=> "/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 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/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 ../bias links 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]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/bias' /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/cltools' Verify modules and create links in /tmp/work/math/plumed/work/plumed-2.8.0/src/cltools gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/analysis' /opt/local/bin/gmake -C ../colvar links 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/cltools' /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]: 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]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/core' /opt/local/bin/gmake -C ../generic links 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/function' /opt/local/bin/gmake -C ../gridtools links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/gridtools' 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 ../isdb links gmake[6]: Entering directory '/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/isdb gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/gridtools' /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/lapack' /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/lepton' /opt/local/bin/gmake -C ../main 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]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/isdb' /opt/local/bin/gmake -C ../mapping links gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/main' /opt/local/bin/gmake -C ../molfile links 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]: 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 ../multicolvar links 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/mapping' /opt/local/bin/gmake -C ../reference links gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/multicolvar' /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]: 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]: 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/secondarystructure' /opt/local/bin/gmake -C ../tools links gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/setup' /opt/local/bin/gmake -C ../vatom links 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]: 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]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/vatom' /opt/local/bin/gmake -C ../vesselbase links gmake[6]: Leaving directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/tools' /opt/local/bin/gmake -C ../wrapper links gmake[6]: Entering directory '/tmp/work/math/plumed/work/plumed-2.8.0/src/vesselbase' Verify modules and create links in /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' 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/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 gmake[6]: Entering directory '/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/asmjit' compiling AnalysisBase.cpp compiling arch.cpp compiling assembler.cpp compiling codebuilder.cpp compiling codecompiler.cpp compiling Average.cpp compiling codeemitter.cpp compiling codeholder.cpp compiling constpool.cpp compiling cpuinfo.cpp compiling AverageVessel.cpp compiling func.cpp compiling Committor.cpp compiling DataCollectionObject.cpp compiling globals.cpp compiling inst.cpp compiling EuclideanDissimilarityMatrix.cpp compiling logging.cpp compiling operand.cpp compiling osutils.cpp compiling regalloc.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 LandmarkSelectionBase.cpp compiling x86builder.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 x86compiler.cpp compiling x86inst.cpp compiling x86instimpl.cpp compiling x86internal.cpp compiling x86logging.cpp 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 { | ^~~~~~~~~~~~~~~~~~~~~~~~ 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