* Package: sci-biology/amos-3.1.0-r4 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_musl kernel_linux python_single_target_python2_7 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox * Using python2.7 to build >>> Unpacking source... >>> Unpacking amos-3.1.0.tar.gz to /var/tmp/portage/sci-biology/amos-3.1.0-r4/work >>> Unpacking amos-3.1.0-fix-c++14.patch.bz2 to /var/tmp/portage/sci-biology/amos-3.1.0-r4/work >>> Source unpacked in /var/tmp/portage/sci-biology/amos-3.1.0-r4/work >>> Preparing source in /var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0 ... * Applying amos-3.1.0-gcc-4.7.patch ... [ ok ] * Applying amos-3.1.0-goBambus2.py-indent-and-cleanup.patch ... [ ok ] * Applying amos-3.1.0-fix-c++14.patch ... [ ok ] * Applying amos-3.1.0-qa-Wformat.patch ... [ ok ] * Applying amos-3.1.0-fix-build-system.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0' ... * Running aclocal -I config ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --foreign --force-missing ... [ ok ] * Running elibtoolize in: amos-3.1.0/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0 ... * econf: updating amos-3.1.0/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating amos-3.1.0/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/amos-3.1.0-r4 --htmldir=/usr/share/doc/amos-3.1.0-r4/html --libdir=/usr/lib --with-qmake-qt4=no 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 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 we are using the GNU C++ compiler... yes checking whether x86_64-gentoo-linux-musl-g++ accepts -g... yes 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 we are using the GNU C compiler... yes checking whether x86_64-gentoo-linux-musl-gcc accepts -g... yes checking for x86_64-gentoo-linux-musl-gcc option to accept ISO C89... 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 x86_64-gentoo-linux-musl-ar... x86_64-gentoo-linux-musl-ar checking the archiver (x86_64-gentoo-linux-musl-ar) interface... ar checking how to run the C preprocessor... x86_64-gentoo-linux-musl-gcc -E checking for perl... /usr/bin/perl checking for python... /usr/bin/python2.7 checking for nucmer... /usr/bin/nucmer checking for delta-filter... /usr/bin/delta-filter checking for show-coords... /usr/bin/show-coords checking for blat... : checking for perl module Statistics::Descriptive... ok checking for perl module XML::Parser... ok checking for perl module DBI... ok checking for pow in -lm... yes checking for fopen in -lc... yes checking for main in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... 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 fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for mode_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking whether byte ordering is bigendian... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking whether bitfields are packed htol... no checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for Qt4... disabled checking whether Qt4 works... no checking for Boost... yes checking whether Boost works... yes checking for CA... no checking whether CA works... no checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking for getopt_long_only... yes checking for working strtod... yes checking for isascii... yes checking for strtol... 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 sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking types of arguments for select... int,fd_set *,struct timeval * checking for strftime... yes checking for dup2... yes checking for floor... yes checking for localtime... yes checking for lstat... yes checking for memmove... yes checking for memset... yes checking for mkdir... yes checking for pow... yes checking for rmdir... yes checking for sqrt... yes checking for stat... yes checking for strchr... yes checking for strdup... yes checking for strstr... yes checking build system type... x86_64-gentoo-linux-musl checking host system type... x86_64-gentoo-linux-musl checking whether to build AMOScmp... (cached) no checking whether to build minimus... (cached) no checking whether to build Simulator... (cached) no checking whether to build Experimental... (cached) no checking whether to build all... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/GNU/Makefile config.status: creating src/AMOS/Makefile config.status: creating src/Bambus/Makefile config.status: creating src/Bambus/Bundler/Makefile config.status: creating src/Bambus/Output/Makefile config.status: creating src/Bambus/Untangler/Makefile config.status: creating src/Common/Makefile config.status: creating src/Graph/Makefile config.status: creating src/Slice/Makefile config.status: creating src/CelMsg/Makefile config.status: creating src/Message/Makefile config.status: creating src/Bank/Makefile config.status: creating src/Align/Makefile config.status: creating src/Tigger/Makefile config.status: creating src/Compare/Makefile config.status: creating src/Casm/Makefile config.status: creating src/CtgTrim/Makefile config.status: creating src/Sim/Makefile config.status: creating src/Validation/Makefile config.status: creating src/Converters/Makefile config.status: creating src/Utils/Makefile config.status: creating src/PerlModules/Makefile config.status: creating src/PythonModules/Makefile config.status: creating src/Pipeline/Makefile config.status: creating src/Staden/Makefile config.status: creating src/Staden/read/Makefile config.status: creating src/Staden/progs/Makefile config.status: creating src/Contig/Makefile config.status: creating src/Foundation/Makefile config.status: creating src/hawkeye/Makefile config.status: creating src/Experimental/Makefile config.status: creating config.h config.status: executing depfiles commands -- AMOS Assembler 3.1.0 Configuration Results -- C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native C++ compiler: x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp GCC version: x86_64-gentoo-linux-musl-gcc (Gentoo 9.3.0 p1) 9.3.0 Host System type: x86_64-gentoo-linux-musl Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. WARNING! BLAT was not found but is required to run minimus2-blat install BLAT if planning on using minimus2-blat WARNING! Qt4 toolkit was not found but is required to run AMOS GUIs install Qt4 or locate Qt4 with configure to build GUIs see config.log for more information on what went wrong >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0 ... make -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src' Making all in GNU make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/GNU' make all-am make[4]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/GNU' x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -c -o gnu.o gnu.c rm -f libGNU.a x86_64-gentoo-linux-musl-ar cru libGNU.a gnu.o x86_64-gentoo-linux-musl-ranlib libGNU.a make[4]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/GNU' make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/GNU' Making all in AMOS make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/AMOS' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-BankStream_AMOS.o `test -f 'BankStream_AMOS.cc' || echo './'`BankStream_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Bank_AMOS.o `test -f 'Bank_AMOS.cc' || echo './'`Bank_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-ContigEdge_AMOS.o `test -f 'ContigEdge_AMOS.cc' || echo './'`ContigEdge_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-ContigIterator_AMOS.o `test -f 'ContigIterator_AMOS.cc' || echo './'`ContigIterator_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-ContigLink_AMOS.o `test -f 'ContigLink_AMOS.cc' || echo './'`ContigLink_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Motif_AMOS.o `test -f 'Motif_AMOS.cc' || echo './'`Motif_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Contig_AMOS.o `test -f 'Contig_AMOS.cc' || echo './'`Contig_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Edge_AMOS.o `test -f 'Edge_AMOS.cc' || echo './'`Edge_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Feature_AMOS.o `test -f 'Feature_AMOS.cc' || echo './'`Feature_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Fragment_AMOS.o `test -f 'Fragment_AMOS.cc' || echo './'`Fragment_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Group_AMOS.o `test -f 'Group_AMOS.cc' || echo './'`Group_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-IDMap_AMOS.o `test -f 'IDMap_AMOS.cc' || echo './'`IDMap_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Index_AMOS.o `test -f 'Index_AMOS.cc' || echo './'`Index_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Kmer_AMOS.o `test -f 'Kmer_AMOS.cc' || echo './'`Kmer_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Layout_AMOS.o `test -f 'Layout_AMOS.cc' || echo './'`Layout_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Library_AMOS.o `test -f 'Library_AMOS.cc' || echo './'`Library_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Link_AMOS.o `test -f 'Link_AMOS.cc' || echo './'`Link_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Message_AMOS.o `test -f 'Message_AMOS.cc' || echo './'`Message_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Overlap_AMOS.o `test -f 'Overlap_AMOS.cc' || echo './'`Overlap_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Read_AMOS.o `test -f 'Read_AMOS.cc' || echo './'`Read_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-ScaffoldEdge_AMOS.o `test -f 'ScaffoldEdge_AMOS.cc' || echo './'`ScaffoldEdge_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-ScaffoldLink_AMOS.o `test -f 'ScaffoldLink_AMOS.cc' || echo './'`ScaffoldLink_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Scaffold_AMOS.o `test -f 'Scaffold_AMOS.cc' || echo './'`Scaffold_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Sequence_AMOS.o `test -f 'Sequence_AMOS.cc' || echo './'`Sequence_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-Universal_AMOS.o `test -f 'Universal_AMOS.cc' || echo './'`Universal_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-datatypes_AMOS.o `test -f 'datatypes_AMOS.cc' || echo './'`datatypes_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-universals_AMOS.o `test -f 'universals_AMOS.cc' || echo './'`universals_AMOS.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -Wno-cpp -c -o libAMOS_a-utility_AMOS.o `test -f 'utility_AMOS.cc' || echo './'`utility_AMOS.cc rm -f libAMOS.a x86_64-gentoo-linux-musl-ar cru libAMOS.a libAMOS_a-BankStream_AMOS.o libAMOS_a-Bank_AMOS.o libAMOS_a-ContigEdge_AMOS.o libAMOS_a-ContigIterator_AMOS.o libAMOS_a-ContigLink_AMOS.o libAMOS_a-Motif_AMOS.o libAMOS_a-Contig_AMOS.o libAMOS_a-Edge_AMOS.o libAMOS_a-Feature_AMOS.o libAMOS_a-Fragment_AMOS.o libAMOS_a-Group_AMOS.o libAMOS_a-IDMap_AMOS.o libAMOS_a-Index_AMOS.o libAMOS_a-Kmer_AMOS.o libAMOS_a-Layout_AMOS.o libAMOS_a-Library_AMOS.o libAMOS_a-Link_AMOS.o libAMOS_a-Message_AMOS.o libAMOS_a-Overlap_AMOS.o libAMOS_a-Read_AMOS.o libAMOS_a-ScaffoldEdge_AMOS.o libAMOS_a-ScaffoldLink_AMOS.o libAMOS_a-Scaffold_AMOS.o libAMOS_a-Sequence_AMOS.o libAMOS_a-Universal_AMOS.o libAMOS_a-datatypes_AMOS.o libAMOS_a-universals_AMOS.o libAMOS_a-utility_AMOS.o x86_64-gentoo-linux-musl-ranlib libAMOS.a make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/AMOS' Making all in Common make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Common' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o amp.o amp.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o delcher.o delcher.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o delta.o delta.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o fasta.o fasta.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o prob.o prob.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o fastq.o fastq.cc rm -f libCommon.a x86_64-gentoo-linux-musl-ar cru libCommon.a amp.o delcher.o delta.o fasta.o prob.o fastq.o x86_64-gentoo-linux-musl-ranlib libCommon.a make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Common' Making all in Foundation make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Foundation' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o CategoryInformation.o CategoryInformation.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o ConfigFile.o ConfigFile.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o ConfigSection.o ConfigSection.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o Exceptions.o Exceptions.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o FileSystem.o FileSystem.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o LogCategory.o LogCategory.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o Logger.o Logger.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o LogMsg.o LogMsg.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o OptionResult.o OptionResult.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o Options.o Options.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o AMOS_Foundation.o AMOS_Foundation.cc rm -f libAMOSFoundation.a x86_64-gentoo-linux-musl-ar cru libAMOSFoundation.a CategoryInformation.o ConfigFile.o ConfigSection.o Exceptions.o FileSystem.o LogCategory.o Logger.o LogMsg.o OptionResult.o Options.o AMOS_Foundation.o x86_64-gentoo-linux-musl-ranlib libAMOSFoundation.a make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Foundation' Making all in Graph make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Graph' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o Edge.o Edge.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o Graph.o Graph.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o Node.o Node.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o SubGraph.o SubGraph.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o CompositeNode.o CompositeNode.cc rm -f libGraph.a x86_64-gentoo-linux-musl-ar cru libGraph.a Edge.o Graph.o Node.o SubGraph.o CompositeNode.o x86_64-gentoo-linux-musl-ranlib libGraph.a make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Graph' Making all in Slice make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Slice' x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -c -o getConsQC.o getConsQC.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -c -o getConsQV.o getConsQV.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -c -o newmem.o newmem.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -march=native -c -o utility.o utility.c rm -f libSlice.a x86_64-gentoo-linux-musl-ar cru libSlice.a getConsQC.o getConsQV.o newmem.o utility.o x86_64-gentoo-linux-musl-ranlib libSlice.a make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Slice' Making all in CelMsg make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/CelMsg' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o CelMsg.o CelMsg.cc rm -f libCelMsg.a x86_64-gentoo-linux-musl-ar cru libCelMsg.a CelMsg.o x86_64-gentoo-linux-musl-ranlib libCelMsg.a make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/CelMsg' Making all in Message make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Message' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o message-count.o message-count.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o message-count message-count.o ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o message-extract.o message-extract.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o message-extract message-extract.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o message-validate.o message-validate.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o message-validate message-validate.o ../../src/AMOS/libAMOS.a -lz -lc -lm make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Message' Making all in Bank make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bank' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank2contig.o bank2contig.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank2contig bank2contig.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank2lib.o bank2lib.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank2lib bank2lib.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank2coverage.o bank2coverage.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank2coverage bank2coverage.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Slice/libSlice.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o bank2fasta-bank2fasta.o `test -f 'bank2fasta.cc' || echo './'`bank2fasta.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank2fasta bank2fasta-bank2fasta.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank2scaff.o bank2scaff.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank2scaff bank2scaff.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank-clean.o bank-clean.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank-clean bank-clean.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank-combine.o bank-combine.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank-combine bank-combine.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank-mapping.o bank-mapping.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank-mapping bank-mapping.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank-report.o bank-report.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank-report bank-report.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank-transact.o bank-transact.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank-transact bank-transact.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o bank-tutorial.o bank-tutorial.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bank-tutorial bank-tutorial.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o dumpFeatures.o dumpFeatures.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o dumpFeatures dumpFeatures.o ../../src/Foundation/libAMOSFoundation.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o dumpmates.o dumpmates.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o dumpmates dumpmates.o ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o dumpreads.o dumpreads.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o dumpreads dumpreads.o ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o extractContig.o extractContig.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o extractContig extractContig.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o findMissingMates.o findMissingMates.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o findMissingMates findMissingMates.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o grow-readbank.o grow-readbank.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o grow-readbank grow-readbank.o ../../src/CelMsg/libCelMsg.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o listReadPlacedStatus.o listReadPlacedStatus.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o listReadPlacedStatus listReadPlacedStatus.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o listGCContent.o listGCContent.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o listGCContent listGCContent.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o load-overlaps.o load-overlaps.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o load-overlaps load-overlaps.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o loadFeatures.o loadFeatures.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o loadFeatures loadFeatures.o ../../src/Foundation/libAMOSFoundation.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o normalizeScaffold.o normalizeScaffold.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o normalizeScaffold normalizeScaffold.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o renameReads.o renameReads.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o renameReads renameReads.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o resetFragLibrary.o resetFragLibrary.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o resetFragLibrary resetFragLibrary.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o revScaffold.o revScaffold.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o revScaffold revScaffold.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o select-reads.o select-reads.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o select-reads select-reads.o ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o simplifyLibraries-simplifyLibraries.o `test -f 'simplifyLibraries.cc' || echo './'`simplifyLibraries.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o simplifyLibraries simplifyLibraries-simplifyLibraries.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o simpleContigLoader.o simpleContigLoader.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o simpleContigLoader simpleContigLoader.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o updateBankPositions.o updateBankPositions.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o updateBankPositions updateBankPositions.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o updateClrRanges.o updateClrRanges.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o updateClrRanges updateClrRanges.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o updateLibSizes.o updateLibSizes.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o updateLibSizes updateLibSizes.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o dumpContigsAsReads-dumpContigsAsReads.o `test -f 'dumpContigsAsReads.cc' || echo './'`dumpContigsAsReads.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o dumpContigsAsReads dumpContigsAsReads-dumpContigsAsReads.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o partitionBank-partitionBank.o `test -f 'partitionBank.cc' || echo './'`partitionBank.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o partitionBank partitionBank-partitionBank.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bank' Making all in Align make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Align' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o arrive.o arrive.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o arrive arrive.o -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o arrive2.o arrive2.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o arrive2 arrive2.o ../../src/Common/libCommon.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o genome-complexity-fast.o genome-complexity-fast.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o genome-complexity genome-complexity-fast.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a ../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o genome-complexity-fast genome-complexity-fast.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a ../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o count-kmers.o count-kmers.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o count-kmers count-kmers.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o find-tandem.o find-tandem.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o find-tandem find-tandem.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o count-qmers.o count-qmers.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o count-qmers count-qmers.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o qmer-filter.o qmer-filter.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o qmer-filter qmer-filter.o -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o frg-umd-merge.o frg-umd-merge.cc frg-umd-merge.cc: In function ‘int main(int, char**)’: frg-umd-merge.cc:115:24: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 115 | p = "XXX"; | ^~~~~ x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o frg-umd-merge frg-umd-merge.o ../../src/CelMsg/libCelMsg.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o gap-links.o gap-links.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gap-links gap-links.o ../../src/Common/libCommon.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o hash-overlap.o hash-overlap.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o align.o align.cc rm -f libAlign.a x86_64-gentoo-linux-musl-ar cru libAlign.a align.o x86_64-gentoo-linux-musl-ranlib libAlign.a x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o hash-overlap hash-overlap.o libAlign.a ../../src/CelMsg/libCelMsg.a ../../src/Slice/libSlice.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o kmer-count.o kmer-count.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o kmer-count kmer-count.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o kmer-cov.o kmer-cov.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o kmer-cov kmer-cov.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o kmer-cov-plot.o kmer-cov-plot.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o kmer-cov-plot kmer-cov-plot.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o make-consensus.o make-consensus.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o make-consensus make-consensus.o libAlign.a ../../src/CelMsg/libCelMsg.a ../../src/Slice/libSlice.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o make-consensus_poly.o make-consensus_poly.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o align_poly.o align_poly.cc rm -f libAlign_poly.a x86_64-gentoo-linux-musl-ar cru libAlign_poly.a align_poly.o x86_64-gentoo-linux-musl-ranlib libAlign_poly.a x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o make-consensus_poly make-consensus_poly.o libAlign_poly.a ../../src/CelMsg/libCelMsg.a ../../src/Slice/libSlice.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o merge-contigs.o merge-contigs.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o merge-contigs merge-contigs.o libAlign.a ../../src/CelMsg/libCelMsg.a ../../src/Slice/libSlice.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o missing-reads.o missing-reads.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o missing-reads missing-reads.o -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o ovl-degr-dist.o ovl-degr-dist.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ovl-degr-dist ovl-degr-dist.o ../../src/Common/libCommon.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o overlap-align.o overlap-align.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o overlap-align overlap-align.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o readinfo2cam.o readinfo2cam.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o readinfo2cam readinfo2cam.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o running-cmp.o running-cmp.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o running-cmp running-cmp.o ../../src/Common/libCommon.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o show-ma-asm.o show-ma-asm.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o show-ma-asm show-ma-asm.o libAlign.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o sim-cover-depth.o sim-cover-depth.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o sim-cover-depth sim-cover-depth.o ../../src/Common/libCommon.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o sim-cover2.o sim-cover2.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o sim-cover2 sim-cover2.o ../../src/Common/libCommon.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o sim-shotgun.o sim-shotgun.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o sim-shotgun sim-shotgun.o ../../src/Common/libCommon.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o simple-overlap.o simple-overlap.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o simple-overlap simple-overlap.o libAlign.a ../../src/CelMsg/libCelMsg.a ../../src/Slice/libSlice.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -march=native -Wno-cpp -c -o verify-layout.o verify-layout.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o verify-layout verify-layout.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a ../../src/GNU/libGNU.a -lz -lc -lm make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Align' Making all in Tigger make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Tigger' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -I../../src/Graph -O2 -pipe -march=native -Wno-cpp -c -o Unitigger.o Unitigger.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -I../../src/Graph -O2 -pipe -march=native -Wno-cpp -c -o TiggerIO.o TiggerIO.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o tigger Unitigger.o TiggerIO.o ../../src/Graph/libGraph.a ../../src/AMOS/libAMOS.a -lz -lc -lm make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Tigger' Making all in Compare make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Compare' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -O2 -pipe -march=native -Wno-cpp -c -o contig-cmp.o contig-cmp.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o contig-cmp contig-cmp.o ../../src/Common/libCommon.a -lz -lc -lm make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Compare' Making all in Bambus make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus' Making all in Bundler make[4]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus/Bundler' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o Bundler.o Bundler.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o Bundler Bundler.o ../../../src/Common/libCommon.a ../../../src/AMOS/libAMOS.a ../../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o clk.o clk.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o clk clk.o ../../../src/Common/libCommon.a ../../../src/AMOS/libAMOS.a ../../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o MarkRepeats.o MarkRepeats.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I/usr/include -DAMOS_HAVE_BOOST -I../../../src/GNU -I../../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o libBundler_a-Utilities_Bundler.o `test -f 'Utilities_Bundler.cc' || echo './'`Utilities_Bundler.cc rm -f libBundler.a x86_64-gentoo-linux-musl-ar cru libBundler.a libBundler_a-Utilities_Bundler.o x86_64-gentoo-linux-musl-ranlib libBundler.a x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o MarkRepeats MarkRepeats.o libBundler.a ../../../src/Common/libCommon.a ../../../src/AMOS/libAMOS.a ../../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o FilterEdgesByCluster.o FilterEdgesByCluster.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o FilterEdgesByCluster FilterEdgesByCluster.o libBundler.a ../../../src/Common/libCommon.a ../../../src/AMOS/libAMOS.a ../../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o OrientContigs.o OrientContigs.cc OrientContigs.cc: In function ‘int32_t computeContigPositionUsingAllEdges(AMOS::ID_t, __gnu_cxx::hash_map, std::equal_to >&, __gnu_cxx::hash_map, std::equal_to >&, __gnu_cxx::hash_map*, __gnu_cxx::hash, std::equal_to >&, AMOS::Bank_t&, AMOS::Bank_t&, double, bool)’: OrientContigs.cc:600:1: warning: no return statement in function returning non-void [-Wreturn-type] 600 | } | ^ x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o OrientContigs OrientContigs.o libBundler.a ../../../src/Common/libCommon.a ../../../src/AMOS/libAMOS.a ../../../src/GNU/libGNU.a -lz -lc -lm make[4]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus/Bundler' Making all in Output make[4]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus/Output' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I../../../src/Bambus/Bundler -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o Position.o Position.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I../../../src/Bambus/Bundler -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o OutputMotifs.o OutputMotifs.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o OutputMotifs Position.o OutputMotifs.o ../../../src/Bambus/Bundler/libBundler.a ../../../src/Common/libCommon.a ../../../src/AMOS/libAMOS.a ../../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I../../../src/Bambus/Bundler -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o OutputScaffolds.o OutputScaffolds.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o OutputScaffolds Position.o OutputScaffolds.o ../../../src/Bambus/Bundler/libBundler.a ../../../src/Common/libCommon.a ../../../src/AMOS/libAMOS.a ../../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I../../../src/Bambus/Bundler -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o Linearize.o Linearize.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o Linearize Linearize.o ../../../src/Bambus/Bundler/libBundler.a ../../../src/Common/libCommon.a ../../../src/AMOS/libAMOS.a ../../../src/GNU/libGNU.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I../../../src/Bambus/Bundler -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o Output_Utils.o Output_Utils.cc x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../../.. -I../../../src/Common -I../../../src/AMOS -I../../../src/GNU -I../../../src/Bambus/Bundler -I/usr/include -DAMOS_HAVE_BOOST -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pedantic -O2 -pipe -march=native -Wno-cpp -c -o OutputResults.o OutputResults.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o OutputResults Output_Utils.o OutputResults.o ../../../src/Bambus/Bundler/libBundler.a ../../../src/Common/libCommon.a ../../../src/AMOS/libAMOS.a ../../../src/GNU/libGNU.a -lz -lc -lm make[4]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus/Output' Making all in Untangler make[4]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus/Untangler' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus/Untangler' make[4]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus' make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Bambus' Making all in Casm make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Casm' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o casm-layout.o casm-layout.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o casm-layout casm-layout.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o casm-breaks.o casm-breaks.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o casm-breaks casm-breaks.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -march=native -Wno-cpp -c -o casm-libsize.o casm-libsize.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o casm-libsize casm-libsize.o ../../src/AMOS/libAMOS.a -lz -lc -lm make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Casm' Making all in CtgTrim make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/CtgTrim' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/CtgTrim' Making all in Sim make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Sim' x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o pyrosim.o pyrosim.cc x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o pyrosim pyrosim.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/GNU -O2 -pipe -march=native -Wno-cpp -c -o tandemCollapse.o tandemCollapse.cc tandemCollapse.cc: In function ‘bool GetOptions(int, char**)’: tandemCollapse.cc:117:1: warning: control reaches end of non-void function [-Wreturn-type] 117 | } // GetOptions | ^ x86_64-gentoo-linux-musl-g++ -O2 -pipe -march=native -Wno-cpp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o tandemCollapse tandemCollapse.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Sim' Making all in Staden make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Staden' Making all in read make[4]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Staden/read' x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o Read.o Read.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o array.o array.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o compress.o compress.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o ctfCompress.o ctfCompress.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o error.o error.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o expFileIO.o expFileIO.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o files.o files.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o find.o find.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o fpoint.o fpoint.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o mach-io.o mach-io.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o misc_scf.o misc_scf.c x86_64-gentoo-linux-musl-gcc -DHAVE_CONFIG_H -I. -I../../.. -O2 -pipe -march=native -c -o open_trace_file.o open_trace_file.c open_trace_file.c: In function ‘find_file_dir’: open_trace_file.c:296:16: error: ‘MAXNAMLEN’ undeclared (first use in this function) 296 | char fname[MAXNAMLEN + 1], filename[MAXNAMLEN + 1], *sptr; | ^~~~~~~~~ open_trace_file.c:296:16: note: each undeclared identifier is reported only once for each function it appears in make[4]: *** [Makefile:464: open_trace_file.o] Error 1 make[4]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Staden/read' make[3]: *** [Makefile:362: all-recursive] Error 1 make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src/Staden' make[2]: *** [Makefile:422: all-recursive] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0/src' make[1]: *** [Makefile:413: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0' make: *** [Makefile:354: all] Error 2 * ERROR: sci-biology/amos-3.1.0-r4::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/amos-3.1.0-r4::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/amos-3.1.0-r4::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:amos-3.1.0-r4:20200330-074528.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/amos-3.1.0-r4/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/amos-3.1.0-r4/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0' * S: '/var/tmp/portage/sci-biology/amos-3.1.0-r4/work/amos-3.1.0'