* Package: sci-biology/embassy-phylipnew-3.69.660 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * 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 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 -falign-functions=32:25:16 -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 -falign-functions=32:25:16 -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 -falign-functions=32:25:16 -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 -falign-functions=32:25:16 -fno-common -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -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 -falign-functions=32:25:16 -fno-common -O2 -Wl,-O1 -Wl,--defsym=__gentoo_check_ldflags__=0 -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/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: error: disc.o: multiple definition of 'phylostates' /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: clique.o: previous definition here /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: error: phylip.o: multiple definition of 'embossouttree' /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: clique.o: previous definition here /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: error: phylip.o: multiple definition of 'embossoutfile' /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: clique.o: previous definition here /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: warning: skipping incompatible /usr/lib/libm.so while searching for m /usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: warning: skipping incompatible /usr/lib/libc.so while searching for c 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-3.69.660:20200504-190241.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'