + CPPTRAJ: Cluster command test, read ASCII pairwise distances. CPPTRAJ: Unwrap orthogonal test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST - CPPTRAJ: Modes analysis, dipole correlation - -All 11 comparisons passed. + CPPTRAJ: CRD Replica Trajectory Run with remdout + CPPTRAJ: Partial Surface calculation test - CPPTRAJ: Closest command test, using mask center and solvent mask -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams + CPPTRAJ: GIST water-water interaction test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF - CPPTRAJ: Read vector data test (no origins, origins) + CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. - CPPTRAJ: Test updating topology with Charmm parameters (single residue) + CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test - CPPTRAJ: GIST water-water interaction test + CPPTRAJ: Modes analysis, dipole correlation + + CPPTRAJ: Data file group by name test + + CPPTRAJ: Read vector data set (origins, no origins) + VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. + Skipped test: VMD VolMap Algorithm longer tests All 2 comparisons passed. +1 comparisons skipped. + + CPPTRAJ: Momentum/velocity vector test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF - CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test + CPPTRAJ: CHARMM COORdinates test - CPPTRAJ: Momentum/velocity vector test. + CPPTRAJ: STFC Diffusion Test - CPPTRAJ: Randomize (around, overlap) + CPPTRAJ: Closest command test, using mask center - CPPTRAJ: RMS fit to previous test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr +All 5 comparisons passed. - CPPTRAJ: AutoCorr test. -All 5 comparisons passed. +All 9 comparisons passed. - CPPTRAJ: Atomicfluct test with ADP output - VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. - Skipped test: VMD VolMap Algorithm longer tests +All 6 comparisons passed. -All 2 comparisons passed. -1 comparisons skipped. + +All 1 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr - CPPTRAJ: Box Test (Add box info) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve +All 4 comparisons passed. - CPPTRAJ: Radial test, orthogonal and no imaging +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box -All 1 comparisons passed. +All 2 comparisons passed. - CPPTRAJ: Outtraj Test with maxmin. + CPPTRAJ: Cluster, nosieve - CPPTRAJ: Read vector data set (origins, no origins) + CPPTRAJ: AutoCorr test. - CPPTRAJ: RMS: imaging after unit cell rotation + CPPTRAJ: Box Test (Add box info) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect + +All 8 comparisons passed. +All 6 comparisons passed. + + + CPPTRAJ: Selection by atom type test. - CPPTRAJ: OpenDX Grid read test +All 6 comparisons passed. - CPPTRAJ: Hbond, no angle cutoff test + +All 10 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd -All 3 comparisons passed. + CPPTRAJ: RMSD Test with averaged reference coordinates. + CPPTRAJ: Crankshaft test - CPPTRAJ: Force vector test. - CPPTRAJ: RMSD Test with averaged reference coordinates. -All 2 comparisons passed. + CPPTRAJ: OpenDX Grid read test + CPPTRAJ: Structure Check with PBC + CPPTRAJ: Data file group by aspect test + CPPTRAJ: Radial test, orthogonal and no imaging - CPPTRAJ: Read Amber output test + CPPTRAJ: RMS fit to previous test + + CPPTRAJ: Hbond, specified solute masks ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar + CPPTRAJ: Read Amber output test CPPTRAJ: COORDS data set creation and CRDFLUCT test. -All 9 comparisons passed. + CPPTRAJ: Multi-frame density along axis test + CPPTRAJ: Force vector test. - CPPTRAJ: Closest command test, solvent mask, water oxygen only -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat + CPPTRAJ: Atomicfluct test with ADP output - CPPTRAJ: Crankshaft test + CPPTRAJ: Basic lipid order parameter test + + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage -All 2 comparisons passed. - - CPPTRAJ: AutoImage test (split DNA duplex) - - CPPTRAJ: Box test (remove box info) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams CPPTRAJ: Pairdist test, orthogonal imaging. - CPPTRAJ: LoadCrd test. - - CPPTRAJ: Read CHARMM output test + CPPTRAJ: Test updating topology with Charmm parameters (single residue) All 1 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector - -All 12 comparisons passed. +All 2 comparisons passed. -All 15 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM All 1 comparisons passed. @@ -2503,829 +2527,831 @@ All 14 comparisons passed. - CPPTRAJ: Multivector test +All 15 comparisons passed. - CPPTRAJ: COORDS data set creation with velocities test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime - CPPTRAJ: Multi-frame density along axis test +All 9 comparisons passed. - CPPTRAJ: Hbond, Bridge nointramol test - CPPTRAJ: Lifetime test. +All 6 comparisons passed. - CPPTRAJ: Box test (Modify box length) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel - CPPTRAJ: Parallel tests. +All 3 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr - - CPPTRAJ: CrossCorr test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector - CPPTRAJ: Grid with specified center test. - CPPTRAJ: Modes analysis, pseudo trajectory creation test -All 3 comparisons passed. + CPPTRAJ: Grid with specified center test. + CPPTRAJ: RMS: imaging after unit cell rotation + CPPTRAJ: STFC Diffusion Test with individual distances -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr + CPPTRAJ: Read CHARMM output test -All 4 comparisons passed. - CPPTRAJ: Timecorr test. + CPPTRAJ: Box test (remove box info) + CPPTRAJ: Modes analysis, pseudo trajectory creation test - CPPTRAJ: LoadTraj test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT + CPPTRAJ: SPAM Pure Solvent Test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime - CPPTRAJ: FFT test. + CPPTRAJ: Multivector test - CPPTRAJ: 3D data read/write test + CPPTRAJ: LoadCrd test. -All 1 comparisons passed. + CPPTRAJ: FFT test. + CPPTRAJ: Lifetime test. -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_Parallel +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd - CPPTRAJ: SymmRmsd + CPPTRAJ: CrossCorr test -All 6 comparisons passed. + CPPTRAJ: Parallel tests. + CPPTRAJ: SymmRmsd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral - - CPPTRAJ: Lifetime test with data set caching. - - CPPTRAJ: Multidihedral test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD - - CPPTRAJ: Generate matrix with trajectory start/stop/offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure - - CPPTRAJ: M-REMD sort test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate - CPPTRAJ: Basic makestructure test + CPPTRAJ: Multidihedral test - CPPTRAJ: Rotation (and inverse) of coords from matrices - CPPTRAJ: Parallel test with trajectory offset + CPPTRAJ: M-REMD sort test. + CPPTRAJ: Basic makestructure test - CPPTRAJ: Box test (auto orthogonal box, no radii) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD + CPPTRAJ: Rotation (and inverse) of coords from matrices - CPPTRAJ: Basic lipid order parameter test +All 1 comparisons passed. - CPPTRAJ: Total system density test - CPPTRAJ: STFC Diffusion Test +All 1 comparisons passed. - CPPTRAJ: LoadTraj from trajin test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr - CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test - CPPTRAJ: Standard 3D data write test +All 6 comparisons passed. + CPPTRAJ: Timecorr test. - CPPTRAJ: Generate matrix with action stop/start/offset +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts CPPTRAJ: ASP symmetry-corrected RMSD test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate -All 6 comparisons passed. - - - CPPTRAJ: SPAM Pure Solvent Test + CPPTRAJ: NativeContacts test. - CPPTRAJ: Standard 3D data read test +All 12 comparisons passed. - CPPTRAJ: Grid with box center offset test. - CPPTRAJ: Box test (auto orthogonal box, VDW radii) + CPPTRAJ: Integration test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral - CPPTRAJ: Lifetime average and cumulative average test. + CPPTRAJ: Check chirality test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy - CPPTRAJ: Integration test. +All 1 comparisons passed. - CPPTRAJ: STFC Diffusion Test with individual distances All 5 comparisons passed. - -All 1 comparisons passed. + CPPTRAJ: Simple energy tests -All 7 comparisons passed. - CPPTRAJ: Multidihedral Nucleotide CHI test - - CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. + CPPTRAJ: Parallel test with trajectory offset + CPPTRAJ: Makestructure test with reference. - CPPTRAJ: GLU symmetry-corrected RMSD test + CPPTRAJ: Generate matrix with trajectory start/stop/offset - CPPTRAJ: LoadCrd append from multiple files test + CPPTRAJ: Lifetime test with data set caching. -All 7 comparisons passed. + CPPTRAJ: Total system density test - CPPTRAJ: Rotate with defined axis + CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. + CPPTRAJ: Box test (Modify box length) -All 6 comparisons passed. + CPPTRAJ: Closest command test, using mask center and solvent mask + CPPTRAJ: LoadTraj test. + CPPTRAJ: Multidihedral Nucleotide CHI test -All 15 comparisons passed. + CPPTRAJ: Randomize (around) - CPPTRAJ: Makestructure test with reference. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve - CPPTRAJ: TRAJ data set creation and CRDFLUCT test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts + CPPTRAJ: 3D data read/write test + CPPTRAJ: Hbond, no angle cutoff test + CPPTRAJ: COORDS data set creation with velocities test - CPPTRAJ: Cluster, nosieve -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy + CPPTRAJ: LCPO test with GAFF atom types - CPPTRAJ: Simple energy tests + CPPTRAJ: STFC Diffusion Test with COM - CPPTRAJ: NativeContacts test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit + CPPTRAJ: New Lipid Order Parameter Test, DOPC. All 1 comparisons passed. - CPPTRAJ: Standard 3D data read/append test - -All 12 comparisons passed. - + CPPTRAJ: Cluster, sieve5 +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: LES split/average test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals - CPPTRAJ: Check chirality test +All 2 comparisons passed. -All 4 comparisons passed. + CPPTRAJ: PermuteDihedrals interval -120, phi psi -All 2 comparisons passed. + CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test +All 1 comparisons passed. -All 7 comparisons passed. + CPPTRAJ: Rotate with defined axis ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 - CPPTRAJ: LCPO test with GAFF atom types + CPPTRAJ: GLU symmetry-corrected RMSD test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals - - CPPTRAJ: PermuteDihedrals interval -120, phi psi -******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar CPPTRAJ: Dihedral Covariance Matrix Test - CPPTRAJ: TYR symmetry-corrected RMSD test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit - CPPTRAJ: Curve fitting test. +All 5 comparisons passed. +All 3 comparisons passed. - CPPTRAJ: Multidihedral protein dihedrals test - CPPTRAJ: TRAJ data set creation with velocities test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage - SANDER energy tests (long) requires SANDER API from AmberTools. - Cpptraj was compiled without SANDER API from AmberTools support. - SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. - SKIP: SANDER energy tests (long) - +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath - CPPTRAJ: Data set averaging and averaging over all sets test. +All 7 comparisons passed. -All 5 comparisons passed. + CPPTRAJ: Curve fitting test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage -All 7 comparisons passed. + CPPTRAJ: Vector dot/cross product test + CPPTRAJ: Data set averaging and averaging over all sets test. -All 3 comparisons passed. +All 13 comparisons passed. - CPPTRAJ: Vector dot/cross product test +All 7 comparisons passed. -All 3 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander + SANDER energy tests (long) requires SANDER API from AmberTools. + Cpptraj was compiled without SANDER API from AmberTools support. + SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. + SKIP: SANDER energy tests (long) - CPPTRAJ: STFC Diffusion Test with COM +All 6 comparisons passed. - CPPTRAJ: Standard 3D data, sparse ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline CPPTRAJ: Temperature test. -All 1 comparisons passed. - CPPTRAJ: Spline test + CPPTRAJ: Lifetime average and cumulative average test. + CPPTRAJ: STFC Diffusion Test with second mask + CPPTRAJ: Grid with box center offset test. - CPPTRAJ: Grid with mask center offset test. + CPPTRAJ: PermuteDihedrals, random rotations ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet - CPPTRAJ: Wavelet analysis test + CPPTRAJ: Box test (auto orthogonal box, no radii) +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline + + CPPTRAJ: M-REMD actions test. + + CPPTRAJ: Multidihedral protein dihedrals test + + CPPTRAJ: Hbond, Bridge nointramol test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short + + CPPTRAJ: Standard 3D data write test Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SKIP: Energy via sander API short tests (GB/PME) - CPPTRAJ: Cluster, sieve5 -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE + CPPTRAJ: Generate matrix with action stop/start/offset - CPPTRAJ: M-REMD actions test. + CPPTRAJ: Spline test + +All 3 comparisons passed. - CPPTRAJ: KDE test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE - CPPTRAJ: New Lipid Order Parameter Test, DOPC. + CPPTRAJ: KDE test. -All 13 comparisons passed. +All 2 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF - - CPPTRAJ: PDB format read/write test - - CPPTRAJ: Multidihedral cyclic molecule test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet - CPPTRAJ: CIF read test + CPPTRAJ: Wavelet analysis test - CPPTRAJ: Nonorthogonal grid standard write/read tests. +All 2 comparisons passed. - CPPTRAJ: Longer symmetry-corrected RMSD test. All 2 comparisons passed. - - CPPTRAJ: Temperature with SHAKE on hydrogens. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF -All 2 comparisons passed. +All 4 comparisons passed. - CPPTRAJ: Curve fitting multi-exponential tests. - CPPTRAJ: PermuteDihedrals, random rotations - - CPPTRAJ: Align Tests. +All 3 comparisons passed. + CPPTRAJ: CIF read test -All 2 comparisons passed. + CPPTRAJ: Curve fitting multi-exponential tests. -All 1 comparisons passed. + CPPTRAJ: TYR symmetry-corrected RMSD test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr - CPPTRAJ: STFC Diffusion Test with second mask + CPPTRAJ: Closest command test, solvent mask, water oxygen only + CPPTRAJ: Cluster, nosieve savepairdist - CPPTRAJ: Velocity autocorrelation test + CPPTRAJ: LoadTraj from trajin test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB - CPPTRAJ: Test combining coordinates, velocities, and forces. +All 15 comparisons passed. - CPPTRAJ: Temperature with SHAKE on all atoms. ******************************************************************************** -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: Rotate dihedral to target value. + CPPTRAJ: PDB format read/write test -All 6 comparisons passed. +All 1 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc - CPPTRAJ: Data Set commands test + CPPTRAJ: Velocity autocorrelation test -All 1 comparisons passed. + CPPTRAJ: Test combining coordinates, velocities, and forces. + CPPTRAJ: Rotate dihedral to target value. -All 3 comparisons passed. +All 7 comparisons passed. -All 8 comparisons passed. +All 12 comparisons passed. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap - CPPTRAJ: COORDS data set append test + CPPTRAJ: Data Set commands test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align - CPPTRAJ: Remap Test +All 4 comparisons passed. - CPPTRAJ: M-REMD ensemble outtraj test. - CPPTRAJ: Rotate dihedral by increment + CPPTRAJ: Remap Test - CPPTRAJ: Temperature calc with extra points. + CPPTRAJ: Align Tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop - - CPPTRAJ: Test using velocities as coordinates. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter CPPTRAJ: Compare topology test + + CPPTRAJ: Basic filter test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd CPPTRAJ: Combine COORDS test. - CPPTRAJ: Basic filter test - CPPTRAJ: Non-orthogonal grid test. + CPPTRAJ: TRAJ data set creation and CRDFLUCT test. + CPPTRAJ: Multidihedral cyclic molecule test -All 1 comparisons passed. + CPPTRAJ: Grid with mask center offset test. + CPPTRAJ: Longer symmetry-corrected RMSD test. - CPPTRAJ: Cluster, nosieve savepairdist + CPPTRAJ: Temperature with SHAKE on hydrogens. - CPPTRAJ: Align, unit cell rotation/imaging test. + CPPTRAJ: Standard 3D data read test - CPPTRAJ: M-REMD no sort, running average test + CPPTRAJ: Box test (auto orthogonal box, VDW radii) - CPPTRAJ: Rotate dihedral in TRAJ data set +All 1 comparisons passed. - CPPTRAJ: Wavelet WAFEX test -All 4 comparisons passed. +All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Topology info print test. - CPPTRAJ: Test kinetic energy calculation +All 6 comparisons passed. + + +All 7 comparisons passed. + + +All 8 comparisons passed. - CPPTRAJ: COORDS test storing frame metadata ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: TRR force/velocity read -> NetCDF write test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI - CPPTRAJ: Combine COORDS test with box info. - -All 1 comparisons passed. + CPPTRAJ: Direct sum test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds + CPPTRAJ: TI analysis test. - CPPTRAJ: Test writing velocities (MDVEL) + CPPTRAJ: Wavelet WAFEX test -All 2 comparisons passed. + CPPTRAJ: NativeContacts test, save non-native contacts, residue time series + CPPTRAJ: Curve fitting, custom output range. - CPPTRAJ: M-REMD, generate RMS data + CPPTRAJ: Fix imaged bonds test (Ortho.) - CPPTRAJ: Curve fitting, custom output range. + CPPTRAJ: Align, unit cell rotation/imaging test. - CPPTRAJ: Randomize (around) + CPPTRAJ: Temperature with SHAKE on all atoms. -All 4 comparisons passed. + CPPTRAJ: Combine COORDS test with box info. + CPPTRAJ: Standard 3D data read/append test +All 10 comparisons passed. -All 3 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Test kinetic energy calculation -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI + CPPTRAJ: Test using velocities as coordinates. - CPPTRAJ: Direct sum test + CPPTRAJ: Rotate dihedral by increment + CPPTRAJ: LoadCrd append from multiple files test -All 10 comparisons passed. - CPPTRAJ: TI analysis test. + CPPTRAJ: M-REMD ensemble outtraj test. +All 3 comparisons passed. - CPPTRAJ: Generate offset traj from PDB +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance - CPPTRAJ: Test total energy calculation +All 4 comparisons passed. - CPPTRAJ: PQR file write with various radii - CPPTRAJ: Test using forces as coordinates. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds +All 6 comparisons passed. - CPPTRAJ: Fix imaged bonds test (Ortho.) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Distance tests ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity - - CPPTRAJ: NativeContacts test, save non-native contacts, residue time series - - CPPTRAJ: Set Velocity test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: Data filter test. - CPPTRAJ: Volume tests - CPPTRAJ: Cluster, nosieve loadpairdist + CPPTRAJ: Temperature calc with extra points. CPPTRAJ: KDE with Kullback-Leibler divergence test + CPPTRAJ: TRAJ data set creation with velocities test. - CPPTRAJ: AutoImage test, use anchor mask - - CPPTRAJ: M-REMD, meltcurve analysis -All 6 comparisons passed. + CPPTRAJ: Test writing velocities (MDVEL) + CPPTRAJ: Test total energy calculation + CPPTRAJ: Rotate dihedral in TRAJ data set - CPPTRAJ: TRAJ test storing frame metadata + CPPTRAJ: Volume tests -All 5 comparisons passed. + CPPTRAJ: Non-orthogonal grid test. + CPPTRAJ: Generate offset traj from PDB - CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test - CPPTRAJ: Split coords and recombine test. - CPPTRAJ: Generate offset traj from CIF + CPPTRAJ: PQR file write with various radii - CPPTRAJ: Test writing forces (MDFRC) + CPPTRAJ: AutoImage test, use anchor mask ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve - - CPPTRAJ: Orthogonal imaged distance +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity CPPTRAJ: Multicurve test - CPPTRAJ: Test partial energy calculation -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog + CPPTRAJ: Set Velocity test All 5 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog CPPTRAJ: Replica log read/analyze test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol - CPPTRAJ: PDB filter alternate atom location IDs test + CPPTRAJ: Area per molecule test - CPPTRAJ: Scale velocity test +All 3 comparisons passed. -All 17 comparisons passed. +All 16 comparisons passed. - CPPTRAJ: Filter matrix test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol -All 1 comparisons passed. +All 4 comparisons passed. - CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. - CPPTRAJ: Non-orthogonal imaged distance + CPPTRAJ: Structure Check with Around + CPPTRAJ: NativeContacts test, orthorhombic imaging. - CPPTRAJ: Area per molecule test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask + CPPTRAJ: Generate offset traj from CIF -All 3 comparisons passed. - CPPTRAJ: Distance-based atom mask tests (atom, residue) + CPPTRAJ: Standard 3D data, sparse + CPPTRAJ: Fix imaged bonds test (Non-ortho.) + CPPTRAJ: Test partial energy calculation -All 4 comparisons passed. + CPPTRAJ: Pairdist test, nonorthogonal imaging. + CPPTRAJ: Test using forces as coordinates. + + CPPTRAJ: Split coords and recombine test. + + CPPTRAJ: M-REMD no sort, running average test + + CPPTRAJ: Orthogonal imaged distance +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc - CPPTRAJ: Fix imaged bonds test (Non-ortho.) +All 1 comparisons passed. -All 2 comparisons passed. + CPPTRAJ: Distance-based atom mask tests (atom, residue) CPPTRAJ: Calc test ******************************************************************************** -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: NativeContacts test, orthorhombic imaging. + CPPTRAJ: Calcstate test - CPPTRAJ: Change atom and residue name tests +All 2 comparisons passed. -All 3 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change + CPPTRAJ: Change atom and residue name tests +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir + CPPTRAJ: Create RREMD NetCDF reservoir test -All 5 comparisons passed. - CPPTRAJ: Cluster, sieve5 savepairdist +All 3 comparisons passed. - CPPTRAJ: Calcstate test +All 2 comparisons passed. - CPPTRAJ: Grid generation from 'bounds' test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir - CPPTRAJ: Create RREMD NetCDF reservoir test +All 7 comparisons passed. - CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. -All 6 comparisons passed. +All 5 comparisons passed. + CPPTRAJ: Topology info with reference coords test -All 2 comparisons passed. + CPPTRAJ: M-REMD, generate RMS data -All 2 comparisons passed. + CPPTRAJ: Filter matrix test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve + CPPTRAJ: Calc test with data sets -All 16 comparisons passed. + CPPTRAJ: Nonorthogonal grid standard write/read tests. + CPPTRAJ: Test writing forces (MDFRC) -All 1 comparisons passed. + CPPTRAJ: COORDS data set append test + CPPTRAJ: PDB filter alternate atom location IDs test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder - CPPTRAJ: TRR force/velocity read -> TRR write test + CPPTRAJ: Cluster, nosieve loadpairdist CPPTRAJ: LowestCurve test -All 3 comparisons passed. - - - CPPTRAJ: Calc test with data sets + CPPTRAJ: Scale velocity test +g++ -o a.out main.o NameType.o CpptrajStdio.o ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise - - CPPTRAJ: Generate restraints (rst) test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent CPPTRAJ: Minimum Image test. + CPPTRAJ: Out of order molecules test + +All 1 comparisons passed. + + +All 2 comparisons passed. + + +All 2 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress - CPPTRAJ: Parmbox test - CPPTRAJ: Pairwise tests +All 1 comparisons passed. - CPPTRAJ: Test solvent command with closest CPPTRAJ: Linear regression test. -All 7 comparisons passed. +All 12 comparisons passed. - CPPTRAJ: Change chain ID test - CPPTRAJ: Adding PDB info to topology + CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. + CPPTRAJ: M-REMD, meltcurve analysis -All 4 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder + CPPTRAJ: Change chain ID test + CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test - CPPTRAJ: Distance-based atom mask tests (molecule) + CPPTRAJ: COORDS test storing frame metadata -All 1 comparisons passed. +All 5 comparisons passed. + +All 6 comparisons passed. - CPPTRAJ: Out of order molecules test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst + + CPPTRAJ: Pairwise tests + CPPTRAJ: Translate test +All 3 comparisons passed. -All 8 comparisons passed. +make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell + CPPTRAJ: Test solvent command with closest - CPPTRAJ: Replicate cell test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK + CPPTRAJ: Generate restraints (rst) test - CPPTRAJ: Scale dihedral force constant test +All 4 comparisons passed. - CPPTRAJ: Topology info with reference coords test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox - CPPTRAJ: Test math functions +All 17 comparisons passed. All 1 comparisons passed. - CPPTRAJ: Structure Check with Around - - CPPTRAJ: Phipsi test - -All 1 comparisons passed. + 'ZN' 'HA2' 'HA' 'HA' 'CT11' +Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' +Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' + CPPTRAJ: Parmbox test -All 1 comparisons passed. + Unit test passed. All 8 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_ReplicateCell - CPPTRAJ: CRD => TRR +All 2 comparisons passed. -All 10 comparisons passed. + CPPTRAJ: Scale dihedral force constant test -All 2 comparisons passed. + CPPTRAJ: Replicate cell test +All 6 comparisons passed. - CPPTRAJ: Change chain ID of COORDS set test -All 13 comparisons passed. +All 3 comparisons passed. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control - CPPTRAJ: Loop tests - -All 1 comparisons passed. - + CPPTRAJ: Phipsi test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine + CPPTRAJ: Loop tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats - CPPTRAJ: Scale dihedral force constant with 'useall' + CPPTRAJ: Command line trajectory args test, part 1 + CPPTRAJ: Infrared spectrum calculation test + + CPPTRAJ: Explicit pH REMD ensemble data read / sort ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff - CPPTRAJ: Explicit pH REMD ensemble data read / sort + CPPTRAJ: XtalSymm Reference -All 5 comparisons passed. + CPPTRAJ: Concatenate COORDS data set test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat +All 17 comparisons passed. - CPPTRAJ: Command line trajectory args test, part 1 -All 6 comparisons passed. +All 1 comparisons passed. All 1 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: Simple Hausdorff distance test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: XYZ format write - CPPTRAJ: Concatenate COORDS data set test - -All 3 comparisons passed. - +All 1 comparisons passed. - CPPTRAJ: Hbond with imaging -All 4 comparisons passed. +All 1 comparisons passed. -All 12 comparisons passed. +All 1 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time - - CPPTRAJ: Pairwise test, partial system - - CPPTRAJ: XtalSymm Reference +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords + CPPTRAJ: Add time to restart test -All 1 comparisons passed. + CPPTRAJ: SplitCoords test CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) - CPPTRAJ: Add time to restart test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords +All 1 comparisons passed. - CPPTRAJ: Pairdist test, nonorthogonal imaging. -All 3 comparisons passed. +All 1 comparisons passed. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope - CPPTRAJ: Finite difference test. - -All 1 comparisons passed. + CPPTRAJ: MW covariance matrix thermo analysis test + CPPTRAJ: Finite difference test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin - CPPTRAJ: SplitCoords test -g++ -o a.out main.o NameType.o CpptrajStdio.o -******************************************************************************** + CPPTRAJ: Command line test trajectory args test, part 2 - CPPTRAJ: Evalulate plateau test +All 8 comparisons passed. -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin - CPPTRAJ: MW covariance matrix thermo analysis test CPPTRAJ: Basic energy minimization test. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau + + CPPTRAJ: Evalulate plateau test +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft CPPTRAJ: Graft test -All 2 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Hbond, orthogonal imaging + CPPTRAJ: Randomize (overlap) - CPPTRAJ: Test set command + CPPTRAJ: Adding PDB info to topology + + CPPTRAJ: Hbond with imaging + + + CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. + CPPTRAJ: Pairwise test, partial system + + CPPTRAJ: TRR force/velocity read -> TRR write test + + CPPTRAJ: Test math functions + + + CPPTRAJ: Scale dihedral force constant with 'useall' + CPPTRAJ: Ewald test (NaCl crystal) + + CPPTRAJ: Grid generation from 'bounds' test. + + CPPTRAJ: Distance-based atom mask tests (molecule) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten - CPPTRAJ: Hausdorff distance of 2D rms output test. + CPPTRAJ: Non-orthogonal imaged distance + CPPTRAJ: Change chain ID of COORDS set test CPPTRAJ: Flatten test. - CPPTRAJ: Dihedral RMSD test (to previous) - CPPTRAJ: Command line test trajectory args test, part 2 -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random + CPPTRAJ: Hausdorff distance of 2D rms output test. All 1 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random - CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs -All 1 comparisons passed. + CPPTRAJ: Atom XYZ format read, test 1 + CPPTRAJ: TRAJ test storing frame metadata + CPPTRAJ: Remove time from restart test -All 17 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Remove time from restart test +All 2 comparisons passed. All 1 comparisons passed. @@ -3333,338 +3359,366 @@ All 2 comparisons passed. - CPPTRAJ: Constant pH stats test - CPPTRAJ: Atom XYZ format read, test 1 + CPPTRAJ: Test set command - CPPTRAJ: Energy minimization with angle term test. + CPPTRAJ: Dihedral RMSD test (to previous) + + CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs + +All 4 comparisons passed. All 1 comparisons passed. -All 6 comparisons passed. +All 3 comparisons passed. + + +All 3 comparisons passed. - CPPTRAJ: PCG32 RNG test. All 1 comparisons passed. All 2 comparisons passed. - CPPTRAJ: Dihedral RMS fluctuation test. +All 10 comparisons passed. -All 1 comparisons passed. +All 10 comparisons passed. - CPPTRAJ: TRR => CRD + +All 4 comparisons passed. + + + CPPTRAJ: PCG32 RNG test. + + CPPTRAJ: Ewald test (trunc. oct) CPPTRAJ: Add time to trajectory test - CPPTRAJ: Cluster, sieve5 loadpairdist -All 10 comparisons passed. + CPPTRAJ: Atom XYZ format read, test 2 + CPPTRAJ: Energy minimization with angle term test. + CPPTRAJ: Constant pH stats test -All 1 comparisons passed. + CPPTRAJ: Dihedral RMS fluctuation test. + CPPTRAJ: CRD => TRR CPPTRAJ: Command line wildcard test, part 1 - CPPTRAJ: Sorted implicit constant pH stats test + CPPTRAJ: Hbond, orthogonal imaging - CPPTRAJ: Test Stdlib RNG + CPPTRAJ: Hausdorff distance of 2D rms output test. -All 23 comparisons passed. +All 13 comparisons passed. - CPPTRAJ: Atom XYZ format read, test 2 +All 6 comparisons passed. - CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. All 5 comparisons passed. - CPPTRAJ: Test reading comma-separated list of strings +All 8 comparisons passed. - CPPTRAJ: Command line wildcard test, part 2 - CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats +All 5 comparisons passed. - CPPTRAJ: Hausdorff distance of 2D rms output test. - CPPTRAJ: Ewald test (NaCl crystal) -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' +All 23 comparisons passed. - CPPTRAJ: Atom XYZ format read, test 3 - CPPTRAJ: Test Mersenne Twister RNG - -All 8 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Cluster, nosieve pairwisecache none - 'ZN' 'HA2' 'HA' 'HA' 'CT11' -Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' -Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' +All 3 comparisons passed. - Unit test passed. + CPPTRAJ: TRR => CRD - CPPTRAJ: CRD(1-5) => TRR + CPPTRAJ: Test reading comma-separated list of strings -All 2 comparisons passed. + CPPTRAJ: Watershell Test, orthorhombic imaging. - CPPTRAJ: Test nested loops and variables in loops + CPPTRAJ: XtalSymm Reimaging by Atom -All 4 comparisons passed. + CPPTRAJ: Read specific columns test. + CPPTRAJ: Pairdist test, 2 masks. - CPPTRAJ: Ewald test (trunc. oct) + CPPTRAJ: Command line wildcard test, part 2 - CPPTRAJ: Unsorted pH read/write test + CPPTRAJ: Atom XYZ format read, test 3 + CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. + CPPTRAJ: Randomize (no restrictions) CPPTRAJ: Modify time info test. - CPPTRAJ: Energy minimization with nonbond term test. - CPPTRAJ: Atom XYZ format read, test 4 + CPPTRAJ: Test Stdlib RNG - CPPTRAJ: Randomize (overlap) + CPPTRAJ: Sorted implicit constant pH stats test All 4 comparisons passed. +All 2 comparisons passed. - CPPTRAJ: Read specific columns test. +All 4 comparisons passed. -All 16 comparisons passed. +All 5 comparisons passed. - CPPTRAJ: Test loop over data set blocks - CPPTRAJ: Atom XYZ format read, test 5 + CPPTRAJ: CRD(1-5) => TRR - CPPTRAJ: OpenMM basic energy minimization tests (bonds) + CPPTRAJ: Test nested loops and variables in loops - CPPTRAJ: Write non-square matrix + CPPTRAJ: Test Mersenne Twister RNG - CPPTRAJ: Test for filename wildcards and oversets + CPPTRAJ: Energy minimization with nonbond term test. - CPPTRAJ: CRD(6-10) => TRR - CPPTRAJ: Atom XYZ format read, test 6 - CPPTRAJ: Cluster, sieve5 pairwisecache none + CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats + CPPTRAJ: Atom XYZ format read, test 4 + CPPTRAJ: Ewald test (partial system, trunc. oct) -All 3 comparisons passed. + CPPTRAJ: Write non-square matrix +All 4 comparisons passed. - CPPTRAJ: Read non-square matrix + 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 6 comparisons passed. +All 4 comparisons passed. +2 comparisons skipped. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME - CPPTRAJ: OpenMM basic energy minimization tests (angles) + CPPTRAJ: Particle mesh Ewald test (NaCl crystal) -All 13 comparisons passed. +All 5 comparisons passed. - CPPTRAJ: Read square matrix + CPPTRAJ: Particle mesh Ewald test (trunc. oct) - CPPTRAJ: Randomize (no restrictions) - CPPTRAJ: TRR (appended) => CRD + CPPTRAJ: Watershell Test, no imaging. + CPPTRAJ: Unsorted pH read/write test - CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) + CPPTRAJ: Test loop over data set blocks - CPPTRAJ: Cluster, random + CPPTRAJ: Read non-square matrix -All 15 comparisons passed. + CPPTRAJ: Atom XYZ format read, test 5 + CPPTRAJ: OpenMM basic energy minimization tests (bonds) - CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) + CPPTRAJ: GIST test, orthogonal cell - CPPTRAJ: XtalSymm Reimaging by Atom + CPPTRAJ: CRD(6-10) => TRR -All 28 comparisons passed. + CPPTRAJ: OpenMM basic energy minimization tests (angles) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve +All 16 comparisons passed. - CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). -All 5 comparisons passed. +All 3 comparisons passed. - CPPTRAJ: Ewald test (partial system, trunc. oct) - CPPTRAJ: GMX: CRD with offset + CPPTRAJ: Test for filename wildcards and oversets + CPPTRAJ: Cluster, sieve5 savepairdist -All 1 comparisons passed. + CPPTRAJ: Read square matrix + CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) -All 4 comparisons passed. + CPPTRAJ: Atom XYZ format read, test 6 - CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). + CPPTRAJ: TRR (appended) => CRD +All 15 comparisons passed. - CPPTRAJ: GMX: TRR with offset - Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. - Skipped test: Ewald test (trunc. oct), 10 frames - Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. - Skipped test: Ewald test (ortho), 10 frames -All 4 comparisons passed. -2 comparisons skipped. +All 13 comparisons passed. - CPPTRAJ: Watershell Test, orthorhombic imaging. +All 6 comparisons passed. -All 4 comparisons passed. +g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME + CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) - CPPTRAJ: Particle mesh Ewald test (NaCl crystal) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet + CPPTRAJ: Particle mesh Ewald test (ortho) - CPPTRAJ: Clustering, One DataSet + CPPTRAJ: GMX: CRD with offset +make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' - CPPTRAJ: Particle mesh Ewald test (trunc. oct) + Unit test passed. + +make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' +make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' All 5 comparisons passed. - CPPTRAJ: Clustering, Two DataSets -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc - CPPTRAJ: Pairdist test, 2 masks. - - CPPTRAJ: XTC read test + CPPTRAJ: GMX: TRR with offset + CPPTRAJ: Particle mesh Ewald test (ortho, with mask) - CPPTRAJ: Clustering, dihedral DataSet + CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) - CPPTRAJ: Clustering, two dihedral DataSets +All 5 comparisons passed. -All 4 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc + CPPTRAJ: XTC read test - CPPTRAJ: Watershell Test, no imaging. + CPPTRAJ: PME test (partial system, trunc. oct) - CPPTRAJ: Clustering, dihedral DataSet, K-means + CPPTRAJ: Cluster, sieve5 loadpairdist - CPPTRAJ: CRD => XTC + CPPTRAJ: XtalSymm Reimaging by Molecule - CPPTRAJ: Clustering, two dihedral DataSets, K-means + CPPTRAJ: Cluster, nosieve pairwisecache none -All 8 comparisons passed. + CPPTRAJ: CRD => XTC + 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 +All 5 comparisons passed. +1 comparisons skipped. - CPPTRAJ: Particle mesh Ewald test (ortho) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LJ_PME - CPPTRAJ: DBSCAN test + CPPTRAJ: LJ PME test. CPPTRAJ: XTC => CRD -All 3 comparisons passed. + CPPTRAJ: LJ PME kappa sweep test, 0.25 + CPPTRAJ: Cluster, sieve5 pairwisecache none - CPPTRAJ: DBSCAN automatic parameter determination test. + CPPTRAJ: Cluster, random - CPPTRAJ: DBSCAN kdist map test + CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: CRD(1-5) => XTC - CPPTRAJ: DBSCAN with sieve - - CPPTRAJ: Particle mesh Ewald test (ortho, with mask) +All 28 comparisons passed. - CPPTRAJ: CRD(6-10) => XTC +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve -All 4 comparisons passed. + CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans + CPPTRAJ: LJ PME kappa sweep test, 0.45 - CPPTRAJ: Cpptraj Kmeans + CPPTRAJ: CRD(6-10) => XTC - CPPTRAJ: PME test (partial system, trunc. oct) + CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). CPPTRAJ: XTC (appended) => CRD - CPPTRAJ: Cpptraj Kmeans random - 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 + CPPTRAJ: LJ PME kappa sweep test, 0.5 -All 5 comparisons passed. -1 comparisons skipped. +All 4 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LJ_PME - - CPPTRAJ: LJ PME test. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet - CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) + CPPTRAJ: Clustering, One DataSet -All 6 comparisons passed. + CPPTRAJ: Clustering, Two DataSets + CPPTRAJ: LJ with switch function test CPPTRAJ: GMX: CRD with offset -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD - CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) + CPPTRAJ: Clustering, dihedral DataSet - CPPTRAJ: LJ PME kappa sweep test, 0.25 +All 5 comparisons passed. - CPPTRAJ: GIST test, orthogonal cell + + CPPTRAJ: Clustering, two dihedral DataSets + + CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: GMX: XTC with offset - CPPTRAJ: LJ PME kappa sweep test, 0.35 + CPPTRAJ: Clustering, two dihedral DataSets, K-means + +All 8 comparisons passed. + All 4 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN - CPPTRAJ: LJ PME kappa sweep test, 0.45 + CPPTRAJ: DBSCAN test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG +All 9 comparisons passed. + + CPPTRAJ: TNG read test -All 5 comparisons passed. + CPPTRAJ: DBSCAN automatic parameter determination test. + CPPTRAJ: DBSCAN kdist map test - CPPTRAJ: LJ PME kappa sweep test, 0.5 -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites + CPPTRAJ: DBSCAN with sieve - CPPTRAJ: XtalSymm Reimaging by Molecule +All 4 comparisons passed. - CPPTRAJ: Cluster command test, coordinate writes. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans - CPPTRAJ: LJ with switch function test + CPPTRAJ: Cpptraj Kmeans + + CPPTRAJ: GIST test, nonorthogonal cell CPPTRAJ: TNG read test (with offset) -All 5 comparisons passed. + CPPTRAJ: Cpptraj Kmeans random +All 6 comparisons passed. - CPPTRAJ: Cluster command test, coordinate writes using info file. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD + + CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) All 6 comparisons passed. +All 3 comparisons passed. + + All 5 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites + + CPPTRAJ: Cluster command test, coordinate writes. + + CPPTRAJ: Cluster command test, coordinate writes using info file. All 8 comparisons passed. @@ -3682,24 +3736,6 @@ All 2 comparisons passed. -g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' - - Unit test passed. - -make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' -make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' - -All 5 comparisons passed. - - -All 9 comparisons passed. - - -All 3 comparisons passed. - - - CPPTRAJ: GIST test, nonorthogonal cell All 11 comparisons passed. @@ -3719,7 +3755,7 @@ make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' /usr/bin/make -C test summary make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' --rwxr-xr-x 1 pbuilder1 pbuilder1 184920736 Oct 19 09:20 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 184920736 Nov 21 15:54 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. @@ -3731,14 +3767,14 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/cpptraj/ - make -j40 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no + make -j42 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' -Skipping bundled ARPACK build Skipping bundled READLINE build +Skipping bundled ARPACK build g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro @@ -3776,12 +3812,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1551618/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1551618/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/754418 and its subdirectories -I: Current time: Sat Oct 18 21:24:37 -12 2025 -I: pbuilder-time-stamp: 1760865877 +I: removing directory /srv/workspace/pbuilder/1551618 and its subdirectories +I: Current time: Sun Nov 22 05:55:07 +14 2026 +I: pbuilder-time-stamp: 1795276507