+ 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]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis' gmake[6]: Leaving 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/bias /opt/pkg/bin/gmake -C ../cltools links 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/asmjit' 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/cltools' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar' Verify modules and create links in /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' 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/colvar' /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/cltools' /opt/pkg/bin/gmake -C ../generic links gmake[6]: Entering directory '/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/generic 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/gridtools' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/gridtools 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/isdb' 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/generic' /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/gridtools' /opt/pkg/bin/gmake -C ../main links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack' /opt/pkg/bin/gmake -C ../mapping links 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' Verify modules and create links in /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' /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/main' /opt/pkg/bin/gmake -C ../multicolvar links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile' /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/reference Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar 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]: 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/mapping' /opt/pkg/bin/gmake -C ../tools links 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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/setup' /opt/pkg/bin/gmake -C ../vesselbase 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' 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/secondarystructure' /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]: 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/vatom' 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/analysis' compiling AnalysisBase.cpp gmake[6]: Entering directory '/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' compiling ABMD.cpp compiling arch.cpp gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas' /opt/pkg/bin/gmake -C ../cltools obj gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools' compiling CLTool.cpp compiling assembler.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 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 codebuilder.cpp compiling Average.cpp compiling codecompiler.cpp compiling Bias.cpp compiling DriverDouble.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 codeemitter.cpp compiling BiasValue.cpp compiling codeholder.cpp compiling constpool.cpp compiling AverageVessel.cpp compiling cpuinfo.cpp compiling ExtendedLagrangian.cpp compiling func.cpp compiling Committor.cpp compiling DriverFloat.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 External.cpp compiling DataCollectionObject.cpp compiling globals.cpp compiling LWalls.cpp compiling EuclideanDissimilarityMatrix.cpp compiling inst.cpp compiling logging.cpp compiling operand.cpp compiling osutils.cpp compiling MaxEnt.cpp compiling regalloc.cpp compiling GenExample.cpp compiling runtime.cpp compiling FarthestPointSampling.cpp compiling string.cpp compiling utils.cpp compiling vmem.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 Histogram.cpp compiling MetaD.cpp compiling GenTemplate.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 Info.cpp compiling Manual.cpp compiling LandmarkSelectionBase.cpp compiling PdbRenumber.cpp compiling x86builder.cpp compiling LandmarkStaged.cpp compiling SimpleMD.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 SumHills.cpp compiling kT.cpp compiling x86compiler.cpp compiling x86inst.cpp compiling MovingRestraint.cpp compiling pesmd.cpp compiling x86instimpl.cpp compiling Completion.cpp compiling x86internal.cpp compiling x86logging.cpp compiling PBMetaD.cpp gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools' compiling x86operand.cpp compiling x86operand_regs.cpp compiling x86regalloc.cpp compiling zone.cpp 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 { | ^~~~~~~~~~~~~~~~~~~~~~~~ compiling Restraint.cpp compiling ReweightBase.cpp compiling ReweightBias.cpp compiling ReweightMetad.cpp compiling ReweightTemperaturePressure.cpp compiling ReweightWham.cpp compiling UWalls.cpp gmake[6]: Leaving directory '/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/bias' 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