=> Bootstrap dependency digest>=20211023: found digest-20220214 => Checksum BLAKE2s OK for plumed-2.8.0.tgz => Checksum SHA512 OK for plumed-2.8.0.tgz ===> Installing dependencies for plumed-2.8.0 ========================================================================== 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-2.8.0. 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 (not defined) * BLAS_LIBS = -lblas * BLAS_TYPE = netlib * CBLAS_LIBS = -lcblas -lblas * LAPACKE_LIBS = -llapacke -llapack -lblas * LAPACK_LIBS = -llapack -lblas 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 `/usr/bin/make clean' after the changes. ========================================================================== => Tool dependency mktools-[0-9]*: found mktools-20220614 => Tool dependency bash-[0-9]*: found bash-5.1.16 => Tool dependency gmake>=3.81: found gmake-4.3nb4 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Full dependency lapack>=3.9.0nb1: found lapack-3.10.1 => Full dependency fftw>=3.3.10nb1: found fftw-3.3.10nb1 => Full dependency gsl>=2.6: found gsl-2.7.1 => Full dependency gcc7>=7.5.0nb6: found gcc7-7.5.0nb6 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Overriding tools for plumed-2.8.0 ===> Extracting for plumed-2.8.0 ===> Patching for plumed-2.8.0 => Applying pkgsrc patches for plumed-2.8.0 => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/math/plumed/patches/patch-Makefile.conf.in => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/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 /amd/pkgsrc/CHROOT/P/pkgsrc/math/plumed/patches/patch-configure => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/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 /amd/pkgsrc/CHROOT/P/pkgsrc/math/plumed/patches/patch-configure.ac => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/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-2.8.0 ===> Configuring for plumed-2.8.0 => 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 c++ accepts -g... yes checking for x86_64--netbsd-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--netbsd-gfortran... gfortran checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes configure: Initial CXX: c++ configure: Initial CXXFLAGS: -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include configure: Initial CPPFLAGS: -I/usr/include -I/usr/pkg/include configure: Initial CFLAGS: -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include configure: Initial LDFLAGS: -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib configure: Initial LIBS: -llapack -lblas configure: Initial STATIC_LIBS: configure: Initial LD: configure: Initial LDSHARED: c++ configure: Initial SOEXT: checking whether c++ accepts -fPIC... yes checking whether gcc accepts -fPIC... yes checking whether c++ accepts -Wall... yes checking whether c++ accepts -pedantic... yes checking whether c++ accepts -std=c++11... yes checking whether c++ declares c++11 support... yes checking whether C++ library supports C++11 exceptions... yes checking whether c++ 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... c++ -E checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep 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... no checking for c++ 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... no configure: WARNING: cannot enable __PLUMED_HAS_EXECINFO 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... -lgslcblas 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 ld -r -o... yes checking whether static libraries can be created with 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... /tmp/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: /usr/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