=> "/opt/local/bin/bmake" ["-C", "/data/jenkins/workspace/pkgsrc-trunk-x86_64/math/plumed", "all", "BATCH=1", "DEPENDS_TARGET=/nonexistent"] ===> Building for plumed-2.8.0nb2 /opt/local/bin/gmake lib gmake[1]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0' /opt/local/bin/gmake -C src gmake[2]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src' /opt/local/bin/gmake -C lib gmake[3]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' /opt/local/bin/gmake dirslinks gmake[4]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' *** Updating links to used modules in all directories *** /opt/local/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 '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' /opt/local/bin/gmake -C ../analysis links /opt/local/bin/gmake -C ../asmjit links /opt/local/bin/gmake -C ../bias links /opt/local/bin/gmake -C ../blas links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/blas' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/blas gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/blas' /opt/local/bin/gmake -C ../cltools links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/asmjit' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/asmjit gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/asmjit' /opt/local/bin/gmake -C ../colvar links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/cltools' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/cltools gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/bias' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/bias gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/analysis' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/analysis gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/colvar' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/colvar gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/bias' /opt/local/bin/gmake -C ../config links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/config' Nothing to do in /tmp/work/math/plumed/work/plumed-2.8.0/src/config gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/config' /opt/local/bin/gmake -C ../core links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/core' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/core gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/colvar' /opt/local/bin/gmake -C ../function links gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/cltools' /opt/local/bin/gmake -C ../generic links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/function' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/function gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/generic' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/generic gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/core' gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/analysis' /opt/local/bin/gmake -C ../gridtools links /opt/local/bin/gmake -C ../isdb links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/isdb' Verify gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/gridtools' modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/isdb Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/gridtools gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/generic' /opt/local/bin/gmake -C ../lapack links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lapack' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/lapack gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/function' /opt/local/bin/gmake -C ../lepton links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lepton' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/lepton gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lapack' /opt/local/bin/gmake -C ../main links gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/gridtools' /opt/local/bin/gmake -C ../mapping links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/main' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/main gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/mapping' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/mapping gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lepton' /opt/local/bin/gmake -C ../molfile links gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/main' /opt/local/bin/gmake -C ../multicolvar links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/molfile' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/molfile gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/molfile' /opt/local/bin/gmake -C ../reference links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/reference' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/reference gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/multicolvar' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/multicolvar gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/isdb' /opt/local/bin/gmake -C ../secondarystructure links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/secondarystructure' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/secondarystructure gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/reference' /opt/local/bin/gmake -C ../setup links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/setup' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/setup gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/mapping' /opt/local/bin/gmake -C ../tools links gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/multicolvar' /opt/local/bin/gmake -C ../vatom links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/vatom' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/vatom gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/tools' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/tools gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/setup' /opt/local/bin/gmake -C ../vesselbase links gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/secondarystructure' /opt/local/bin/gmake -C ../wrapper links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/vesselbase' gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/wrapper' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/vesselbase Nothing to do in /tmp/work/math/plumed/work/plumed-2.8.0/src/wrapper gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/wrapper' /opt/local/bin/gmake -C ../xdrfile links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/xdrfile' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/xdrfile gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/xdrfile' gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/vatom' gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/tools' gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/vesselbase' gmake[5]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' gmake[4]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' /opt/local/bin/gmake dirs gmake[4]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' *** Compiling all directories *** /opt/local/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 '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' /opt/local/bin/gmake -C ../analysis obj /opt/local/bin/gmake -C ../asmjit obj /opt/local/bin/gmake -C ../bias obj /opt/local/bin/gmake -C ../blas obj gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/blas' compiling blas.cpp gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/bias' gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/asmjit' compiling ABMD.cpp compiling arch.cpp gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/analysis' compiling AnalysisBase.cpp gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/blas' compiling Average.cpp compiling assembler.cpp compiling codebuilder.cpp compiling codecompiler.cpp compiling Bias.cpp compiling AverageVessel.cpp compiling codeemitter.cpp compiling Committor.cpp compiling codeholder.cpp compiling BiasValue.cpp compiling constpool.cpp /opt/local/bin/gmake -C ../cltools obj gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/cltools' compiling CLTool.cpp compiling cpuinfo.cpp compiling ExtendedLagrangian.cpp compiling func.cpp compiling DataCollectionObject.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 EuclideanDissimilarityMatrix.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 External.cpp compiling FarthestPointSampling.cpp compiling LWalls.cpp compiling MaxEnt.cpp compiling Histogram.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 globals.cpp compiling inst.cpp compiling logging.cpp compiling operand.cpp compiling osutils.cpp compiling regalloc.cpp compiling MetaD.cpp compiling runtime.cpp compiling string.cpp compiling utils.cpp compiling LandmarkSelectionBase.cpp compiling GenExample.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!"); | ~~~~~~^~~~~~~~~ compiling vmem.cpp 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!"); | ~~~~~~^~~~~~~~~ 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 LandmarkStaged.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/local/gcc13/include/c++/13.4.0/bits/std_abs.h:40, from /opt/local/gcc13/include/c++/13.4.0/cstdlib:81, from /opt/local/gcc13/include/c++/13.4.0/ext/string_conversions.h:43, from /opt/local/gcc13/include/c++/13.4.0/bits/basic_string.h:4109, from /opt/local/gcc13/include/c++/13.4.0/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 '/tmp/work/math/plumed/work/plumed-2.8.0/src/analysis' gmake[5]: *** [Makefile:426: ../analysis] Error 2 gmake[5]: *** Waiting for unfinished jobs.... compiling GenTemplate.cpp compiling MovingRestraint.cpp compiling Info.cpp compiling Manual.cpp compiling PdbRenumber.cpp compiling SimpleMD.cpp compiling x86builder.cpp compiling SumHills.cpp compiling PBMetaD.cpp compiling x86compiler.cpp compiling kT.cpp compiling x86inst.cpp compiling pesmd.cpp compiling Completion.cpp compiling x86instimpl.cpp compiling x86internal.cpp gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/cltools' compiling x86logging.cpp compiling x86operand.cpp compiling Restraint.cpp compiling ReweightBase.cpp compiling ReweightBias.cpp compiling x86operand_regs.cpp compiling x86regalloc.cpp compiling ReweightMetad.cpp compiling ReweightTemperaturePressure.cpp compiling ReweightWham.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 UWalls.cpp gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/bias' gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/asmjit' gmake[5]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' gmake[4]: *** [Makefile:128: dirs] Error 2 gmake[4]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' gmake[3]: *** [Makefile:111: all] Error 2 gmake[3]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/lib' gmake[2]: *** [Makefile:8: lib] Error 2 gmake[2]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src' gmake[1]: *** [Makefile:32: lib] Error 2 gmake[1]: Leaving directory '/tmp/work/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-trunk-x86_64/math/plumed *** Error code 1 Stop. bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-trunk-x86_64/math/plumed