[package - 121i386-default][science/plumed] Failed for plumed-2.6.0 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue May 12 15:05:46 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri at FreeBSD.org
Last committer: linimon at FreeBSD.org
Ident: $FreeBSD: head/science/plumed/Makefile 534167 2020-05-06 12:00:53Z linimon $
Log URL: http://beefy5.nyi.freebsd.org/data/121i386-default/534969/logs/plumed-2.6.0.log
Build URL: http://beefy5.nyi.freebsd.org/build.html?mastername=121i386-default&build=534969
Log:
=>> Building science/plumed
build started at Tue May 12 14:46:02 UTC 2020
port directory: /usr/ports/science/plumed
package name: plumed-2.6.0
building for: FreeBSD 121i386-default-job-07 12.1-RELEASE-p4 FreeBSD 12.1-RELEASE-p4 i386
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/science/plumed/Makefile 534167 2020-05-06 12:00:53Z linimon $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300089
Jail OSVERSION: 1201000
Job Id: 07
---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1201000
UNAME_v=FreeBSD 12.1-RELEASE-p4
UNAME_r=12.1-RELEASE-p4
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-5-gc81843e5
MASTERMNT=/usr/local/poudriere/data/.m/121i386-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/121i386-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=121i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/121i386-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
yuri at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--enable-shared --disable-python --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/science/plumed/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/plumed/work HOME=/wrkdirs/usr/ports/science/plumed/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/plumed/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/science/plumed/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/plumed/work HOME=/wrkdirs/usr/ports/science/plumed/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/plumed/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
OSREL=12.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/plumed" EXAMPLESDIR="share/examples/plumed" DATADIR="share/plumed" WWWDIR="www/plumed" ETCDIR="etc/plumed"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/plumed DOCSDIR=/usr/local/share/doc/plumed EXAMPLESDIR=/usr/local/share/examples/plumed WWWDIR=/usr/local/www/plumed ETCDIR=/usr/local/etc/plumed
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: i386-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: i386-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: i386-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=12.1-RELEASE-p4
OSREL=12.1
OSVERSION=1201000
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 1024
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===> License LGPL3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> plumed-2.6.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.4.txz
[121i386-default-job-07] Installing pkg-1.14.4...
[121i386-default-job-07] Extracting pkg-1.14.4: .......... done
===> plumed-2.6.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of plumed-2.6.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by plumed-2.6.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by plumed-2.6.0 for building
=> SHA256 Checksum OK for plumed-plumed2-v2.6.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by plumed-2.6.0 for building
===> Extracting for plumed-2.6.0
=> SHA256 Checksum OK for plumed-plumed2-v2.6.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for plumed-2.6.0
===> Applying FreeBSD patches for plumed-2.6.0
===> Cleanly applied FreeBSD patch(es) patch-configure.ac
===========================================================================
=======================<phase: build-depends >============================
===> plumed-2.6.0 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.0.17.txz
[121i386-default-job-07] Installing bash-5.0.17...
[121i386-default-job-07] `-- Installing gettext-runtime-0.20.2...
[121i386-default-job-07] | `-- Installing indexinfo-0.3.1...
[121i386-default-job-07] | `-- Extracting indexinfo-0.3.1: .... done
[121i386-default-job-07] `-- Extracting gettext-runtime-0.20.2: .......... done
[121i386-default-job-07] Extracting bash-5.0.17: .......... done
===> plumed-2.6.0 depends on executable: bash - found
===> Returning to build of plumed-2.6.0
===> plumed-2.6.0 depends on executable: xxd - not found
===> Installing existing package /packages/All/vim-console-8.2.0491_1.txz
[121i386-default-job-07] Installing vim-console-8.2.0491_1...
[121i386-default-job-07] Extracting vim-console-8.2.0491_1: .......... done
<snip>
compiling ERMSD.cpp
compiling Exception.cpp
compiling FileBase.cpp
compiling ForwardDecl.cpp
compiling Grid.cpp
compiling HistogramBead.cpp
compiling IFile.cpp
compiling KernelFunctions.cpp
compiling Keywords.cpp
compiling LatticeReduction.cpp
compiling LinkCells.cpp
compiling Log.cpp
compiling LoopUnroller.cpp
compiling Matrix.cpp
compiling MatrixSquareBracketsAccess.cpp
compiling Minimise1DBrent.cpp
compiling MinimiseBase.cpp
compiling MolDataClass.cpp
compiling MultiValue.cpp
compiling NeighborList.cpp
compiling OFile.cpp
compiling OpenMP.cpp
compiling PDB.cpp
compiling Pbc.cpp
compiling PlumedHandle.cpp
compiling RMSD.cpp
RMSD.cpp:93:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSD::setReference(const vector<Vector> & reference) {
^
RMSD.cpp:112:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSD::setAlign(const vector<double> & align, bool normalize_weights, bool remove_center) {
^
RMSD.cpp:112:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
RMSD.cpp:147:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSD::setDisplace(const vector<double> & displace, bool normalize_weights) {
^
RMSD.cpp:147:12: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
RMSD.cpp:958:20: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSDCoreData::doCoreCalc(bool safe,bool alEqDis, bool only_rotation) {
^
RMSD.cpp:1106:22: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
double RMSDCoreData::getDistance( bool squared) {
^
RMSD.cpp:1134:20: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void RMSDCoreData::doCoreCalcWithCloseStructure(bool safe,bool alEqDis, Tensor & rotationPosClose, Tensor & rotationRefClose, std::array<std::array<Tensor,3>,3> & drotationPosCloseDrr01) {
^
RMSD.cpp:1169:35: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
std::vector<Vector> RMSDCoreData::getDDistanceDPositions() {
^
RMSD.cpp:1205:36: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
std::vector<Vector> RMSDCoreData::getDDistanceDReference() {
^
10 warnings generated.
compiling Random.cpp
compiling RootFindingBase.cpp
compiling Stopwatch.cpp
compiling Subprocess.cpp
compiling SwitchingFunction.cpp
compiling Tensor.cpp
compiling Tools.cpp
compiling Torsion.cpp
compiling Units.cpp
compiling Vector.cpp
compiling h36.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/tools'
gmake -C ../vatom obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vatom'
compiling ActionWithVirtualAtom.cpp
compiling Center.cpp
compiling FixedAtom.cpp
compiling Ghost.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vatom'
gmake -C ../vesselbase obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vesselbase'
compiling ActionWithAveraging.cpp
compiling ActionWithInputVessel.cpp
compiling ActionWithVessel.cpp
compiling AltMin.cpp
compiling AveragingVessel.cpp
compiling Between.cpp
compiling BridgeVessel.cpp
compiling FunctionVessel.cpp
compiling Highest.cpp
compiling Histogram.cpp
compiling LessThan.cpp
compiling Lowest.cpp
compiling Max.cpp
compiling Mean.cpp
compiling Min.cpp
compiling Moments.cpp
compiling MoreThan.cpp
compiling OrderingVessel.cpp
compiling ShortcutVessel.cpp
compiling StoreDataVessel.cpp
compiling Sum.cpp
compiling ValueVessel.cpp
compiling Vessel.cpp
compiling VesselRegister.cpp
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/vesselbase'
gmake -C ../wrapper obj
gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/wrapper'
compiling PlumedStatic.cpp
compiling Plumed.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/wrapper'
gmake[6]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
gmake lib
gmake[5]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/ope
rand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.
o ../cltools/kT.o ../cltools/pesmd.o ../colv!
ar/Angle..o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/Exchan
gePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/Actio
nWithInputGrid.o ../gridtools/ActionWithInte!
gral.o ../!
gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ..
/mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../mul
ticolvar/MultiColvarFilter.o ../multicolvar/!
MultiColv!
arProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/Sim
pleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.
o ../tools/PlumedHandle.o ../tools/RMSD.o ..!
/tools/Ra!
ndom.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o ../wrapper/PlumedStatic.o -o
plumed-static -ldl -lstdc++ -lz -ldl -fstack-protector-strong -rdynamic -Wl,-Bsymbolic -fopenmp
ld: error: undefined symbol: __atomic_load
>>> referenced by CoordinationBase.cpp
>>> ../colvar/CoordinationBase.o:(.omp_outlined.)
ld: error: undefined symbol: __atomic_load
>>> referenced by EEFSolv.cpp
>>> ../colvar/EEFSolv.o:(.omp_outlined.)
ld: error: undefined symbol: __atomic_load
>>> referenced by EffectiveEnergyDrift.cpp
>>> ../generic/EffectiveEnergyDrift.o:(.omp_outlined..27)
ld: error: undefined symbol: __atomic_load
>>> referenced by Metainference.cpp
>>> ../isdb/Metainference.o:(.omp_outlined.)
ld: error: undefined symbol: __atomic_load
>>> referenced by Metainference.cpp
>>> ../isdb/Metainference.o:(.omp_outlined..188)
ld: error: undefined symbol: __atomic_load
>>> referenced by Metainference.cpp
>>> ../isdb/Metainference.o:(.omp_outlined..190)
ld: error: undefined symbol: __atomic_load
>>> referenced by Metainference.cpp
>>> ../isdb/Metainference.o:(.omp_outlined..192)
ld: error: undefined symbol: __atomic_load
>>> referenced by Metainference.cpp
>>> ../isdb/Metainference.o:(.omp_outlined..194)
ld: error: undefined symbol: __atomic_load
>>> referenced by Metainference.cpp
>>> ../isdb/Metainference.o:(.omp_outlined..198)
ld: error: undefined symbol: __atomic_load
>>> referenced by Metainference.cpp
>>> ../isdb/Metainference.o:(.omp_outlined..200)
ld: error: undefined symbol: __atomic_load
>>> referenced by Metainference.cpp
>>> ../isdb/Metainference.o:(.omp_outlined..202)
ld: error: undefined symbol: __atomic_load
>>> referenced by MetainferenceBase.cpp
>>> ../isdb/MetainferenceBase.o:(.omp_outlined.)
ld: error: undefined symbol: __atomic_load
>>> referenced by MetainferenceBase.cpp
>>> ../isdb/MetainferenceBase.o:(.omp_outlined..186)
ld: error: undefined symbol: __atomic_load
>>> referenced by MetainferenceBase.cpp
>>> ../isdb/MetainferenceBase.o:(.omp_outlined..188)
ld: error: undefined symbol: __atomic_load
>>> referenced by MetainferenceBase.cpp
>>> ../isdb/MetainferenceBase.o:(.omp_outlined..190)
ld: error: undefined symbol: __atomic_load
>>> referenced by MetainferenceBase.cpp
>>> ../isdb/MetainferenceBase.o:(.omp_outlined..192)
ld: error: undefined symbol: __atomic_load
>>> referenced by MetainferenceBase.cpp
>>> ../isdb/MetainferenceBase.o:(.omp_outlined..196)
ld: error: undefined symbol: __atomic_load
>>> referenced by MetainferenceBase.cpp
>>> ../isdb/MetainferenceBase.o:(.omp_outlined..198)
ld: error: undefined symbol: __atomic_load
>>> referenced by MetainferenceBase.cpp
>>> ../isdb/MetainferenceBase.o:(.omp_outlined..200)
c++: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[5]: *** [Makefile:484: plumed-static] Error 1
gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
gmake[4]: *** [Makefile:112: all] Error 2
gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/lib'
gmake[3]: *** [Makefile:8: lib] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src'
gmake[2]: *** [Makefile:32: lib] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0'
gmake[1]: *** [Makefile:21: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0'
*** Error code 1
Stop.
make: stopped in /usr/ports/science/plumed
More information about the freebsd-pkg-fallout
mailing list