* Package: sci-biology/abyss-2.3.4 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_musl kernel_linux openmp userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking abyss-2.3.4.tar.gz to /var/tmp/portage/sci-biology/abyss-2.3.4/work >>> Source unpacked in /var/tmp/portage/sci-biology/abyss-2.3.4/work >>> Preparing source in /var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 ... * Running eautoreconf in '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' ... * Running 'aclocal' ... [ ok ] * Running 'autoconf --force' ... [ ok ] * Running 'autoheader' ... [ ok ] * Running 'automake --add-missing --copy --foreign --force-missing' ... [ ok ] * Running elibtoolize in: abyss-2.3.4/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 ... * econf: updating abyss-2.3.4/config.sub with /usr/share/gnuconfig/config.sub * econf: updating abyss-2.3.4/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 --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/abyss-2.3.4 --htmldir=/usr/share/doc/abyss-2.3.4/html --libdir=/usr/lib --enable-openmp --enable-maxk=256 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 x86_64-gentoo-linux-musl-g++ supports C++11 features with -std=c++11... yes 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 the include directive... yes (GNU style) checking whether make supports nested variables... yes checking whether UID '250' is supported by ustar format... yes checking whether GID '250' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking dependency style of x86_64-gentoo-linux-musl-g++ -std=c++11... none checking for gawk... (cached) gawk 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 how to run the C preprocessor... x86_64-gentoo-linux-musl-gcc -E checking whether the compiler supports GNU C++... (cached) yes checking whether x86_64-gentoo-linux-musl-g++ -std=c++11 accepts -g... (cached) yes checking for x86_64-gentoo-linux-musl-g++ -std=c++11 option to enable C++11 features... (cached) none needed checking for x86_64-gentoo-linux-musl-ranlib... x86_64-gentoo-linux-musl-ranlib checking for x86_64-gentoo-linux-musl-ghc... no checking for ghc... (cached) no ./configure: line 7029: : command not found checking for pandoc... no checking for x86_64-gentoo-linux-musl-ar... x86_64-gentoo-linux-musl-ar checking the archiver (x86_64-gentoo-linux-musl-ar) interface... ar 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 vfork.h... no checking for dlfcn.h... yes checking for fcntl.h... yes checking for float.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for sys/param.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking for fork... yes checking for vfork... yes checking for vprintf... yes checking for working fork... yes checking for working vfork... (cached) 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 for working memcmp... yes checking for GNU libc compatible realloc... yes checking for x86_64-gentoo-linux-musl-gcc options needed to detect all undeclared functions... none needed checking whether HOST_NAME_MAX is declared... yes checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking for functional... yes checking for tr1/functional... yes checking for boost/functional/hash.hpp... yes checking for boost/property_map/property_map.hpp... yes checking for google/sparse_hash_map... yes checking for unordered_map... yes checking for tr1/unordered_map... yes checking for unordered_set... yes checking for tr1/unordered_set... yes checking for boost/unordered_set.hpp... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for x86_64-gentoo-linux-musl-g++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating RResolver/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating config.h config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 ... make -j4 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' Making all in bin make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/bin' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/bin' Making all in doc make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/doc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/doc' Making all in Common make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/Common' x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc In file included from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/cstdio:42, from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/ext/string_conversions.h:43, from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/bits/basic_string.h:6606, from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/string:55, from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/bits/locale_classes.h:40, from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/bits/ios_base.h:41, from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/iomanip:40, from StringUtil.h:5, from Uncompress.cpp:15: Uncompress.cpp:160:7: error: redefinition of 'FILE* fopen(const char*, const char*)' 160 | FILE *fopen64(const char *path, const char *mode) | ^~~~~~~ Uncompress.cpp:133:7: note: 'FILE* fopen(const char*, const char*)' previously defined here 133 | FILE *fopen(const char *path, const char *mode) | ^~~~~ Uncompress.cpp:184:52: error: 'mode_t' has not been declared 184 | typedef int (*open_t)(const char *path, int flags, mode_t mode); | ^~~~~~ Uncompress.cpp:189:39: error: 'mode_t' has not been declared 189 | int open(const char *path, int flags, mode_t mode) | ^~~~~~ make[2]: *** [Makefile:572: libcommon_a-Uncompress.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/Common' make[1]: *** [Makefile:488: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' make: *** [Makefile:408: all] Error 2 * ERROR: sci-biology/abyss-2.3.4::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/abyss-2.3.4::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/abyss-2.3.4::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:abyss-2.3.4:20220113-131801.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/abyss-2.3.4/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/abyss-2.3.4/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' * S: '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4'