* Package: sci-biology/allpathslg-52488-r2 * 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 allpathslg-52488.tar.gz to /var/tmp/portage/sci-biology/allpathslg-52488-r2/work >>> Unpacking allpathslg-52488-patchset.tar.bz2 to /var/tmp/portage/sci-biology/allpathslg-52488-r2/work >>> Source unpacked in /var/tmp/portage/sci-biology/allpathslg-52488-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488 ... * Applying allpathslg-52488_fix-buildsystem.patch ... [ ok ] * Applying allpathslg-52488_remove-namespace-std.patch ... [ ok ] * Applying allpathslg-52488-gcc7.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488' ... * Running libtoolize --install --copy --force --automake ... [ ok ] * Running aclocal -I m4 ... [ ok ] * Running autoconf --force ... [ ok ] * Running automake --add-missing --copy --foreign --force-missing ... [ ok ] * Running elibtoolize in: allpathslg-52488/ * 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/allpathslg-52488-r2/work/allpathslg-52488 ... * econf: updating allpathslg-52488/config.sub with /usr/share/gnuconfig/config.sub * econf: updating allpathslg-52488/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/allpathslg-52488-r2 --htmldir=/usr/share/doc/allpathslg-52488-r2/html --libdir=/usr/lib64 checking for a BSD-compatible install... /usr/lib/portage/python3.6/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 whether make supports the include directive... yes (GNU style) 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 dependency style of x86_64-pc-linux-gnu-gcc... none 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 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 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... 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 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 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 dependency style of x86_64-pc-linux-gnu-g++... none 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 whether byte ordering is bigendian... no g++ version is >= 4.7... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp checking validity of OpenMP configuation.... checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: executing depfiles commands config.status: executing libtool commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488 ... make -j1 Making all in src make[1]: Entering directory '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488/src' x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -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_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=5.1.1 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -fno-strict-aliasing -iquote . -DNDEBUG -c -o RemodelGaps.o `test -f 'paths/RemodelGaps.cc' || echo './'`paths/RemodelGaps.cc In file included from paths/RemodelGaps.cc:27: ./Superb.h:240:18: error: friend declaration of ‘void WriteSuperbsAndSummary(const String&, const vec&, Bool, const String&)’ specifies default arguments and isn’t a definition [-fpermissive] 240 | friend void WriteSuperbsAndSummary( const String & dir, | ^~~~~~~~~~~~~~~~~~~~~~ ./Superb.h:245:18: error: friend declaration of ‘void WriteSummary(const String&, const vec&, const vecBoolvector&)’ specifies default arguments and isn’t a definition [-fpermissive] 245 | friend void WriteSummary( const String & fn, const vec & s, | ^~~~~~~~~~~~ ./Superb.h:252:18: error: friend declaration of ‘void WriteSupercontigFiles(const String&, const vec&, Bool)’ specifies default arguments and isn’t a definition [-fpermissive] 252 | friend void WriteSupercontigFiles( const String& dir, | ^~~~~~~~~~~~~~~~~~~~~ In file included from ./efasta/EfastaTools.h:15, from paths/RemodelGaps.cc:28: ./Fastavector.h:302:18: error: friend declaration of ‘void LoadRegionsFromIndexedFastaFile(const String&, const String&, const vec >, int, int> >&, vec&, int, vec, std::allocator > >*)’ specifies default arguments and isn’t a definition [-fpermissive] 302 | friend void LoadRegionsFromIndexedFastaFile( const String& fasta, const String& index, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./Fastavector.h:323:18: error: friend declaration of ‘void WriteScaffoldedFasta(const String&, const vec&, const vec&, const vec&, int, char, Bool)’ specifies default arguments and isn’t a definition [-fpermissive] 323 | friend void WriteScaffoldedFasta( const String &out_file, | ^~~~~~~~~~~~~~~~~~~~ In file included from paths/RemodelGaps.cc:28: ./efasta/EfastaTools.h:202:19: error: friend declaration of ‘void WriteScaffoldedEFasta(const String&, const VecEFasta&, const vec&, Bool)’ specifies default arguments and isn’t a definition [-fpermissive] 202 | friend void WriteScaffoldedEFasta( const String &out_file, | ^~~~~~~~~~~~~~~~~~~~~ In file included from ./kmers/KmerRecord.h:15, from paths/RemodelGaps.cc:29: ./kmers/KmerShape.h: In static member function ‘static KmerShapeId kmer_shape_zebra::getId()’: ./kmers/KmerShape.h:566:49: error: could not convert ‘kmer_shape_zebra::getStringId()’ from ‘String’ {aka ‘FeudalString’} to ‘KmerShapeId’ 566 | static KmerShapeId getId() { return getStringId(); } | ~~~~~~~~~~~^~ | | | String {aka FeudalString} make[1]: *** [Makefile:8801: RemodelGaps.o] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488/src' make: *** [Makefile:388: all-recursive] Error 1 * ERROR: sci-biology/allpathslg-52488-r2::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/allpathslg-52488-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/allpathslg-52488-r2::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:allpathslg-52488-r2:20190513-213427.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/allpathslg-52488-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/allpathslg-52488-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488' * S: '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488'