* Package: sci-biology/amos-3.1.0-r1 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 qt4 userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking amos-3.1.0.tar.gz to /var/tmp/portage/sci-biology/amos-3.1.0-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/amos-3.1.0-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/amos-3.1.0-r1/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 ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/amos-3.1.0-r1/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-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --libdir=/usr/lib64 checking for a BSD-compatible install... /usr/lib/portage/python3.4/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 for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-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-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-g++... none checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for gawk... (cached) gawk checking whether ln -s works... yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for perl... /usr/bin/perl checking for python... /usr/bin/python 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... /usr/bin/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... yes checking whether Qt4 works... no checking for Boost... no checking whether Boost works... no 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-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu 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 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-pc-linux-gnu-gcc -march=native -O2 -pipe C++ compiler: x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe GCC version: x86_64-pc-linux-gnu-gcc (Gentoo 6.2.0-r1 p1.1) 6.2.0 Host System type: x86_64-pc-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. WARNING! Qt4 toolkit malfunctioning but is required to run AMOS GUIs try compiling GUIs manually or reinstall Qt4 toolkit to build GUIs see config.log for more information on what went wrong WARNING! Boost graph toolkit was not found but is required to run parts of the AMOS Scaffolder (Bambus 2) install Boost or locate Boost with configure to build Scaffolder see config.log for more information on what went wrong >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0 ... make -j1 -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0/src' Making all in GNU make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0/src/GNU' make all-am make[4]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0/src/GNU' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c gnu.c rm -f libGNU.a ar cru libGNU.a gnu.o x86_64-pc-linux-gnu-ranlib libGNU.a make[4]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0/src/GNU' make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0/src/GNU' Making all in AMOS make[3]: Entering directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0/src/AMOS' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-BankStream_AMOS.o `test -f 'BankStream_AMOS.cc' || echo './'`BankStream_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Bank_AMOS.hh:22, from BankStream_AMOS.hh:13, from BankStream_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Bank_AMOS.hh:22, from BankStream_AMOS.hh:13, from BankStream_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Bank_AMOS.o `test -f 'Bank_AMOS.cc' || echo './'`Bank_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Bank_AMOS.hh:22, from Bank_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Bank_AMOS.hh:22, from Bank_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-ContigEdge_AMOS.o `test -f 'ContigEdge_AMOS.cc' || echo './'`ContigEdge_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from ContigEdge_AMOS.hh:13, from ContigEdge_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from ContigEdge_AMOS.hh:13, from ContigEdge_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-ContigIterator_AMOS.o `test -f 'ContigIterator_AMOS.cc' || echo './'`ContigIterator_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Sequence_AMOS.hh:13, from Contig_AMOS.hh:13, from ContigIterator_AMOS.hh:15, from ContigIterator_AMOS.cc:3: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Sequence_AMOS.hh:13, from Contig_AMOS.hh:13, from ContigIterator_AMOS.hh:15, from ContigIterator_AMOS.cc:3: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-ContigLink_AMOS.o `test -f 'ContigLink_AMOS.cc' || echo './'`ContigLink_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from ContigLink_AMOS.hh:13, from ContigLink_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from ContigLink_AMOS.hh:13, from ContigLink_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Motif_AMOS.o `test -f 'Motif_AMOS.cc' || echo './'`Motif_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Motif_AMOS.hh:13, from Motif_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Motif_AMOS.hh:13, from Motif_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Contig_AMOS.o `test -f 'Contig_AMOS.cc' || echo './'`Contig_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Sequence_AMOS.hh:13, from Contig_AMOS.hh:13, from Contig_AMOS.cc:11: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Sequence_AMOS.hh:13, from Contig_AMOS.hh:13, from Contig_AMOS.cc:11: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Edge_AMOS.o `test -f 'Edge_AMOS.cc' || echo './'`Edge_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from Edge_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from Edge_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Feature_AMOS.o `test -f 'Feature_AMOS.cc' || echo './'`Feature_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Feature_AMOS.hh:13, from Feature_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Feature_AMOS.hh:13, from Feature_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Fragment_AMOS.o `test -f 'Fragment_AMOS.cc' || echo './'`Fragment_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Fragment_AMOS.hh:13, from Fragment_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Fragment_AMOS.hh:13, from Fragment_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Group_AMOS.o `test -f 'Group_AMOS.cc' || echo './'`Group_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Group_AMOS.hh:13, from Group_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Group_AMOS.hh:13, from Group_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-IDMap_AMOS.o `test -f 'IDMap_AMOS.cc' || echo './'`IDMap_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from IDMap_AMOS.hh:13, from IDMap_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from IDMap_AMOS.hh:13, from IDMap_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Index_AMOS.o `test -f 'Index_AMOS.cc' || echo './'`Index_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from ContigEdge_AMOS.hh:13, from universals_AMOS.hh:13, from Index_AMOS.hh:13, from Index_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from ContigEdge_AMOS.hh:13, from universals_AMOS.hh:13, from Index_AMOS.hh:13, from Index_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Kmer_AMOS.o `test -f 'Kmer_AMOS.cc' || echo './'`Kmer_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Kmer_AMOS.hh:13, from Kmer_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Kmer_AMOS.hh:13, from Kmer_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Layout_AMOS.o `test -f 'Layout_AMOS.cc' || echo './'`Layout_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Layout_AMOS.hh:13, from Layout_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Layout_AMOS.hh:13, from Layout_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Library_AMOS.o `test -f 'Library_AMOS.cc' || echo './'`Library_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Library_AMOS.hh:13, from Library_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Library_AMOS.hh:13, from Library_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Link_AMOS.o `test -f 'Link_AMOS.cc' || echo './'`Link_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Link_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Link_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Message_AMOS.o `test -f 'Message_AMOS.cc' || echo './'`Message_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Message_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Message_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Overlap_AMOS.o `test -f 'Overlap_AMOS.cc' || echo './'`Overlap_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Overlap_AMOS.hh:13, from Overlap_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Overlap_AMOS.hh:13, from Overlap_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Read_AMOS.o `test -f 'Read_AMOS.cc' || echo './'`Read_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Sequence_AMOS.hh:13, from Read_AMOS.hh:13, from Read_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Sequence_AMOS.hh:13, from Read_AMOS.hh:13, from Read_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-ScaffoldEdge_AMOS.o `test -f 'ScaffoldEdge_AMOS.cc' || echo './'`ScaffoldEdge_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from ScaffoldEdge_AMOS.hh:13, from ScaffoldEdge_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from ScaffoldEdge_AMOS.hh:13, from ScaffoldEdge_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-ScaffoldLink_AMOS.o `test -f 'ScaffoldLink_AMOS.cc' || echo './'`ScaffoldLink_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from ScaffoldLink_AMOS.hh:13, from ScaffoldLink_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from ScaffoldLink_AMOS.hh:13, from ScaffoldLink_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Scaffold_AMOS.o `test -f 'Scaffold_AMOS.cc' || echo './'`Scaffold_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Scaffold_AMOS.hh:13, from Scaffold_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Scaffold_AMOS.hh:13, from Scaffold_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Sequence_AMOS.o `test -f 'Sequence_AMOS.cc' || echo './'`Sequence_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Sequence_AMOS.hh:13, from Sequence_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Sequence_AMOS.hh:13, from Sequence_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-Universal_AMOS.o `test -f 'Universal_AMOS.cc' || echo './'`Universal_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Universal_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Universal_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-datatypes_AMOS.o `test -f 'datatypes_AMOS.cc' || echo './'`datatypes_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from datatypes_AMOS.hh:17, from datatypes_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from datatypes_AMOS.hh:17, from datatypes_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-universals_AMOS.o `test -f 'universals_AMOS.cc' || echo './'`universals_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from ContigEdge_AMOS.hh:13, from universals_AMOS.hh:13, from universals_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from Message_AMOS.hh:14, from Universal_AMOS.hh:13, from Link_AMOS.hh:13, from Edge_AMOS.hh:13, from ContigEdge_AMOS.hh:13, from universals_AMOS.hh:13, from universals_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -march=native -O2 -pipe -c -o libAMOS_a-utility_AMOS.o `test -f 'utility_AMOS.cc' || echo './'`utility_AMOS.cc In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ext/hash_map:60:0, from utility_AMOS.hh:48, from utility_AMOS.cc:10: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from utility_AMOS.hh:13:0, from utility_AMOS.cc:10: inttypes_AMOS.hh: In function ‘std::__cxx11::string AMOS::Decode(AMOS::NCode_t)’: inttypes_AMOS.hh:78:25: warning: narrowing conversion of ‘(ncode & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:78:55: warning: narrowing conversion of ‘((ncode >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ inttypes_AMOS.hh:79:35: warning: narrowing conversion of ‘(((ncode >> 8) >> 8) & 127u)’ from ‘AMOS::NCode_t {aka unsigned int}’ to ‘char’ inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ utility_AMOS.cc: At global scope: utility_AMOS.cc:35:3: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] }; ^ utility_AMOS.cc:35:3: error: narrowing conversion of ‘129’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘130’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘131’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘132’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘133’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘134’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘135’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘136’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘137’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘138’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘139’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘140’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘141’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘142’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘143’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘144’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘145’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘146’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘147’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘148’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘149’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘150’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘151’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘152’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘153’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘154’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘155’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘156’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘157’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘158’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘159’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘160’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘161’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘162’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘163’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘164’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘165’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘166’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘167’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘168’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘169’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘170’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘171’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘172’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘173’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘174’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘175’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘176’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘177’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘178’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘179’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘180’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘181’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘182’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘183’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘184’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘185’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘186’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘187’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘188’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘189’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘190’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘191’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘192’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘193’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘194’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘195’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘196’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘197’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘198’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘199’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘200’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘201’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘202’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘203’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘204’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘205’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘206’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘207’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘208’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘209’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘210’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘211’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘212’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘213’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘214’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘215’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘216’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘217’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘218’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘219’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘220’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘221’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘222’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘223’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘224’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘225’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘226’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘227’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘228’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘229’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘230’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘231’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘232’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘233’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘234’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘235’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘236’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘237’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘238’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘239’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘240’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘241’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘242’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘243’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘244’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘245’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘246’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘247’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘248’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘249’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘250’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘251’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘252’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘253’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘254’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] utility_AMOS.cc:35:3: error: narrowing conversion of ‘255’ from ‘int’ to ‘char’ inside { } [-Wnarrowing] make[3]: *** [Makefile:899: libAMOS_a-utility_AMOS.o] Error 1 make[3]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0/src/AMOS' make[2]: *** [Makefile:325: all-recursive] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0/src' make[1]: *** [Makefile:306: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0' make: *** [Makefile:244: all] Error 2 * ERROR: sci-biology/amos-3.1.0-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/amos-3.1.0-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/amos-3.1.0-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:amos-3.1.0-r1:20160923-145247.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/amos-3.1.0-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/amos-3.1.0-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0' * S: '/var/tmp/portage/sci-biology/amos-3.1.0-r1/work/amos-3.1.0'