* Package: sci-biology/eugene-4.1d * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_musl kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking eugene-4.1d.tar.gz to /var/tmp/portage/sci-biology/eugene-4.1d/work >>> Source unpacked in /var/tmp/portage/sci-biology/eugene-4.1d/work >>> Preparing source in /var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d ... * Applying eugene-3.6-overflow.patch ... [ ok ] * Applying eugene-3.6-plugins.patch ... [ ok ] * Applying eugene-4.1-format-security.patch ... [ ok ] * Applying eugene-4.1d-fix-c++14.patch ... [ ok ] * Applying eugene-4.1d-Wformat.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d' ... * Running 'aclocal' ... [ ok ] * Running 'autoconf --force' ... [ ok ] * Running 'autoheader' ... [ ok ] * Running 'automake --add-missing --copy --force-missing' ... [ ok ] * Running elibtoolize in: eugene-4.1d/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d ... * econf: updating eugene-4.1d/config.sub with /usr/share/gnuconfig/config.sub * econf: updating eugene-4.1d/config.guess with /usr/share/gnuconfig/config.guess * econf: updating eugene-4.1d/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating eugene-4.1d/config/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-gentoo-linux-musl --host=x86_64-gentoo-linux-musl --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/eugene-4.1d --htmldir=/usr/share/doc/eugene-4.1d/html --libdir=/usr/lib checking for a BSD-compatible install... /usr/lib/portage/python3.9/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for x86_64-gentoo-linux-musl-g++... x86_64-gentoo-linux-musl-g++ 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 the compiler supports GNU C++... yes checking whether x86_64-gentoo-linux-musl-g++ accepts -g... yes checking for x86_64-gentoo-linux-musl-g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of x86_64-gentoo-linux-musl-g++... none checking for x86_64-gentoo-linux-musl-gcc... x86_64-gentoo-linux-musl-gcc checking whether the compiler supports GNU C... yes checking whether x86_64-gentoo-linux-musl-gcc accepts -g... yes checking for x86_64-gentoo-linux-musl-gcc option to enable C11 features... none needed checking whether x86_64-gentoo-linux-musl-gcc understands -c and -o together... yes checking dependency style of x86_64-gentoo-linux-musl-gcc... none checking for gawk... (cached) gawk checking whether ln -s works... yes checking for x86_64-gentoo-linux-musl-ranlib... x86_64-gentoo-linux-musl-ranlib checking for main in -lc... yes checking for main in -ldl... yes checking for main in -lgcc... yes checking for main in -lgd... yes checking for main in -lm... yes checking for main in -lpng... yes checking for main in -lz... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for netdb.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for values.h... yes checking for getopt.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking whether struct tm is in sys/time.h or time.h... time.h checking for size_t... yes checking build system type... x86_64-gentoo-linux-musl checking host system type... x86_64-gentoo-linux-musl checking for GNU libc compatible malloc... yes checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for floor... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strspn... yes checking for uname... yes checking for getopt... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating README config.status: creating src/Makefile config.status: creating src/GDIF/Makefile config.status: creating src/Parametrization/Makefile config.status: creating src/SensorPlugins/Makefile config.status: creating src/SensorPlugins/0_SensorTk/Makefile config.status: creating src/SensorPlugins/0_SensorTk/GetData/Makefile config.status: creating src/SensorPlugins/AnnotaStruct/Makefile config.status: creating src/SensorPlugins/BlastX/Makefile config.status: creating src/SensorPlugins/Est/Makefile config.status: creating src/SensorPlugins/EuStop/Makefile config.status: creating src/SensorPlugins/FrameShift/Makefile config.status: creating src/SensorPlugins/GCPlot/Makefile config.status: creating src/SensorPlugins/GFF/Makefile config.status: creating src/SensorPlugins/GSplicer/Makefile config.status: creating src/SensorPlugins/Homology/Makefile config.status: creating src/SensorPlugins/IfElse/Makefile config.status: creating src/SensorPlugins/MarkovConst/Makefile config.status: creating src/SensorPlugins/MarkovIMM/Makefile config.status: creating src/SensorPlugins/MarkovIMM/GetData/Makefile config.status: creating src/SensorPlugins/MarkovProt/Makefile config.status: creating src/SensorPlugins/MarkovProt/GetData/Makefile config.status: creating src/SensorPlugins/NcRNA/Makefile config.status: creating src/SensorPlugins/NG2/Makefile config.status: creating src/SensorPlugins/NStart/Makefile config.status: creating src/SensorPlugins/NStretch/Makefile config.status: creating src/SensorPlugins/PatConst/Makefile config.status: creating src/SensorPlugins/PepSignal/Makefile config.status: creating src/SensorPlugins/ProStart/Makefile config.status: creating src/SensorPlugins/Plotter/Makefile config.status: creating src/SensorPlugins/QualData/Makefile config.status: creating src/SensorPlugins/Repeat/Makefile config.status: creating src/SensorPlugins/RibosomalFrameShift/Makefile config.status: creating src/SensorPlugins/Riken/Makefile config.status: creating src/SensorPlugins/SMachine/Makefile config.status: creating src/SensorPlugins/SPred/Makefile config.status: creating src/SensorPlugins/SpliceWAM/Makefile config.status: creating src/SensorPlugins/StartWAM/Makefile config.status: creating src/SensorPlugins/Tester/Makefile config.status: creating src/SensorPlugins/Transcript/Makefile config.status: creating plugins/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d ... make -j4 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src' Making all in Parametrization make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/Parametrization' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o ParaOptimization.o ParaOptimization.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o OptiAlgorithm.o OptiAlgorithm.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o Random.o Random.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o LineSearch.o LineSearch.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o Genetic.o Genetic.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o CrossingOver.o CrossingOver.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o Mutating.o Mutating.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o Scaling.o Scaling.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o Selecting.o Selecting.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o Sharing.o Sharing.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o SimulatedAnnealing.o SimulatedAnnealing.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -pipe -march=native -fno-diagnostics-color -O2 -c -o Chromosome.o Chromosome.cc rm -f libParametrization.a ar cru libParametrization.a ParaOptimization.o OptiAlgorithm.o Random.o LineSearch.o Genetic.o CrossingOver.o Mutating.o Scaling.o Selecting.o Sharing.o SimulatedAnnealing.o Chromosome.o x86_64-gentoo-linux-musl-ranlib libParametrization.a make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/Parametrization' Making all in GDIF make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/GDIF' x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../.. -pipe -march=native -fno-diagnostics-color -O2 -c -o gdIF.o gdIF.c rm -f libGDIF.a ar cru libGDIF.a gdIF.o x86_64-gentoo-linux-musl-ranlib libGDIF.a make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/GDIF' Making all in . make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib\" -pipe -march=native -fno-diagnostics-color -O2 -c -o AltEst.o AltEst.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib\" -pipe -march=native -fno-diagnostics-color -O2 -c -o Attributes.o Attributes.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib\" -pipe -march=native -fno-diagnostics-color -O2 -c -o BackP.o BackP.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib\" -pipe -march=native -fno-diagnostics-color -O2 -c -o DAG.o DAG.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib\" -pipe -march=native -fno-diagnostics-color -O2 -c -o DNASeq.o DNASeq.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib\" -pipe -march=native -fno-diagnostics-color -O2 -c -o Dll.o Dll.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib\" -pipe -march=native -fno-diagnostics-color -O2 -c -o EuGene.o EuGene.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib\" -pipe -march=native -fno-diagnostics-color -O2 -c -o Gap.o Gap.cc In file included from Param.h:37, from Prediction.h:32, from DAG.h:26, from EuGene.cc:58: ./getopt.h:104:12: error: conflicting declaration of C function 'int getopt()' 104 | extern int getopt (); | ^~~~~~ In file included from EuGene.cc:50: /usr/include/unistd.h:123:5: note: previous declaration 'int getopt(int, char* const*, const char*)' 123 | int getopt(int, char * const [], const char *); | ^~~~~~ x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib\" -pipe -march=native -fno-diagnostics-color -O2 -c -o GeneFeature.o GeneFeature.cc make[3]: *** [Makefile:493: EuGene.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src' make[2]: *** [Makefile:509: all-recursive] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src' make[1]: *** [Makefile:477: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d' make: *** [Makefile:416: all] Error 2 * ERROR: sci-biology/eugene-4.1d::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/eugene-4.1d::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/eugene-4.1d::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:eugene-4.1d:20211222-152522.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/eugene-4.1d/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/eugene-4.1d/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d' * S: '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d'