From owner-freebsd-pkg-fallout@freebsd.org Tue May 5 16:13:55 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 EB34413B4B1 for ; Tue, 5 May 2020 16:13:55 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id 49GlCR6CW6z4BVw for ; Tue, 5 May 2020 16:13:55 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id D517D13B4B0; Tue, 5 May 2020 16:13:55 +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 D4D4E13B4AF for ; Tue, 5 May 2020 16:13:55 +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) server-signature RSA-PSS (4096 bits) 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 49GlCR5lRpz4BVv; Tue, 5 May 2020 16:13:55 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy10.nyi.freebsd.org (beefy10.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:ed]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id C05D318AC3; Tue, 5 May 2020 16:13:55 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy10.nyi.freebsd.org (localhost [127.0.0.1]) by beefy10.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id 045GDt92095593; Tue, 5 May 2020 16:13:55 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy10.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 045GDtwL095592; Tue, 5 May 2020 16:13:55 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 5 May 2020 16:13:55 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202005051613.045GDtwL095592@beefy10.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - 113i386-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: 2.1.30 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 05 May 2020 16:13:56 -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: yuri@FreeBSD.org Ident: $FreeBSD: head/science/plumed/Makefile 533981 2020-05-04 19:55:51Z yuri $ Log URL: http://beefy10.nyi.freebsd.org/data/113i386-default/534000/logs/plumed-2.6.0.log Build URL: http://beefy10.nyi.freebsd.org/build.html?mastername=113i386-default&build=534000 Log: =>> Building science/plumed build started at Tue May 5 15:58:12 UTC 2020 port directory: /usr/ports/science/plumed package name: plumed-2.6.0 building for: FreeBSD 113i386-default-job-07 11.3-RELEASE-p8 FreeBSD 11.3-RELEASE-p8 i386 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/science/plumed/Makefile 533981 2020-05-04 19:55:51Z yuri $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300089 Jail OSVERSION: 1103000 Job Id: 07 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1103000 UNAME_v=FreeBSD 11.3-RELEASE-p8 UNAME_r=11.3-RELEASE-p8 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/113i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/113i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=113i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/113i386-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=11.3 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 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: i386-unknown-freebsd11.3 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: i386-unknown-freebsd11.3 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 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: i386-unknown-freebsd11.3 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=11.3-RELEASE-p8 OSREL=11.3 OSVERSION=1103000 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 [113i386-default-job-07] Installing pkg-1.14.4... [113i386-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 =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL3 accepted by the user => plumed-plumed2-v2.6.0_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/plumed/plumed2/tar.gz/v2.6.0?dummy=/plumed-plumed2-v2.6.0_GH0.tar.gz fetch: https://codeload.github.com/plumed/plumed2/tar.gz/v2.6.0?dummy=/plumed-plumed2-v2.6.0_GH0.tar.gz: size unknown fetch: https://codeload.github.com/plumed/plumed2/tar.gz/v2.6.0?dummy=/plumed-plumed2-v2.6.0_GH0.tar.gz: size of remote file is not known plumed-plumed2-v2.6.0_GH0.tar.gz 71 MB 5183 kBps 14s ===> 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 ===> Cleanly applied FreeBSD patch(es) patch-configure.ac =========================================================================== =================================================== ===> plumed-2.6.0 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.0.17.txz [113i386-default-job-07] Installing bash-5.0.17... [113i386-default-job-07] `-- Installing gettext-runtime-0.20.2... [113i386-default-job-07] | `-- Installing indexinfo-0.3.1... [113i386-default-job-07] | `-- Extracting indexinfo-0.3.1: .... done [113i386-default-job-07] `-- Extracting gettext-runtime-0.20.2: .......... done [113i386-default-job-07] Extracting bash-5.0.17: .......... done ===> plumed-2.6.0 depends on executable: bash - found compiling VolumeCavity.cpp compiling CoordinationNumbers.cpp compiling DistanceFromContour.cpp compiling Angles.cpp compiling AtomValuePack.cpp compiling CatomPack.cpp compiling CenterOfMultiColvar.cpp compiling InPlaneDistances.cpp compiling XAngle.cpp compiling VolumeBetweenContours.cpp compiling VolumeInSphere.cpp compiling AlphaBeta.cpp compiling Torsions.cpp compiling BridgedMultiColvarFunction.cpp compiling MultiColvarBase.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/multicolvar' gmake -C ../reference obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/reference' compiling NormalizedEuclideanDistance.cpp compiling DotProductDistance.cpp compiling ReferenceAtoms.cpp compiling MetricRegister.cpp compiling OptimalRMSD.cpp compiling ReferenceArguments.cpp compiling SingleDomainRMSD.cpp compiling ReferenceValuePack.cpp compiling RMSDBase.cpp compiling SimpleRMSD.cpp compiling MultiDomainRMSD.cpp compiling IntermolecularDRMSD.cpp compiling ArgumentOnlyDistance.cpp compiling MahalanobisDistance.cpp compiling DRMSD.cpp compiling EuclideanDistance.cpp compiling ReferenceConfiguration.cpp compiling Direction.cpp compiling IntramolecularDRMSD.cpp compiling FakeFrame.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/reference' gmake -C ../secondarystructure obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/secondarystructure' compiling SecondaryStructureRMSD.cpp compiling AlphaRMSD.cpp compiling AntibetaRMSD.cpp compiling ParabetaRMSD.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/secondarystructure' gmake -C ../setup obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/setup' compiling Load.cpp compiling MolInfo.cpp compiling Restart.cpp compiling Units.cpp gmake[7]: Leaving directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/setup' gmake -C ../tools obj gmake[7]: Entering directory '/wrkdirs/usr/ports/science/plumed/work/plumed2-2.6.0/src/tools' compiling DynamicList.cpp compiling Exception.cpp compiling SwitchingFunction.cpp compiling Angle.cpp compiling Vector.cpp compiling Communicator.cpp compiling Pbc.cpp compiling AtomNumber.cpp compiling Keywords.cpp compiling OFile.cpp compiling PlumedHandle.cpp compiling MolDataClass.cpp compiling Subprocess.cpp compiling Torsion.cpp compiling Log.cpp compiling RootFindingBase.cpp compiling Citations.cpp compiling Matrix.cpp compiling Brent1DRootSearch.cpp compiling FileBase.cpp compiling DLLoader.cpp compiling KernelFunctions.cpp compiling LatticeReduction.cpp compiling ConjugateGradient.cpp compiling PDB.cpp compiling Minimise1DBrent.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 h36.cpp compiling Random.cpp compiling OpenMP.cpp compiling Tools.cpp compiling LinkCells.cpp compiling MinimiseBase.cpp compiling BiasRepresentation.cpp compiling ERMSD.cpp compiling Units.cpp compiling MatrixSquareBracketsAccess.cpp compiling Grid.cpp compiling ForwardDecl.cpp compiling MultiValue.cpp compiling LoopUnroller.cpp compiling Stopwatch.cpp compiling IFile.cpp compiling NeighborList.cpp compiling HistogramBead.cpp compiling Tensor.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 Center.cpp compiling ActionWithVirtualAtom.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 Highest.cpp compiling VesselRegister.cpp compiling Sum.cpp compiling ActionWithInputVessel.cpp compiling AveragingVessel.cpp compiling ActionWithAveraging.cpp compiling ValueVessel.cpp compiling Histogram.cpp compiling MoreThan.cpp compiling Min.cpp compiling ShortcutVessel.cpp compiling OrderingVessel.cpp compiling Between.cpp compiling BridgeVessel.cpp compiling Max.cpp compiling StoreDataVessel.cpp compiling AltMin.cpp compiling Moments.cpp compiling Mean.cpp compiling ActionWithVessel.cpp compiling Lowest.cpp compiling FunctionVessel.cpp compiling Vessel.cpp compiling LessThan.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 ./colvar/CoordinationBase.o: In function `.omp_outlined.': CoordinationBase.cpp:(.text+0x2191): undefined reference to `__atomic_load' ./colvar/EEFSolv.o: In function `.omp_outlined.': EEFSolv.cpp:(.text+0x3b64): undefined reference to `__atomic_load' ./generic/EffectiveEnergyDrift.o: In function `.omp_outlined..27': EffectiveEnergyDrift.cpp:(.text+0x3ed3): undefined reference to `__atomic_load' ./isdb/Metainference.o: In function `.omp_outlined.': Metainference.cpp:(.text+0x16ed9): undefined reference to `__atomic_load' ./isdb/Metainference.o: In function `.omp_outlined..188': Metainference.cpp:(.text+0x17383): undefined reference to `__atomic_load' ./isdb/Metainference.o:Metainference.cpp:(.text+0x1788e): more undefined references to `__atomic_load' follow 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