+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb2/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb2/work.log ===> Building for plumed-2.8.0nb2 /opt/pkg/bin/gmake lib gmake[1]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0' /opt/pkg/bin/gmake -C src gmake[2]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src' /opt/pkg/bin/gmake -C lib gmake[3]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' /opt/pkg/bin/gmake dirslinks gmake[4]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' *** Updating links to used modules in all directories *** /opt/pkg/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links gmake[5]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' /opt/pkg/bin/gmake -C ../analysis links /opt/pkg/bin/gmake -C ../asmjit links /opt/pkg/bin/gmake -C ../bias links /opt/pkg/bin/gmake -C ../blas links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas' gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis' /opt/pkg/bin/gmake -C ../cltools links Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit' /opt/pkg/bin/gmake -C ../colvar links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias' /opt/pkg/bin/gmake -C ../config links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/config' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar Nothing to do in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/config gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/config' /opt/pkg/bin/gmake -C ../core links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/core' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/core gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools' /opt/pkg/bin/gmake -C ../function links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/function' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/function gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar' /opt/pkg/bin/gmake -C ../generic links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/core' /opt/pkg/bin/gmake -C ../gridtools links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/generic' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis' /opt/pkg/bin/gmake -C ../isdb links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/gridtools' gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/isdb' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/gridtools Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/generic Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/isdb gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/function' /opt/pkg/bin/gmake -C ../lapack links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack' /opt/pkg/bin/gmake -C ../lepton links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lepton' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lepton gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/generic' /opt/pkg/bin/gmake -C ../main links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/gridtools' /opt/pkg/bin/gmake -C ../mapping links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/mapping' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lepton' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/mapping /opt/pkg/bin/gmake -C ../molfile links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile' /opt/pkg/bin/gmake -C ../multicolvar links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main' /opt/pkg/bin/gmake -C ../reference links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/reference' gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/reference gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/isdb' /opt/pkg/bin/gmake -C ../secondarystructure links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/secondarystructure' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/secondarystructure gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/reference' /opt/pkg/bin/gmake -C ../setup links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/mapping' /opt/pkg/bin/gmake -C ../tools links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/setup' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/setup gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar' /opt/pkg/bin/gmake -C ../vatom links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vatom' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vatom gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/tools' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/secondarystructure' /opt/pkg/bin/gmake -C ../vesselbase links Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/tools gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vesselbase' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vesselbase gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/setup' /opt/pkg/bin/gmake -C ../wrapper links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/wrapper' Nothing to do in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/wrapper gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/wrapper' /opt/pkg/bin/gmake -C ../xdrfile links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vatom' gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/xdrfile' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/xdrfile gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/xdrfile' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/tools' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vesselbase' gmake[5]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' gmake[4]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' /opt/pkg/bin/gmake dirs gmake[4]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' *** Compiling all directories *** /opt/pkg/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile gmake[5]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' /opt/pkg/bin/gmake -C ../analysis obj /opt/pkg/bin/gmake -C ../asmjit obj /opt/pkg/bin/gmake -C ../bias obj /opt/pkg/bin/gmake -C ../blas obj gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas' compiling blas.cpp gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias' compiling ABMD.cpp gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit' gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis' compiling arch.cpp compiling AnalysisBase.cpp gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas' compiling assembler.cpp compiling codebuilder.cpp compiling codecompiler.cpp compiling Bias.cpp compiling codeemitter.cpp /opt/pkg/bin/gmake -C ../cltools obj gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools' compiling Average.cpp compiling CLTool.cpp compiling codeholder.cpp compiling BiasValue.cpp compiling constpool.cpp { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| ../maketools/xxd > completion.xxd ../../scripts/selector.sh: line 219: python: command not found compiling Driver.cpp compiling cpuinfo.cpp In file included from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38: xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37: xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | In file included from xdrfile/xdrfile_xtc.h:1, from Driver.cpp:39: xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | compiling func.cpp compiling ExtendedLagrangian.cpp compiling DriverDouble.cpp compiling AverageVessel.cpp In file included from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38, from DriverDouble.cpp:23: xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37: xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | In file included from xdrfile/xdrfile_xtc.h:1, from Driver.cpp:39: xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | compiling Committor.cpp compiling External.cpp compiling globals.cpp compiling inst.cpp compiling LWalls.cpp compiling DataCollectionObject.cpp compiling logging.cpp compiling DriverFloat.cpp compiling operand.cpp In file included from xdrfile/xdrfile_trr.h:1, from Driver.cpp:38, from DriverFloat.cpp:23: xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37: xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | In file included from xdrfile/xdrfile_xtc.h:1, from Driver.cpp:39: xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | compiling osutils.cpp compiling EuclideanDissimilarityMatrix.cpp compiling regalloc.cpp compiling MaxEnt.cpp compiling runtime.cpp compiling string.cpp compiling utils.cpp compiling vmem.cpp compiling FarthestPointSampling.cpp vmem.cpp:284:13: warning: 'bool PLMD::asmjit::vMemMgrCheckTree(VMemMgr*)' defined but not used [-Wunused-function] 284 | static bool vMemMgrCheckTree(VMemMgr* self) noexcept { | ^~~~~~~~~~~~~~~~ vmem.cpp: In member function 'PLMD::asmjit::Error PLMD::asmjit::VMemMgr::release(void*)': vmem.cpp:883:1: warning: dangling pointer 'q' to 'head' may be used [-Wdangling-pointer=] 883 | } | ^ vmem.cpp:420:10: note: 'head' declared here 420 | RbNode head = { { nullptr, nullptr }, 0, 0 }; | ^~~~ compiling x86assembler.cpp compiling MetaD.cpp compiling GenExample.cpp compiling Histogram.cpp MetaD.cpp: In constructor 'PLMD::bias::MetaD::MetaD(const PLMD::ActionOptions&)': MetaD.cpp:1232:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 1232 | if(result!=0&&result!=mpi_nw_) error("in this WALKERS_MPI run some replica have restarted from GRID while other do not!"); | ~~~~~~^~~~~~~~~ MetaD.cpp:1297:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 1297 | if(result!=0&&result!=mpi_nw_) error("in this WALKERS_MPI run some replica have restarted from FILE while other do not!"); | ~~~~~~^~~~~~~~~ compiling GenTemplate.cpp compiling Info.cpp compiling x86builder.cpp compiling LandmarkSelectionBase.cpp compiling Manual.cpp compiling LandmarkStaged.cpp compiling PdbRenumber.cpp LandmarkStaged.cpp: In member function 'virtual void PLMD::analysis::LandmarkStaged::selectLandmarks()': LandmarkStaged.cpp:69:42: error: call of overloaded 'sqrt(unsigned int)' is ambiguous 69 | unsigned int m = static_cast( sqrt(n*N) ); | ~~~~^~~~~ In file included from /usr/include/math.h:35, from /opt/tools/gcc13/include/c++/13.3.0/bits/std_abs.h:40, from /opt/tools/gcc13/include/c++/13.3.0/cstdlib:81, from /opt/tools/gcc13/include/c++/13.3.0/ext/string_conversions.h:43, from /opt/tools/gcc13/include/c++/13.3.0/bits/basic_string.h:4109, from /opt/tools/gcc13/include/c++/13.3.0/string:54, from core/../../core/Action.h:25, from core/../../core/ActionPilot.h:25, from core/ActionPilot.h:1, from AnalysisBase.h:25, from LandmarkSelectionBase.h:25, from LandmarkStaged.cpp:22: /usr/include/iso/math_iso.h:232:28: note: candidate: 'long double std::sqrt(long double)' 232 | inline long double sqrt(long double __X) { return __sqrtl(__X); } | ^~~~ /usr/include/iso/math_iso.h:183:22: note: candidate: 'float std::sqrt(float)' 183 | inline float sqrt(float __X) { return __sqrtf(__X); } | ^~~~ /usr/include/iso/math_iso.h:77:15: note: candidate: 'double std::sqrt(double)' 77 | extern double sqrt(double); | ^~~~ gmake[6]: *** [../maketools/make.rules:21: LandmarkStaged.o] Error 1 gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis' gmake[5]: *** [Makefile:426: ../analysis] Error 2 gmake[5]: *** Waiting for unfinished jobs.... compiling MovingRestraint.cpp compiling x86compiler.cpp compiling SimpleMD.cpp compiling PBMetaD.cpp compiling Restraint.cpp compiling SumHills.cpp compiling ReweightBase.cpp compiling x86inst.cpp compiling x86instimpl.cpp compiling ReweightBias.cpp compiling x86internal.cpp compiling kT.cpp compiling ReweightMetad.cpp compiling ReweightTemperaturePressure.cpp compiling pesmd.cpp compiling ReweightWham.cpp compiling UWalls.cpp compiling Completion.cpp compiling x86logging.cpp compiling x86operand.cpp gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools' compiling x86operand_regs.cpp compiling x86regalloc.cpp compiling zone.cpp gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias' zone.cpp:223:13: warning: 'bool PLMD::asmjit::ZoneHeap_hasDynamicBlock(ZoneHeap*, ZoneHeap::DynamicBlock*)' defined but not used [-Wunused-function] 223 | static bool ZoneHeap_hasDynamicBlock(ZoneHeap* self, ZoneHeap::DynamicBlock* block) noexcept { | ^~~~~~~~~~~~~~~~~~~~~~~~ gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit' gmake[5]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' gmake[4]: *** [Makefile:128: dirs] Error 2 gmake[4]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' gmake[3]: *** [Makefile:111: all] Error 2 gmake[3]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' gmake[2]: *** [Makefile:8: lib] Error 2 gmake[2]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src' gmake[1]: *** [Makefile:32: lib] Error 2 gmake[1]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0' gmake: *** [Makefile:21: all] Error 2 *** Error code 2 Stop. bmake[1]: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed *** Error code 1 Stop. bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed