+ 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 gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis /opt/pkg/bin/gmake -C ../bias links 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' gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias' /opt/pkg/bin/gmake -C ../blas 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/blas' /opt/pkg/bin/gmake -C ../cltools links 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/cltools' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas' /opt/pkg/bin/gmake -C ../colvar links 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/colvar' 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' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis' /opt/pkg/bin/gmake -C ../function links 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 ../generic 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]: 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/cltools' /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/gridtools' /opt/pkg/bin/gmake -C ../isdb links gmake[6]: Leaving directory '/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/function' 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 /opt/pkg/bin/gmake -C ../lapack links gmake[6]: Entering 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/lapack 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]: 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]: Leaving directory '/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/lepton' /opt/pkg/bin/gmake -C ../mapping links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main' /opt/pkg/bin/gmake -C ../molfile links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile' /opt/pkg/bin/gmake -C ../multicolvar links 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/molfile 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/molfile' /opt/pkg/bin/gmake -C ../reference links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar' gmake[6]: Entering directory '/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/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' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/setup' /opt/pkg/bin/gmake -C ../vatom links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vatom' /opt/pkg/bin/gmake -C ../vesselbase links 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/vatom 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' gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/tools' Nothing to do in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/wrapper Verify modules and create links in /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/vesselbase 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/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' /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 compiling codebuilder.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 Average.cpp compiling codecompiler.cpp compiling Bias.cpp compiling DriverDouble.cpp compiling codeemitter.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 BiasValue.cpp compiling codeholder.cpp compiling AverageVessel.cpp compiling constpool.cpp compiling ExtendedLagrangian.cpp compiling cpuinfo.cpp compiling func.cpp compiling Committor.cpp compiling External.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 DataCollectionObject.cpp compiling LWalls.cpp compiling globals.cpp compiling EuclideanDissimilarityMatrix.cpp compiling inst.cpp compiling logging.cpp compiling MaxEnt.cpp compiling operand.cpp compiling osutils.cpp compiling regalloc.cpp compiling GenExample.cpp compiling FarthestPointSampling.cpp compiling runtime.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 { | ^~~~~~~~~~~~~~~~ compiling MetaD.cpp 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 Histogram.cpp compiling x86assembler.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 x86compiler.cpp compiling SumHills.cpp compiling MovingRestraint.cpp compiling kT.cpp compiling x86inst.cpp compiling x86instimpl.cpp compiling x86internal.cpp compiling PBMetaD.cpp compiling x86logging.cpp compiling pesmd.cpp compiling Restraint.cpp compiling ReweightBase.cpp compiling Completion.cpp compiling x86operand.cpp gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools' compiling ReweightBias.cpp compiling x86operand_regs.cpp compiling ReweightMetad.cpp compiling x86regalloc.cpp compiling ReweightTemperaturePressure.cpp compiling ReweightWham.cpp compiling zone.cpp compiling UWalls.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 { | ^~~~~~~~~~~~~~~~~~~~~~~~ gmake[6]: Leaving 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/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