+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb2/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb2/work.log
=> Checksum BLAKE2s OK for plumed-2.8.0.tgz
=> Checksum SHA512 OK for plumed-2.8.0.tgz
===> Installing dependencies for plumed-2.8.0nb2
==========================================================================
The supported build options for plumed are:

	mpi

You can select which build options to use by setting PKG_DEFAULT_OPTIONS
or the following variable.  Its current value is shown:

	PKG_OPTIONS.plumed (not defined)

==========================================================================
==========================================================================
The following variables will affect the build process of this package,
plumed-2.8.0nb2.  Their current value is shown below:

        * PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp

Based on these variables, the following variables have been set:

        * BLAS_INCLUDES = -I/opt/pkg/include/netlib
        * BLAS_LIBS = -lblas
        * BLAS_PC = blas
        * BLAS_TYPE = netlib
        * CBLAS_LIBS = -lcblas -lblas
        * CBLAS_PC = cblas
        * LAPACKE_LIBS = -llapacke -llapack -lblas
        * LAPACKE_PC = lapacke
        * LAPACK_LIBS = -llapack -lblas
        * LAPACK_PC = lapack

You may want to abort the process now with CTRL-C and change the value
of variables in the first group before continuing.  Be sure to run
`/opt/pkg/bin/bmake clean' after the changes.
==========================================================================
=> Tool dependency gmake>=3.81: found gmake-4.4.1
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Full dependency cblas>=3.9.1nb1: found cblas-3.12.0
=> Full dependency fftw>=3.3.10nb1: found fftw-3.3.10nb2
=> Full dependency gsl>=2.6: found gsl-2.7.1
=> Full dependency lapack>=3.9.0nb1: found lapack-3.12.0
=> Full dependency lapacke>=3.9.1nb2: found lapacke-3.12.0
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
=> Full dependency blas>=3.9.0: found blas-3.12.0
===> Overriding tools for plumed-2.8.0nb2
===> Extracting for plumed-2.8.0nb2
===> Patching for plumed-2.8.0nb2
=> Applying pkgsrc patches for plumed-2.8.0nb2
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed/patches/patch-Makefile.conf.in
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed/patches/patch-Makefile.conf.in
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile.conf.in,v 1.1 2022/07/08 19:47:59 thor Exp $
|
|Enable rpath flags also for linking the main binary.
|
|--- Makefile.conf.in.orig	2022-07-08 18:34:07.530823035 +0000
|+++ Makefile.conf.in
--------------------------
Patching file Makefile.conf.in using Plan A...
Hunk #1 succeeded at 11.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed/patches/patch-configure
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed/patches/patch-configure
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-configure,v 1.1 2022/07/08 19:47:59 thor Exp $
|
|Short out the rpath test that fails with pkgsrc wrappers.
|Enable rpath flags also for linking the main binary.
|Fix portability to non-bash with test = instead of test ==.
|
|--- configure.orig	2022-02-22 22:28:39.000000000 +0000
|+++ configure
--------------------------
Patching file configure using Plan A...
Hunk #1 succeeded at 635.
Hunk #2 succeeded at 755.
Hunk #3 succeeded at 2435.
Hunk #4 succeeded at 3325.
Hunk #5 succeeded at 4435.
Hunk #6 succeeded at 4545.
Hunk #7 succeeded at 4691.
Hunk #8 succeeded at 4741.
Hunk #9 succeeded at 4775.
Hunk #10 succeeded at 5797.
Hunk #11 succeeded at 5806.
Hunk #12 succeeded at 5868.
Hunk #13 succeeded at 5926.
Hunk #14 succeeded at 6103.
Hunk #15 succeeded at 6246.
Hunk #16 succeeded at 6389.
Hunk #17 succeeded at 6445.
Hunk #18 succeeded at 6531.
Hunk #19 succeeded at 6539.
Hunk #20 succeeded at 6547.
Hunk #21 succeeded at 6667.
Hunk #22 succeeded at 6732.
Hunk #23 succeeded at 6740.
Hunk #24 succeeded at 6860.
Hunk #25 succeeded at 6945.
Hunk #26 succeeded at 6979.
Hunk #27 succeeded at 7121.
Hunk #28 succeeded at 7129.
Hunk #29 succeeded at 7249.
Hunk #30 succeeded at 7259.
Hunk #31 succeeded at 7267.
Hunk #32 succeeded at 7387.
Hunk #33 succeeded at 7397.
Hunk #34 succeeded at 7405.
Hunk #35 succeeded at 7525.
Hunk #36 succeeded at 7536.
Hunk #37 succeeded at 7579.
Hunk #38 succeeded at 7596.
Hunk #39 succeeded at 7604.
Hunk #40 succeeded at 7724.
Hunk #41 succeeded at 7735.
Hunk #42 succeeded at 7801.
Hunk #43 succeeded at 7818.
Hunk #44 succeeded at 7826.
Hunk #45 succeeded at 7946.
Hunk #46 succeeded at 7957.
Hunk #47 succeeded at 7965.
Hunk #48 succeeded at 8085.
Hunk #49 succeeded at 8096.
Hunk #50 succeeded at 8104.
Hunk #51 succeeded at 8224.
Hunk #52 succeeded at 8234.
Hunk #53 succeeded at 8242.
Hunk #54 succeeded at 8362.
Hunk #55 succeeded at 8373.
Hunk #56 succeeded at 8435.
Hunk #57 succeeded at 8617.
Hunk #58 succeeded at 8742.
Hunk #59 succeeded at 8751.
Hunk #60 succeeded at 8796.
Hunk #61 succeeded at 8813.
Hunk #62 succeeded at 8856.
Hunk #63 succeeded at 8874.
Hunk #64 succeeded at 8882.
Hunk #65 succeeded at 9002.
Hunk #66 succeeded at 9013.
Hunk #67 succeeded at 9096.
Hunk #68 succeeded at 9104.
Hunk #69 succeeded at 9224.
Hunk #70 succeeded at 9234.
Hunk #71 succeeded at 9242.
Hunk #72 succeeded at 9362.
Hunk #73 succeeded at 9372.
Hunk #74 succeeded at 9380.
Hunk #75 succeeded at 9500.
Hunk #76 succeeded at 9512.
Hunk #77 succeeded at 9523.
Hunk #78 succeeded at 9546.
Hunk #79 succeeded at 9598.
Hunk #80 succeeded at 9697.
Hunk #81 succeeded at 9720.
Hunk #82 succeeded at 9763.
Hunk #83 succeeded at 9833.
Hunk #84 succeeded at 9885.
Hunk #85 succeeded at 9924.
Hunk #86 succeeded at 9934.
Hunk #87 succeeded at 9952.
Hunk #88 succeeded at 9964.
Hunk #89 succeeded at 9981.
Hunk #90 succeeded at 10025.
Hunk #91 succeeded at 10070.
Hunk #92 succeeded at 10078.
Hunk #93 succeeded at 10121.
Hunk #94 succeeded at 10162.
Hunk #95 succeeded at 10203.
Hunk #96 succeeded at 10257.
Hunk #97 succeeded at 10353.
Hunk #98 succeeded at 10366.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed/patches/patch-configure.ac
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed/patches/patch-configure.ac
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-configure.ac,v 1.1 2022/07/08 19:47:59 thor Exp $
|
|Short out the rpath test that fails with pkgsrc wrappers.
|Enable rpath flags also for linking the main binary.
|Fix portability to non-bash with test = instead of test ==.
|
|Including the .ac patch here to motivate upstreaming at least
|of the == stuff.
|
|--- configure.ac.orig	2022-02-22 22:28:39.000000000 +0000
|+++ configure.ac
--------------------------
Patching file configure.ac using Plan A...
Hunk #1 succeeded at 89.
Hunk #2 succeeded at 106.
Hunk #3 succeeded at 122.
Hunk #4 succeeded at 141.
Hunk #5 succeeded at 164.
Hunk #6 succeeded at 313.
Hunk #7 succeeded at 346.
Hunk #8 succeeded at 363.
Hunk #9 succeeded at 377.
Hunk #10 succeeded at 499.
Hunk #11 succeeded at 536.
Hunk #12 succeeded at 557.
Hunk #13 succeeded at 596.
Hunk #14 succeeded at 638.
Hunk #15 succeeded at 662.
Hunk #16 succeeded at 675.
Hunk #17 succeeded at 692.
Hunk #18 succeeded at 714.
Hunk #19 succeeded at 736.
Hunk #20 succeeded at 775.
Hunk #21 succeeded at 818.
Hunk #22 succeeded at 831.
Hunk #23 succeeded at 870.
Hunk #24 succeeded at 890.
Hunk #25 succeeded at 903.
Hunk #26 succeeded at 911.
Hunk #27 succeeded at 931.
Hunk #28 succeeded at 962.
Hunk #29 succeeded at 983.
Hunk #30 succeeded at 1019.
Hunk #31 succeeded at 1053.
Hunk #32 succeeded at 1076.
Hunk #33 succeeded at 1084.
Hunk #34 succeeded at 1100.
Hunk #35 succeeded at 1110.
Hunk #36 succeeded at 1125.
Hunk #37 succeeded at 1166.
Hunk #38 succeeded at 1208.
Hunk #39 succeeded at 1255.
Hunk #40 succeeded at 1294.
Hunk #41 succeeded at 1328.
Hunk #42 succeeded at 1338.
Hunk #43 succeeded at 1405.
Hunk #44 succeeded at 1415.
done
===> Creating toolchain wrappers for plumed-2.8.0nb2
===> Configuring for plumed-2.8.0nb2
=> Substituting "envbash" in src/lib/Makefile
=> Modifying GNU configure scripts to avoid --recheck
=> Replacing config-guess with pkgsrc versions
=> Replacing config-sub with pkgsrc versions
=> Replacing install-sh with pkgsrc version
=> Replacing bash interpreter in scripts/*.sh patches/*.sh.
=> Checking for portability problems in extracted files
configure: Optional modules are disabled by default
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for x86_64-sun-solaris2.11-gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for x86_64-sun-solaris2.11-gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
configure: Initial CXX:         g++
configure: Initial CXXFLAGS:    -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include
configure: Initial CPPFLAGS:    -I/opt/pkg/include
configure: Initial CFLAGS:      -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include
configure: Initial LDFLAGS:     -L/opt/pkg/lib -Wl,-R/opt/pkg/lib
configure: Initial LIBS:        -llapack -lblas -lcblas -lblas
configure: Initial STATIC_LIBS: 
configure: Initial LD:          
configure: Initial LDSHARED:    g++
configure: Initial SOEXT:       
checking whether g++ accepts -fPIC... yes
checking whether gcc accepts -fPIC... yes
checking whether g++ accepts -Wall... yes
checking whether g++ accepts -pedantic... yes
checking whether g++ accepts -std=c++11... yes
checking whether g++ declares c++11 support... yes
checking whether C++ library supports C++11 exceptions... yes
checking whether g++ can generate dependency file with -MM -MF... yes
configure: dependency tracking enabled
configure: Now we will check compulsory headers and libraries
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... (cached) /usr/xpg4/bin/grep
checking for egrep... (cached) /usr/xpg4/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... yes
checking for readdir... yes
checking whether dgemv can be linked with no library... no
checking whether dgemv_ can be linked with no library... yes
checking for library containing dsyevr_... none required
checking whether sdot returns float... yes
configure: Now we will check for optional headers and libraries
checking libmolfile_plugin.h usability... no
checking libmolfile_plugin.h presence... no
checking for libmolfile_plugin.h... no
configure: WARNING: cannot enable __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS
configure: WARNING: using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files
checking for dlopen in -ldl... yes
checking for g++ option to support OpenMP... -fopenmp
checking whether architecture is X86/X64... yes
configure: Enabling embedded asmjit
checking regex.h usability... yes
checking regex.h presence... yes
checking for regex.h... yes
checking for library containing regcomp... none required
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for library containing dlopen... none required
checking RTLD_DEFAULT without extra libs... yes
checking for unistd.h... (cached) yes
checking for library containing chdir... none required
checking subprocess without extra libs... yes
checking for unistd.h... (cached) yes
checking for library containing getcwd... none required
checking cstdio usability... yes
checking cstdio presence... yes
checking for cstdio... yes
checking for library containing popen... none required
checking execinfo.h usability... yes
checking execinfo.h presence... yes
checking for execinfo.h... yes
checking for library containing backtrace... none required
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for library containing gzopen... -lz
checking for library containing cblas_dgemv... none required
checking gsl/gsl_vector.h usability... yes
checking gsl/gsl_vector.h presence... yes
checking for gsl/gsl_vector.h... yes
checking for library containing gsl_vector_alloc... -lgsl
checking fftw3.h usability... yes
checking fftw3.h presence... yes
checking for fftw3.h... yes
checking for library containing fftw_execute... -lfftw3
configure: Release mode, adding -DNDEBUG
configure: *** Dynamic library only enabled on OSX and Linux ***
checking for doxygen... no
configure: Manuals will not be generated
configure: A PDF version of the manual will not be generated
checking whether a program can be run on this machine... yes
configure: PLUMED seems to be configured properly!
configure: **************************
checking whether C++ objects can be grouped with /bin/ld -r -o... yes
checking whether static libraries can be created with /usr/ccs/bin/ar cr... yes
checking whether static-object constructors can be linked from a static archive... yes
configure: I will now check if C++ objects can be linked by C/Fortran compilers
configure: This is relevant if you want to use plumed patch --static on a non-C++ code
checking whether C can link a C++ object... no
checking whether C can link a C++ object with library -lstdc++... yes
checking whether FORTRAN can link a C++ object... yes
checking for pkg-config... /home/pbulk/build/math/plumed/work/.tools/bin/pkg-config
configure: bash-completion is not installed or it is installed on a different prefix
configure: bash completion for plumed will not be installed
configure: **** PLUMED will be installed using the following paths:
configure: **** prefix: /opt/pkg
configure: **** exec_prefix: ${prefix}
configure: **** bindir: ${exec_prefix}/bin
configure: **** libdir: ${exec_prefix}/lib
configure: **** includedir: ${prefix}/include
configure: **** datarootdir: ${prefix}/share
configure: **** datadir: ${datarootdir}
configure: **** docdir: ${prefix}/share/doc/plumed
configure: **** htmldir: ${docdir}
configure: **** Executable will be named plumed
configure: **** As of PLUMED 2.5, you cannot change paths anymore during "make install"
configure: **** Please configure and make clean to change the prefix
configure: WARNING: **** Bash completion for plumed will not be installed, please add the following two lines to your bashrc
configure: WARNING: **** _plumed() { eval "$(plumed --no-mpi completion 2>/dev/null)";}
configure: WARNING: **** complete -F _plumed -o default plumed
configure: **** PLUMED will be compiled without MPI
configure: creating ./config.status
config.status: creating Makefile.conf
config.status: creating sourceme.sh
config.status: creating stamp-h