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Gentoo's Bugzilla – Attachment 509002 Details for
Bug 640348
sci-chemistry/freeon-1.0.10 : configure: error: unsupported hdf5 library version: 1.10.5
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sci-chemistry:freeon-1.0.10:20171209-025207.log
sci-chemistry:freeon-1.0.10:20171209-025207.log (text/plain), 14.60 KB, created by
Toralf Förster
on 2017-12-09 08:25:50 UTC
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Description:
sci-chemistry:freeon-1.0.10:20171209-025207.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2017-12-09 08:25:50 UTC
Size:
14.60 KB
patch
obsolete
> * Package: sci-chemistry/freeon-1.0.10 > * Repository: gentoo > * Maintainer: nicolasbock@gentoo.org sci-chemistry@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking freeon-1.0.10.tar.bz2 to /var/tmp/portage/sci-chemistry/freeon-1.0.10/work >>>> Source unpacked in /var/tmp/portage/sci-chemistry/freeon-1.0.10/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/freeon-1.0.10/work/freeon-1.0.10 ... > * Applying freeon-1.0.10-stop.patch ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-chemistry/freeon-1.0.10/work/freeon-1.0.10' ... > * Running libtoolize --install --copy --force --automake ... > [ ok ] > * Running aclocal -I m4 ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --force-missing ... > [ ok ] > * Running elibtoolize in: freeon-1.0.10/ > * Applying portage/1.2.0 patch ... > * Applying sed/1.5.6 patch ... > * Applying as-needed/2.4.3 patch ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/freeon-1.0.10/work/freeon-1.0.10 ... > * econf: updating freeon-1.0.10/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating freeon-1.0.10/config.guess with /usr/share/gnuconfig/config.guess >./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/freeon-1.0.10 --htmldir=/usr/share/doc/freeon-1.0.10/html --libdir=/usr/lib64 >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking target system type... x86_64-pc-linux-gnu >checking for a BSD-compatible install... /usr/lib/portage/python3.5/ebuild-helpers/xattr/install -c >checking whether build environment is sane... yes >checking for a thread-safe mkdir -p... /bin/mkdir -p >checking for gawk... gawk >checking whether make sets $(MAKE)... yes >checking whether make supports nested variables... yes >checking whether make supports nested variables... (cached) yes >configure: configuring local version master:release >checking whether to build fully parallel MPI version... no >checking whether to build MPI version, parallelized across clones only... no >checking for style of include used by make... GNU >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >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 x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes >checking dependency style of x86_64-pc-linux-gnu-gcc... none >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C99... none needed >checking for x86_64-pc-linux-gnu-gcc option to accept ISO Standard C... (cached) none needed >checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ >checking whether we are using the GNU C++ compiler... yes >checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes >checking dependency style of x86_64-pc-linux-gnu-g++... none >checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran compiler... yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes >checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran 77 compiler... yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /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 minix/config.h usability... no >checking minix/config.h presence... no >checking for minix/config.h... no >checking whether it is safe to define __EXTENSIONS__... yes >configure: CC: identified GNU gcc compiler >configure: CXX: identified GNU gcc compiler >configure: F77: identified GNU gcc compiler >configure: FC: identified GNU gcc compiler >configure: C compiler version: x86_64-pc-linux-gnu-gcc (Gentoo 7.2.0 p1.1) 7.2.0 >configure: CXX compiler version: x86_64-pc-linux-gnu-g++ (Gentoo 7.2.0 p1.1) 7.2.0 >configure: F77 compiler version: GNU Fortran (Gentoo 7.2.0 p1.1) 7.2.0 >configure: FC compiler version: GNU Fortran (Gentoo 7.2.0 p1.1) 7.2.0 >checking how to get verbose linking output from x86_64-pc-linux-gnu-gfortran... -v >checking for Fortran 77 libraries of x86_64-pc-linux-gnu-gfortran... -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../.. -lgfortran -lm -lquadmath >checking for dummy main to link with Fortran 77 libraries... none >checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore >checking how to get verbose linking output from x86_64-pc-linux-gnu-gfortran... -v >checking for Fortran libraries of x86_64-pc-linux-gnu-gfortran... -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../.. -lgfortran -lm -lquadmath >checking for dummy main to link with Fortran libraries... none >checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore >checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp >checking for x86_64-pc-linux-gnu-gfortran option to support OpenMP... -fopenmp >checking for Fortran flag to compile .F90 files... none >checking for Fortran flag needed to accept free-form source... none >checking how to print strings... printf >checking for a sed that does not truncate output... /bin/sed >checking for fgrep... /bin/grep -F >checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B >checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm >checking whether ln -s works... yes >checking the maximum length of command line arguments... 1572864 >checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop >checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-dlltool... no >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok >checking for sysroot... no >checking for a working dd... /bin/dd >checking how to truncate binary pipes... /bin/dd bs=4096 count=1 >checking for x86_64-pc-linux-gnu-mt... no >checking for mt... mt >checking if mt is a manifest tool... no >checking for dlfcn.h... yes >checking for objdir... .libs >checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking whether -lc should be explicitly linked in... no >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether stripping libraries is possible... yes >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... yes >checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E >checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (cached) GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... yes >checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC >checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes >checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (cached) GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... yes >checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC >checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes >checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (cached) GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether make sets $(MAKE)... (cached) yes >checking whether to add compiler optimizations... no >checking whether to check for case differences in names... no >checking how to set line length limits of f90 compiler... gfortran detected, setting unlimited line-length limit (-ffree-line-length-none) >checking for ANSI C header files... (cached) yes >checking sys/resource.h usability... yes >checking sys/resource.h presence... yes >checking for sys/resource.h... yes >checking sys/time.h usability... yes >checking sys/time.h presence... yes >checking for sys/time.h... yes >checking for unistd.h... (cached) yes >checking sys/ioctl.h usability... yes >checking sys/ioctl.h presence... yes >checking for sys/ioctl.h... yes >checking for sys/types.h... (cached) yes >checking math.h usability... yes >checking math.h presence... yes >checking for math.h... yes >checking sys/wait.h usability... yes >checking sys/wait.h presence... yes >checking for sys/wait.h... yes >checking for random number generator seed... use random seed >checking whether to use PHiPAC... no >checking whether to debug MD... no >checking for round in -lm... yes >checking for library containing clock_gettime... none required >checking for possible compiler problems... good, none found >checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config >checking pkg-config is at least version 0.9.0... yes >checking for BLAS... yes >checking for LAPACK... yes >checking for hdf5 version... 1.10.1 >configure: error: in `/var/tmp/portage/sci-chemistry/freeon-1.0.10/work/freeon-1.0.10': >configure: error: unsupported hdf5 library version: 1.10.1 >See `config.log' for more details > >!!! Please attach the following file when seeking support: >!!! /var/tmp/portage/sci-chemistry/freeon-1.0.10/work/freeon-1.0.10/config.log > * ERROR: sci-chemistry/freeon-1.0.10::gentoo failed (configure phase): > * econf failed > * > * Call stack: > * ebuild.sh, line 124: Called src_configure > * environment, line 3517: Called default > * phase-functions.sh, line 853: Called default_src_configure > * phase-functions.sh, line 888: Called __eapi2_src_configure > * phase-helpers.sh, line 783: Called econf > * phase-helpers.sh, line 666: Called __helpers_die 'econf failed' > * isolated-functions.sh, line 117: Called die > * The specific snippet of code: > * die "$@" > * > * If you need support, post the output of `emerge --info '=sci-chemistry/freeon-1.0.10::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-chemistry/freeon-1.0.10::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-chemistry:freeon-1.0.10:20171209-025207.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/freeon-1.0.10/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/freeon-1.0.10/temp/environment'. > * Working directory: '/var/tmp/portage/sci-chemistry/freeon-1.0.10/work/freeon-1.0.10' > * S: '/var/tmp/portage/sci-chemistry/freeon-1.0.10/work/freeon-1.0.10'
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