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Gentoo's Bugzilla – Attachment 408546 Details for
Bug 557038
sci-libs/ccp4-libs-6.1.3-r16: In file included from ./condition.c:31:0: ./library.h:201:21: fatal error: g2c.h: No such file or directory
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Build.log
build.log (text/x-log), 33.68 KB, created by
David Kredba
on 2015-08-08 14:00:41 UTC
(
hide
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Description:
Build.log
Filename:
MIME Type:
Creator:
David Kredba
Created:
2015-08-08 14:00:41 UTC
Size:
33.68 KB
patch
obsolete
>[32;01m * [39;49;00mPackage: sci-libs/ccp4-libs-6.1.3-r16 >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: jlec@gentoo.org sci-chemistry@gentoo.org >[32;01m * [39;49;00mUSE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 userland_GNU >[32;01m * [39;49;00mFEATURES: preserve-libs sandbox splitdebug usersandbox >[32;01m * [39;49;00mPackage: sci-libs/ccp4-libs-6.1.3-r16 >[32;01m * [39;49;00mRepository: gentoo >[32;01m * [39;49;00mMaintainer: jlec@gentoo.org sci-chemistry@gentoo.org >[32;01m * [39;49;00mUSE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 userland_GNU >[32;01m * [39;49;00mFEATURES: preserve-libs sandbox splitdebug usersandbox > [32;01m*[0m Using following Fortran compiler: > [32;01m*[0m F77: x86_64-pc-linux-gnu-gfortran > [32;01m*[0m FC: x86_64-pc-linux-gnu-gfortran >>>> Unpacking source... >>>> Unpacking ccp4-6.1.3-core-src.tar.gz to /var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work >>>> Source unpacked in /var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work >>>> Preparing source in /var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 ... > [32;01m*[0m Applying upstream patches ... > [32;01m*[0m Done. > > [32;01m*[0m Applying Gentoo patches ... > [32;01m*[0m 6.1.3-overflows.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.1.3-dont-make-dirs-in-configure.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.0.2-ppc-double-define-gerror.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.1.3-ccif-shared.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.1.3-dont-build-mmdb.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.1.3-unbundle-libs-ng2.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.1.3-noinstall.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.1.3-impl-dec.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.1.3-lapack.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.1.3-cbf.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m 6.1.3-no-pypath.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m ccp4-libs-6.1.3-force.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m ccp4-libs-6.1.3-format-security.patch ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Done. > > [32;01m*[0m Using GNU config files from /usr/share/gnuconfig > [32;01m*[0m Updating x-windows/Mosflm/jpg/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/Mosflm/cbf/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/Mosflm/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/xdl_view/src/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/Rotgen/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/libjwc/libjwc_c/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/libjwc/libjwc_f/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/DiffractionImage/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/fftw/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/ssm/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/ccif/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/clipper/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/rxdispencer/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating src/clipper_progs/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating src/rapper/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating src/pointless/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating src/pisa/config.sub >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/Mosflm/jpg/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/Mosflm/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/Mosflm/cbf/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/xdl_view/src/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/Rotgen/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/libjwc/libjwc_c/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating x-windows/libjwc/libjwc_f/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/DiffractionImage/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/fftw/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/ssm/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/ccif/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/clipper/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating lib/rxdispencer/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating src/clipper_progs/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating src/rapper/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating src/pointless/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Updating src/pisa/config.guess >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3/lib/DiffractionImage' ... > [32;01m*[0m Running libtoolize --install --copy --force --automake ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running aclocal ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running autoconf --force ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running automake --add-missing --copy --force-missing ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running elibtoolize in: ccp4-6.1.3/lib/DiffractionImage/ > [32;01m*[0m Applying portage/1.2.0 patch ... > [32;01m*[0m Applying sed/1.5.6 patch ... > [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3/src/rapper' ... > [32;01m*[0m Running libtoolize --install --copy --force --automake ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running aclocal ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running autoconf --force ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running automake --add-missing --copy --force-missing ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running elibtoolize in: ccp4-6.1.3/src/rapper/ > [32;01m*[0m Applying portage/1.2.0 patch ... > [32;01m*[0m Applying sed/1.5.6 patch ... > [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3/src/pisa' ... > [32;01m*[0m Running aclocal -I macros ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running autoconf --force ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running automake --add-missing --copy --foreign --force-missing ... >[A[127C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Running elibtoolize in: ccp4-6.1.3/src/pisa/ >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 ... >with_fftw='/usr' >srcdir bindir libdir /var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 /usr/libexec/ccp4/bin/ /usr/lib64 >OK, setting up for a system type of `linux'... > >! onlylibs build requested >! >! Only the libraries will be configured and built. >! Configuration of x-windows programs, phaser and mapslicer >! command library have been implicitly disabled. >! (Some messages below regarding re-enabling these options >! are likely to be misleading.) > >! Using gnu fortran compiler. If you have an old fortran compiler, you may be better >! off using f2c, see --with-f2c option. > >! The x-windows programs will not be installed. >! If you want the x-windows programs to be installed re-run >! configure with the --enable-x flag. > > The CCIF library will be built and installed. > This has been tested on the most common systems, but if > you have problems, use the --disable-ccif flag. > > Installation of the CCTBX library has been suppressed. > Some functionality will be lost. > > Installation of Phaser has been suppressed. > > The LAPACK linear algebra package will be included in the installation. > Configure will search for existing LAPACK and BLAS libraries on > on your system - if a version of LAPACK is not found then the NetLib > version will be built for you automatically. > If you want NetLib LAPACK and BLAS to be used regardless of > system libraries then rerun configure using --with-netlib-lapack > > To disable inclusion of LAPACK, use the --disable-lapack flag > (This is not recommended as some programs will fail to build) > > Building of the CCP4i MapSlicer command library has been suppressed. > As a result you will not be able to use the MapSlicer viewer. >! You have specified a non-default Fortran compiler (x86_64-pc-linux-gnu-gfortran). > This probably only makes sense if you have made the appropriate > changes to the Fortran-C interface routines. > >testing linux ABI using: x86_64-pc-linux-gnu-gcc >$ 64-bit > >Testing Fortran90 support. >WARNING: no Fortran90 support. Check setting of FC. >WARNING: compilation of Refmac5, Sfcheck and Molrep disabled. >checking for ctime... > yes > > Testing command for running m4 (m4 -D_g77=1) ... ok > >Running separate configure for CCIF library. > >Updating modification times for configuration files >Please wait... >...done. >configure: loading cache /tmp/22207.cache_file > > > CCCCCC CCCCCC IIII FFFFFFFFFF > CCCCCCCCCC CCCCCCCCCC IIII FFFFFFFFFF > CC C CC C II FF > CC CC II FF > CC CC II FFFFF > CC CC II FFFFF > CC CC II FF > CC C CC C II FF > CCCCCCCCCC CCCCCCCCC IIII FF > CCCCCC CCCCC IIII FF > ======================================================= > > Fortran programmers' tools for mmCIF > >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking for gcc... x86_64-pc-linux-gnu-gcc >checking for C compiler default output file name... a.out >checking whether the C compiler works... yes >checking whether we are cross compiling... no >checking for suffix of executables... >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 for function prototypes... yes >checking for ranlib... x86_64-pc-linux-gnu-ranlib >checking for gawk... gawk >checking for nm... /usr/bin/nm >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 signal.h usability... yes >checking signal.h presence... yes >checking for signal.h... yes >checking time.h usability... yes >checking time.h presence... yes >checking for time.h... yes >checking standards.h usability... no >checking standards.h presence... no >checking for standards.h... no >checking assert.h usability... yes >checking assert.h presence... yes >checking for assert.h... yes >checking for unistd.h... checking for unistd.h... (cached) yes >yes >checking for an ANSI C-conforming const... yes >------------------------------------------------- > Setting up system-dependent stuff >------------------------------------------------- > > >checking for standards.h... (cached) no >checking for working non-fixed mmap... yes >checking whether strdup declared in string.h... yes >------------------------------------------------- > Regular expression package stuff >------------------------------------------------- >checking regex.h usability... yes >checking regex.h presence... yes >checking for regex.h... yes >checking out regular expression package... ok > >------------------------------------------------- >*** Configuring CCIF build for shared library *** >------------------------------------------------- > >------------------------------------------------- > Checking for certain archaic features >------------------------------------------------- > >checking whether we need to define strerror... no >checking for old-style realloc... no >checking for old BSD sprintf... no > >configure: updating cache /tmp/22207.cache_file >configure: creating ./config.status >config.status: creating shlib.csh >config.status: creating shlib.sh >config.status: creating Makefile > >Returning to main configure. > > >********* BLAS AND LAPACK CONFIGURATION *********** > >Warning: this option has not been extensively tested! >Please report problems to ccp4@ccp4.ac.uk > Test C linking for lapack library >x86_64-pc-linux-gnu-gcc -O2 -ggdb -pipe -march=core2 -frecord-gcc-switches -DG77 -DPROTOTYPE -DHAVE_G2C_H -fPIC -o testlink testlink.c -L/usr/lib64/blas/reference -llapack -lblas -L/usr/lib64/blas/reference -llapack -lblas >[01m[Ktestlink.c:[m[K In function '[01m[Kmain[m[K': >[01m[Ktestlink.c:18:4:[m[K [01;35m[Kwarning: [m[Kimplicit declaration of function '[01m[Kdsyev[m[K' [-Wimplicit-function-declaration] > dsyev('N', 'L', &m, B, &ia, eigval, w, 5*MAXBMT, &istat); >[01;32m[K ^[m[K >/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/temp/ccFhVN6j.o: In function `main': >/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3/testlink.c:18: undefined reference to `dsyev' >collect2: error: ld returned 1 exit status > >Linking in LAPACK/BLAS using XLAPACK_LIB="-L/usr/lib64/blas/reference -llapack -lblas -L/usr/lib64/blas/reference -llapack -lblas " > >***** BLAS AND LAPACK CONFIGURATION FINISHED ******* > >********* DIFFRACTION IMAGE LIBRARY CONFIGURATION *********** > >Updating modification times for configuration files >Please wait... >...done. > >configure --exec_prefix=/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 --prefix=/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 --bindir=/usr/libexec/ccp4/bin/ --libdir=/usr/lib64 --with-tcl-module --with-pic >configure: WARNING: unrecognized options: --with-tcl-module >checking for a BSD-compatible install... /usr/lib/portage/python2.7/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 build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking how to print strings... printf >checking for style of include used by make... GNU >checking for 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... gcc3 >checking for a sed that does not truncate output... /bin/sed >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >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/nm -B >checking the name lister (/usr/bin/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 objdump... objdump >checking how to recognize dependent libraries... pass_all >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for archiver @FILE support... @ >checking for strip... strip >checking for ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/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 mt... mt >checking if mt is a manifest tool... no >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -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 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 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++... gcc3 >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 for gcc... (cached) x86_64-pc-linux-gnu-gcc >checking whether we are using the GNU C compiler... (cached) yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed >checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... (cached) yes >checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) gcc3 >checking whether make sets $(MAKE)... (cached) yes >checking for ANSI C header files... (cached) yes >checking for /usr/bin/python2.7... /usr/bin/python2.7 >checking /usr/include/python2.7/Python.h usability... yes >checking /usr/include/python2.7/Python.h presence... yes >checking for /usr/include/python2.7/Python.h... yes >checking tcl.h usability... yes >checking tcl.h presence... yes >checking for tcl.h... yes >checking /etc/java-config-2/current-system-vm/include/jni.h usability... yes >checking /etc/java-config-2/current-system-vm/include/jni.h presence... yes >checking for /etc/java-config-2/current-system-vm/include/jni.h... yes >checking for sqrt in -lm... yes >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating MAR/Makefile >config.status: creating Rigaku/Makefile >config.status: creating Bruker/Makefile >config.status: executing depfiles commands >config.status: executing libtool commands >configure: WARNING: unrecognized options: --with-tcl-module > >***** DIFFRACTION IMAGE LIBRARY CONFIGURATION FINISHED ******* > > >********* RAPPER CONFIGURATION *********** > >Updating modification times for configuration files >Please wait... >touch: cannot touch 'libxml2/configure.in': No such file or directory >touch: cannot touch 'libxml2/Makefile.am': No such file or directory >touch: cannot touch 'libxml2/aclocal.m4': No such file or directory >touch: cannot touch 'libxml2/configure': No such file or directory >touch: cannot touch 'libxml2/Makefile.in': No such file or directory >touch: cannot touch 'libxml2/ltconfig': No such file or directory >touch: cannot touch 'libxml2/ltmain.sh': No such file or directory >touch: cannot touch 'gc7.0/configure.in': No such file or directory >touch: cannot touch 'gc7.0/Makefile.am': No such file or directory >touch: cannot touch 'gc7.0/aclocal.m4': No such file or directory >touch: cannot touch 'gc7.0/configure': No such file or directory >touch: cannot touch 'gc7.0/Makefile.in': No such file or directory >touch: cannot touch 'gc7.0/ltconfig': No such file or directory >touch: cannot touch 'gc7.0/ltmain.sh': No such file or directory >touch: cannot touch 'gc7.0/libatomic_ops-1.2/configure.in': No such file or directory >touch: cannot touch 'gc7.0/libatomic_ops-1.2/Makefile.am': No such file or directory >touch: cannot touch 'gc7.0/libatomic_ops-1.2/aclocal.m4': No such file or directory >touch: cannot touch 'gc7.0/libatomic_ops-1.2/configure': No such file or directory >touch: cannot touch 'gc7.0/libatomic_ops-1.2/Makefile.in': No such file or directory >touch: cannot touch 'gc7.0/libatomic_ops-1.2/ltconfig': No such file or directory >touch: cannot touch 'gc7.0/libatomic_ops-1.2/ltmain.sh': No such file or directory >...done. > >configure --enable-shared=yes --exec_prefix=/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 --prefix=/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 --bindir=/usr/libexec/ccp4/bin/ --libdir=/usr/lib64 --disable-shared >checking for a BSD-compatible install... /usr/lib/portage/python2.7/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 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-g++ accepts -g... yes >checking for style of include used by make... GNU >checking dependency style of x86_64-pc-linux-gnu-g++... gcc3 >checking for gcc... x86_64-pc-linux-gnu-gcc >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... gcc3 >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 bstring.h usability... no >checking bstring.h presence... no >checking for bstring.h... no >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >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/nm -B >checking the name lister (/usr/bin/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 objdump... objdump >checking how to recognize dependent libraries... pass_all >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for archiver @FILE support... @ >checking for strip... strip >checking for ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/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 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 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... no >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 that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating LOOP/Makefile >config.status: creating data/Makefile >config.status: executing depfiles commands >config.status: executing libtool commands > >***** RAPPER CONFIGURATION FINISHED ******* > > > Building of the RCSB PDB_EXTRACT suite has been suppressed. > As a result you will not be able to use the PDB_EXTRACT programs. > >The configuration can be re-built by executing config.status : > >#!/bin/sh ># (Generated automatically by configure) ># CCP4 was configured as follows: >libdir="/usr/lib64" RANLIB="x86_64-pc-linux-gnu-ranlib" \ >FC="x86_64-pc-linux-gnu-gfortran" FOPTIM="-O2 -ggdb -pipe -march=core2 -frecord-gcc-switches" \ >COPTIM="-O2 -ggdb -pipe -march=core2 -frecord-gcc-switches" XFFLAGS="-fno-second-underscore -fno-globals -fno-automatic -fPIC" \ >XCFLAGS="-DG77 -DPROTOTYPE -DHAVE_G2C_H -fPIC" CC="x86_64-pc-linux-gnu-gcc" \ >LNS="ln -s" M4="m4 -D_g77=1" \ >XCXXFLAGS=" -fPIC" CXX="x86_64-pc-linux-gnu-g++" \ >CXXOPTIM="-O2 -ggdb -pipe -march=core2 -frecord-gcc-switches" \ >M4FLAGS="" SETFLAGS="lgglib_FLAGS='-fno-second-underscore -fno-globals -fno-automatic -fPIC -O0' arp_waters_FLAGS='-fno-second-underscore -fno-globals -fno-automatic -fPIC -O2 -ggdb -pipe -march=core2 -frecord-gcc-switches -fforce-mem' " \ >MAKE="make" F="f" \ >INSTALL_PROGRAM="cp -p" INSTALL_DATA="cp -p" \ >XLDFLAGS=" -lm" \ >SHARE_LIB=" x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libccp4c.so -o libccp4c.so ${CORELIBOBJS} ${CGENERALOBJS} ${CUCOBJS} ${CMTZOBJS} ${CMAPOBJS} ${CSYMOBJS} -L../ccif/ -lccif -L/usr/lib/gcc/x86_64-pc-linux-gnu/5.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/5.2.0/32 -lm && x86_64-pc-linux-gnu-gfortran -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libccp4f.so -o libccp4f.so ${FORTRANLOBJS} ${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c -lmmdb -L/usr/lib/gcc/x86_64-pc-linux-gnu/5.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/5.2.0/32 -lstdc++ -lgfortran -lm" \ >SHARED_LIB_CFLAGS='' \ >SHARED_LIB_FFLAGS="" \ >SHARE_INST="$(INSTALL_DATA) `pwd`/libmmdb.so $(DESTDIR)/$(libdir)/libmmdb.so; $(INSTALL_DATA) `pwd`/libccp4c.so $(DESTDIR)/$(libdir)/libccp4c.so; $(INSTALL_DATA) `pwd`/libccp4f.so $(DESTDIR)/$(libdir)/libccp4f.so; " \ >/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3/configure --prefix=/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 --srcdir=/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 --bindir=/usr/libexec/ccp4/bin/ --libdir=/usr/lib64 --onlylibs --with-shared-libs --tmpdir=/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/temp --disable-x --disable-cctbx --disable-phaser --disable-mapslicer --disable-clipper --disable-ssm --disable-fftw --with-fftw=/usr --with-warnings --disable-pdb_extract linux64 -hush > >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3 ... >make -j4 -j1 DESTDIR=/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/image/ onlylib >if test -n ""; then cd /var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3/lib/lapack; \ > make ; else true; fi >if test -n "lib/ccif"; then cd lib/ccif; \ > make ; else true; fi >make[1]: Entering directory '/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3/lib/ccif' >gawk -f ./condition.awk ./condition.list >x86_64-pc-linux-gnu-gcc -c -O2 -ggdb -pipe -march=core2 -frecord-gcc-switches -DG77 -DPROTOTYPE -DHAVE_G2C_H -fPIC -ansi -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPROTOTYPES=1 -D__PROTOTYPES=1 -D__USE_PROTOS=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SIGNAL_H=1 -DHAVE_TIME_H=1 -DHAVE_ASSERT_H=1 -DUPDATE_WARN=1 -DUSER_ZZMODE_STACK=1 -D_XOPEN_SOURCE=500 -DHAVE_MMAP=1 -DSTRDUP_DECL=1 -DHAVE_REGEX_H=1 -I. -o condition.o ./condition.c && \ >x86_64-pc-linux-gnu-ar r libccif.a condition.o && true >In file included from [01m[K./condition.c:31:0[m[K: >[01m[K./library.h:201:21:[m[K [01;31m[Kfatal error: [m[Kg2c.h: No such file or directory >compilation terminated. >Makefile:326: recipe for target 'libccif.a(condition.o)' failed >make[1]: *** [libccif.a(condition.o)] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3/lib/ccif' >Makefile:90: recipe for target 'cciflib' failed >make: *** [cciflib] Error 2 > [31;01m*[0m ERROR: sci-libs/ccp4-libs-6.1.3-r16::gentoo failed (compile phase): > [31;01m*[0m emake failed > [31;01m*[0m > [31;01m*[0m If you need support, post the output of `emerge --info '=sci-libs/ccp4-libs-6.1.3-r16::gentoo'`, > [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-libs/ccp4-libs-6.1.3-r16::gentoo'`. > [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/temp/build.log'. > [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/temp/environment'. > [31;01m*[0m Working directory: '/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3' > [31;01m*[0m S: '/var/tmp/portage/sci-libs/ccp4-libs-6.1.3-r16/work/ccp4-6.1.3'
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