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Gentoo's Bugzilla – Attachment 388052 Details for
Bug 526722
sci-chemistry/freeon-1.0.8-r1: fails to build with sh -> dash
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build.log
build.log (text/plain), 15.04 KB, created by
Ian Stakenvicius (RETIRED)
on 2014-11-01 19:08:17 UTC
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Description:
build.log
Filename:
MIME Type:
Creator:
Ian Stakenvicius (RETIRED)
Created:
2014-11-01 19:08:17 UTC
Size:
15.04 KB
patch
obsolete
> * Package: sci-chemistry/freeon-1.0.8-r1 > * Repository: gentoo > * Maintainer: nicolasbock@gentoo.org sci-chemistry@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: sandbox test userpriv usersandbox >Installed LAPACK for library directory lib64 > [1] reference * >Installed BLAS for library directory lib64 > [1] reference * >Installed CBLAS for library directory lib64 > [1] gsl > [2] reference * >>>> Unpacking source... >>>> Unpacking freeon-1.0.8.tar.bz2 to /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work >>>> Source unpacked in /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work >>>> Preparing source in /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8 ... > * Running eautoreconf in '/tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8' ... > * Running libtoolize --install --copy --force --automake ... > [ ok ] > * Running aclocal -I m4 ... > [ ok ] > * Running autoconf ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --force-missing ... > [ ok ] > * Running elibtoolize in: freeon-1.0.8/ > * Applying portage/1.2.0 patch ... > * Applying sed/1.5.6 patch ... > * Applying as-needed/2.4.2 patch ... > * Applying target-nm/2.4.2 patch ... >>>> Source prepared. >>>> Configuring source in /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8 ... >>>> Working in BUILD_DIR: "/tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8_build" > * econf: updating freeon-1.0.8/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating freeon-1.0.8/config.guess with /usr/share/gnuconfig/config.guess >/tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/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 --libdir=/usr/lib64 --docdir=/usr/share/doc/freeon-1.0.8-r1 >configure: loading site script /usr/share/config.site >/tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: 40: /usr/share/config.site: [[: Permission denied >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/bin/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... -std=gnu99 >checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99 >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 -std=gnu99 -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 4.9.1 p1.0, pie-0.6.0) 4.9.1 >configure: CXX compiler version: x86_64-pc-linux-gnu-g++ (Gentoo 4.9.1 p1.0, pie-0.6.0) 4.9.1 >configure: F77 compiler version: GNU Fortran (Gentoo 4.9.1 p1.0, pie-0.6.0) 4.9.1 >configure: FC compiler version: GNU Fortran (Gentoo 4.9.1 p1.0, pie-0.6.0) 4.9.1 >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/4.9.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../.. -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/4.9.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../.. -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 python version... 2.7 >checking for python platform... linux2 >checking for python script directory... ${prefix}/lib64/python2.7/site-packages >checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages >checking for x86_64-pc-linux-gnu-gcc -std=gnu99 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 -std=gnu99... /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 whether the shell understands some XSI constructs... yes >checking whether the shell understands "+="... no >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 -std=gnu99 object... ok >checking for sysroot... no >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 -std=gnu99 supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc -std=gnu99 static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc -std=gnu99 supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc -std=gnu99 supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc -std=gnu99 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 >/tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: 25266: /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: declare: Permission denied >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 library containing dgemm... -lblas >checking for library containing dsyev... -llapack >checking for hdf5 version... /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: 1: eval: h5cc: Permission denied >configure: error: in `/tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8_build': >configure: error: unsupported hdf5 library version: >See `config.log' for more details >!!! Please attach the following file when seeking support: >!!! /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8_build/config.log > * ERROR: sci-chemistry/freeon-1.0.8-r1::gentoo failed (configure phase): > * econf failed > * > * Call stack: > * ebuild.sh, line 93: Called src_configure > * environment, line 3963: Called autotools-utils_src_configure > * environment, line 974: Called econf '--docdir=/usr/share/doc/freeon-1.0.8-r1' > * phase-helpers.sh, line 584: Called die > * The specific snippet of code: > * die "econf failed" > * > * If you need support, post the output of `emerge --info '=sci-chemistry/freeon-1.0.8-r1::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-chemistry/freeon-1.0.8-r1::gentoo'`. >sed: couldn't open temporary file /etc/portage/package.mask/sedAos7tV: Permission denied
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bug 526722
: 388052