From owner-freebsd-pkg-fallout@freebsd.org Sat May 23 16:40:06 2020 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 16F962CF84D for ; Sat, 23 May 2020 16:40:06 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (mailman.nyi.freebsd.org [IPv6:2610:1c1:1:606c::50:13]) by mx1.freebsd.org (Postfix) with ESMTP id 49TpxL06hhz4Gjf for ; Sat, 23 May 2020 16:40:06 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 023442CF6F9; Sat, 23 May 2020 16:40:06 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 01F7A2CF6F8 for ; Sat, 23 May 2020 16:40:06 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 49TpxK6kTyz4H4r; Sat, 23 May 2020 16:40:05 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy5.nyi.freebsd.org (beefy5.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:e8]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id DDE1712C1B; Sat, 23 May 2020 16:40:05 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy5.nyi.freebsd.org (localhost [127.0.0.1]) by beefy5.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id 04NGe5I5030145; Sat, 23 May 2020 16:40:05 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy5.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 04NGe5s9030144; Sat, 23 May 2020 16:40:05 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 23 May 2020 16:40:05 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202005231640.04NGe5s9030144@beefy5.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - 121i386-default][science/plumed] Failed for plumed-2.6.0 in build Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 23 May 2020 16:40:06 -0000 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@FreeBSD.org Last committer: linimon@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/536258/logs/plumed-2.6.0.log Build URL: http://beefy5.nyi.freebsd.org/build.html?mastername=121i386-default&build=536258 Log: =>> Building science/plumed build started at Sat May 23 16:17:48 UTC 2020 port directory: /usr/ports/science/plumed package name: plumed-2.6.0 building for: FreeBSD 121i386-default-job-02 12.1-RELEASE-p5 FreeBSD 12.1-RELEASE-p5 i386 maintained by: yuri@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: 02 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1201000 UNAME_v=FreeBSD 12.1-RELEASE-p5 UNAME_r=12.1-RELEASE-p5 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@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-p5 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-- =================================================== ===> License LGPL3 accepted by the user =========================================================================== =================================================== ===> 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-02] Installing pkg-1.14.4... [121i386-default-job-02] 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 =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by plumed-2.6.0 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for plumed-2.6.0 ===> Applying FreeBSD patches for plumed-2.6.0 from /usr/ports/science/plumed/files =========================================================================== =================================================== ===> plumed-2.6.0 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.0.17.txz [121i386-default-job-02] Installing bash-5.0.17... [121i386-default-job-02] `-- Installing gettext-runtime-0.20.2... [121i386-default-job-02] | `-- Installing indexinfo-0.3.1... [121i386-default-job-02] | `-- Extracting indexinfo-0.3.1: .... done [121i386-default-job-02] `-- Extracting gettext-runtime-0.20.2: .......... done [121i386-default-job-02] 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-02] Installing vim-console-8.2.0491_1... [121i386-default-job-02] Extracting vim-console-8.2.0491_1: .......... done ===> plumed-2.6.0 depends on executable: xxd - found 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 & 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 & 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 & 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,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 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 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