+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb1/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb1/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Building for plumed-2.8.0nb1
/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
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
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis'
/opt/pkg/bin/gmake -C ../asmjit 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'
/opt/pkg/bin/gmake -C ../bias links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias'
Verify modules and create links in /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/bias'
/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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas'
/opt/pkg/bin/gmake -C ../cltools 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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools'
/opt/pkg/bin/gmake -C ../colvar links
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/colvar'
/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/core'
/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/function'
/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/generic'
/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]: 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/isdb'
/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/lepton'
/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/main'
/opt/pkg/bin/gmake -C ../mapping 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/mapping
gmake[6]: Leaving directory '/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]: 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
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar'
/opt/pkg/bin/gmake -C ../reference links
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
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/reference'
/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/secondarystructure'
/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/setup'
/opt/pkg/bin/gmake -C ../tools links
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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/tools'
/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]: Leaving 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/vesselbase
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vesselbase'
/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[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
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis'
compiling AnalysisBase.cpp
compiling Average.cpp
compiling AverageVessel.cpp
compiling Committor.cpp
compiling DataCollectionObject.cpp
compiling EuclideanDissimilarityMatrix.cpp
compiling FarthestPointSampling.cpp
compiling Histogram.cpp
compiling LandmarkSelectionBase.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<int>( sqrt(n*N) );
| ~~~~^~~~~
In file included from /usr/include/math.h:35,
from /opt/tools/gcc13/include/c++/13.1.0/bits/std_abs.h:40,
from /opt/tools/gcc13/include/c++/13.1.0/cstdlib:81,
from /opt/tools/gcc13/include/c++/13.1.0/ext/string_conversions.h:43,
from /opt/tools/gcc13/include/c++/13.1.0/bits/basic_string.h:4108,
from /opt/tools/gcc13/include/c++/13.1.0/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]: 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 in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed
*** Error code 1
Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed