sci-biology:amos-3.1.0-r4:20200330-074528.log

sci-biology:amos-3.1.0-r4:20200330-074528.log (text/plain), 68.57 KB, created by Toralf Förster on 2020-03-30 08:56:51 UTC

 * Package:    sci-biology/amos-3.1.0-r4
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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 <[e-mail]> 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
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Making all in CelMsg
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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
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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 
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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 
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Making all in Tigger
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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 
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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 
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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<unsigned int, int, __gnu_cxx::hash<unsigned int>, std::equal_to<unsigned int> >&, __gnu_cxx::hash_map<unsigned int, Bundler::contigOrientation, __gnu_cxx::hash<unsigned int>, std::equal_to<unsigned int> >&, __gnu_cxx::hash_map<unsigned int, std::set<unsigned int, Bundler::EdgeWeightCmp>*, __gnu_cxx::hash<unsigned int>, std::equal_to<unsigned int> >&, 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'