sci-biology:embassy-phylipnew-3.69.660:20200126-094738.log

sci-biology:embassy-phylipnew-3.69.660:20200126-094738.log (text/plain), 13.16 KB, created by Toralf Förster on 2020-01-26 10:10:10 UTC

 * Package:    sci-biology/embassy-phylipnew-3.69.660
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking embassy-phylipnew-3.69.660.tar.gz to /var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work
>>> Source unpacked in /var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work
>>> Preparing source in /var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650 ...
 * Applying embassy-phylipnew-3.69.650_fix-build-system.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650' ...
 * 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: PHYLIPNEW-3.69.650/
 *   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-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650 ...
 * econf: updating PHYLIPNEW-3.69.650/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating PHYLIPNEW-3.69.650/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/embassy-phylipnew-3.69.660 --htmldir=/usr/share/doc/embassy-phylipnew-3.69.660/html --libdir=/usr/lib64 --enable-shared --disable-static --without-x --without-pngdriver --without-hpdf --without-mysql --without-postgresql --enable-large --without-java --enable-systemlibs
configure: loading site script /usr/share/config.site
checking for gawk... gawk
checking for x86_64-pc-linux-gnu-icc... no
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 for x86_64-pc-linux-gnu-icpc... no
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 how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether build environment is sane... yes
checking whether make supports the include directive... yes (GNU style)
checking whether make supports nested variables... yes
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking dependency style of x86_64-pc-linux-gnu-g++... none
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 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/x86_64-pc-linux-gnu-nm -B
checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm
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... no
checking if : is a manifest tool... no
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... no
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 X... disabled
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for ANSI C header files... (cached) yes
checking for unistd.h... (cached) yes
checking TargetConfig.h usability... no
checking TargetConfig.h presence... no
checking for TargetConfig.h... no
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking whether getpgrp requires zero arguments... yes
checking for strftime... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for vprintf... yes
checking for _doprnt... no
checking for strdup... yes
checking for strstr... yes
checking for strchr... yes
checking for erand48... yes
checking for memmove... yes
checking for socket in -lc... yes
checking for main in -lm... yes
checking if docroot is given... no
checking if gcc profiling is selected... no
checking for Java JNI... no
checking for Java JNI OS... no
checking for authorisation type... no
checking for threading type... no
checking whether to look for pdf support... no
checking if png driver is wanted... no
checking for large file support... yes
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 PLPLOT... no
checking for PLPLOT... yes
checking for purify... no
checking for cygwin... no
checking for savestats... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating data/Makefile
config.status: creating emboss_acd/Makefile
config.status: creating emboss_doc/Makefile
config.status: creating emboss_doc/html/Makefile
config.status: creating emboss_doc/text/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650 ...
make -j1 
Making all in src
make[1]: Entering directory '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650/src'
make  all-am
make[2]: Entering directory '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650/src'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.  -I../include -I/usr/include  -I/usr/include/plplot  -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64    -O2 -pipe -march=native -fno-common  -O2 -c -o clique.o clique.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.  -I../include -I/usr/include  -I/usr/include/plplot  -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64    -O2 -pipe -march=native -fno-common  -O2 -c -o disc.o disc.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.  -I../include -I/usr/include  -I/usr/include/plplot  -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64    -O2 -pipe -march=native -fno-common  -O2 -c -o phylip.o phylip.c
/bin/sh ../libtool  --tag=CC   --mode=link x86_64-pc-linux-gnu-gcc    -O2 -pipe -march=native -fno-common  -O2  -Wl,-O1 -Wl,--as-needed -o fclique clique.o disc.o phylip.o -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax   -lm 
libtool: link: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -O2 -Wl,-O1 -o fclique clique.o disc.o phylip.o  -Wl,--as-needed -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lm
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: disc.o:(.bss+0x38): multiple definition of `phylostates'; clique.o:(.bss+0x4a0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: phylip.o:(.bss+0x50): multiple definition of `embossouttree'; clique.o:(.bss+0xf8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: phylip.o:(.bss+0x68): multiple definition of `embossoutfile'; clique.o:(.bss+0x100): first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:1185: fclique] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650/src'
make[1]: *** [Makefile:1085: all] Error 2
make[1]: Leaving directory '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650/src'
make: *** [Makefile:421: all-recursive] Error 1
 * ERROR: sci-biology/embassy-phylipnew-3.69.660::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/embassy-phylipnew-3.69.660::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/embassy-phylipnew-3.69.660::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:embassy-phylipnew-3.69.660:20200126-094738.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650'
 * S: '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650'