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Gentoo's Bugzilla – Attachment 519766 Details for
Bug 647878
sci-biology/vaal-46233-r2 : /.../ld: cannot find -lieee
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sci-biology:vaal-46233-r2:20180216-114706.log
sci-biology:vaal-46233-r2:20180216-114706.log (text/plain), 87.92 KB, created by
Toralf Förster
on 2018-02-16 17:21:55 UTC
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hide
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Description:
sci-biology:vaal-46233-r2:20180216-114706.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2018-02-16 17:21:55 UTC
Size:
87.92 KB
patch
obsolete
> * Package: sci-biology/vaal-46233-r2 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux openmp userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking vaal-46233.tar.gz to /var/tmp/portage/sci-biology/vaal-46233-r2/work >>>> Unpacking VAAL_manual.doc to /var/tmp/portage/sci-biology/vaal-46233-r2/work >unpack VAAL_manual.doc: file format not recognized. Ignoring. >>>> Unpacking vaal-46233_remove-namespace-std.patch.bz2 to /var/tmp/portage/sci-biology/vaal-46233-r2/work >>>> Source unpacked in /var/tmp/portage/sci-biology/vaal-46233-r2/work >>>> Preparing source in /var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233 ... > * Applying vaal-46233_remove-namespace-std.patch ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233' ... > * Running libtoolize --install --copy --force --automake ... > [ ok ] > * Running aclocal -I m4 ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --foreign --force-missing ... > [ ok ] > * Running elibtoolize in: vaal-46233/ > * Applying portage/1.2.0 patch ... > * Applying sed/1.5.6 patch ... > * Applying as-needed/2.4.3 patch ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233 ... > * econf: updating vaal-46233/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating vaal-46233/config.guess with /usr/share/gnuconfig/config.guess >./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/vaal-46233-r2 --htmldir=/usr/share/doc/vaal-46233-r2/html --libdir=/usr/lib64 --enable-openmp >checking for a BSD-compatible install... /usr/lib/portage/python3.5/ebuild-helpers/xattr/install -c >checking whether build environment is sane... yes >checking for a thread-safe mkdir -p... /bin/mkdir -p >checking for gawk... gawk >checking whether make sets $(MAKE)... yes >checking whether make supports nested variables... yes >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking how to print strings... printf >checking for style of include used by make... GNU >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking whether the C compiler works... yes >checking for C compiler default output file name... a.out >checking for suffix of executables... >checking whether we are cross compiling... no >checking for suffix of object files... o >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes >checking dependency style of x86_64-pc-linux-gnu-gcc... none >checking for a sed that does not truncate output... /bin/sed >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for fgrep... /bin/grep -F >checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B >checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm >checking whether ln -s works... yes >checking the maximum length of command line arguments... 1572864 >checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop >checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-dlltool... no >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok >checking for sysroot... no >checking for a working dd... /bin/dd >checking how to truncate binary pipes... /bin/dd bs=4096 count=1 >checking for x86_64-pc-linux-gnu-mt... no >checking for mt... no >checking if : is a manifest tool... no >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for ANSI C header files... yes >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking for dlfcn.h... yes >checking for objdir... .libs >checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether stripping libraries is possible... yes >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... no >checking whether to build static libraries... yes >checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ >checking whether we are using the GNU C++ compiler... yes >checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes >checking dependency style of x86_64-pc-linux-gnu-g++... none >checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E >checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (cached) GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether byte ordering is bigendian... no >g++ version is >= 4.7... yes >checking for the pthreads library -lpthreads... no >checking whether pthreads work without any flags... no >checking whether pthreads work with -Kthread... no >checking whether pthreads work with -kthread... no >checking for the pthreads library -llthread... no >checking whether pthreads work with -pthread... yes >checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE >checking if more special flags are required for pthreads... no >checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating src/Makefile >config.status: creating src/config.h >config.status: executing depfiles commands >config.status: executing libtool commands >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233 ... >make -j 1 >Making all in src >make[1]: Entering directory '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233/src' >make all-am >make[2]: Entering directory '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233/src' >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ErrNo.o `test -f 'system/ErrNo.cc' || echo './'`system/ErrNo.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Mutmer.o `test -f 'pairwise_aligners/Mutmer.cc' || echo './'`pairwise_aligners/Mutmer.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LookAlignSort.o `test -f 'lookup/LookAlignSort.cc' || echo './'`lookup/LookAlignSort.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FetchReadsAmb.o FetchReadsAmb.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Floatvector.o Floatvector.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ScoreAlignment.o ScoreAlignment.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Mempool.o `test -f 'feudal/Mempool.cc' || echo './'`feudal/Mempool.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SolexaTools.o `test -f 'solexa/SolexaTools.cc' || echo './'`solexa/SolexaTools.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Basevector.o Basevector.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o KmerBaseBroker.o `test -f 'paths/KmerBaseBroker.cc' || echo './'`paths/KmerBaseBroker.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from paths/KmerBaseBroker.cc:12: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AffineRefiner.o `test -f 'pairwise_aligners/AffineRefiner.cc' || echo './'`pairwise_aligners/AffineRefiner.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o QueryLookupTableCore.o `test -f 'lookup/QueryLookupTableCore.cc' || echo './'`lookup/QueryLookupTableCore.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Permutation.o `test -f 'math/Permutation.cc' || echo './'`math/Permutation.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ParsedArgs.o `test -f 'system/ParsedArgs.cc' || echo './'`system/ParsedArgs.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FeudalFileWriter.o `test -f 'feudal/FeudalFileWriter.cc' || echo './'`feudal/FeudalFileWriter.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Qualvector.o Qualvector.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FileReader.o `test -f 'system/file/FileReader.cc' || echo './'`system/file/FileReader.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Bases.o `test -f 'dna/Bases.cc' || echo './'`dna/Bases.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FeudalControlBlock.o `test -f 'feudal/FeudalControlBlock.cc' || echo './'`feudal/FeudalControlBlock.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AlignCollector.o `test -f 'lookup/AlignCollector.cc' || echo './'`lookup/AlignCollector.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o HoInterval.o `test -f 'math/HoInterval.cc' || echo './'`math/HoInterval.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LookAlignFinder.o `test -f 'lookup/LookAlignFinder.cc' || echo './'`lookup/LookAlignFinder.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Generic.o `test -f 'feudal/Generic.cc' || echo './'`feudal/Generic.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Array.o `test -f 'math/Array.cc' || echo './'`math/Array.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Digraph.o `test -f 'graph/Digraph.cc' || echo './'`graph/Digraph.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Equiv.o Equiv.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ParseRange.o ParseRange.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Vec.o Vec.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o IndexedAlignmentPlusVector.o IndexedAlignmentPlusVector.cc >In file included from IndexedAlignmentPlusVector.h:16:0, > from IndexedAlignmentPlusVector.cc:9: >Alignment.h: In member function âvoid VecAlignmentPlusReader::ReadHalf(vec<alignment_plus>&, vec<unsigned char>&, vec<int>&)â: >Alignment.h:142:7: warning: â<anonymous>.alignment_plus::scoreâ may be used uninitialized in this function [-Wmaybe-uninitialized] > class alignment_plus { > ^~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PerfectCount.o `test -f 'lookup/PerfectCount.cc' || echo './'`lookup/PerfectCount.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FourBase.o `test -f 'solexa/FourBase.cc' || echo './'`solexa/FourBase.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LookAlign.o `test -f 'lookup/LookAlign.cc' || echo './'`lookup/LookAlign.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ProcBuf.o `test -f 'system/ProcBuf.cc' || echo './'`system/ProcBuf.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FieldVec.o `test -f 'feudal/FieldVec.cc' || echo './'`feudal/FieldVec.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FileWriter.o `test -f 'system/file/FileWriter.cc' || echo './'`system/file/FileWriter.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SmithWatAffine.o `test -f 'pairwise_aligners/SmithWatAffine.cc' || echo './'`pairwise_aligners/SmithWatAffine.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ScaffoldAccuracyCore.o `test -f 'reporting/ScaffoldAccuracyCore.cc' || echo './'`reporting/ScaffoldAccuracyCore.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ReadPairing.o ReadPairing.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Misc.o Misc.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PerfStat.o `test -f 'reporting/PerfStat.cc' || echo './'`reporting/PerfStat.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o BaitMap.o `test -f 'util/BaitMap.cc' || echo './'`util/BaitMap.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FeudalTools.o `test -f 'feudal/FeudalTools.cc' || echo './'`feudal/FeudalTools.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PerfectAlignerLG.o `test -f 'pairwise_aligners/PerfectAlignerLG.cc' || echo './'`pairwise_aligners/PerfectAlignerLG.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FetchReads.o FetchReads.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o TraceVal.o `test -f 'system/TraceVal.cc' || echo './'`system/TraceVal.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SortKmersB.o `test -f 'sort_kmers/SortKmersB.cc' || echo './'`sort_kmers/SortKmersB.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SortKmers.o `test -f 'kmers/SortKmers.cc' || echo './'`kmers/SortKmers.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Alignment.o Alignment.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o TempFile.o `test -f 'system/file/TempFile.cc' || echo './'`system/file/TempFile.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ThreadsafeIO.o `test -f 'system/ThreadsafeIO.cc' || echo './'`system/ThreadsafeIO.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Shuffle.o `test -f 'random/Shuffle.cc' || echo './'`random/Shuffle.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AlignSeqsToHyper.o `test -f 'paths/AlignSeqsToHyper.cc' || echo './'`paths/AlignSeqsToHyper.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:19, > from ./paths/AlignSeqsToHyper.h:18, > from paths/AlignSeqsToHyper.cc:9: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >In file included from ./paths/AlignSeqsToHyper.h:20:0, > from paths/AlignSeqsToHyper.cc:9: >./paths/SeqOnHyper.h: In function âvoid AlignSeqsToHyper(const HyperBasevector&, const vecbasevector&, const vec<alignment_plus>&, vec<SeqOnHyper>*, vec<CompressedSeqOnHyper>*)â: >./paths/SeqOnHyper.h:211:37: warning: â<anonymous>.CompressedSeqOnHyper::mp_basesâ may be used uninitialized in this function [-Wmaybe-uninitialized] > : mp_bases ( other.mp_bases ), > ~~~~~~^~~~~~~~ >./paths/SeqOnHyper.h:211:37: warning: â<anonymous>.CompressedSeqOnHyper::mp_basesâ may be used uninitialized in this function [-Wmaybe-uninitialized] > : mp_bases ( other.mp_bases ), > ~~~~~~^~~~~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o KmerPathInterval.o `test -f 'paths/KmerPathInterval.cc' || echo './'`paths/KmerPathInterval.cc >In file included from paths/KmerPathInterval.cc:3:0: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastIfstream.o FastIfstream.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Assert.o `test -f 'system/Assert.cc' || echo './'`system/Assert.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastaConverter.o FastaConverter.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Superb.o Superb.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ArtifactualSequenceDetector.o `test -f 'micro/ArtifactualSequenceDetector.cc' || echo './'`micro/ArtifactualSequenceDetector.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o KmerRecord.o `test -f 'kmers/KmerRecord.cc' || echo './'`kmers/KmerRecord.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LookupTable.o `test -f 'lookup/LookupTable.cc' || echo './'`lookup/LookupTable.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o File.o `test -f 'system/file/File.cc' || echo './'`system/file/File.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SysConf.o `test -f 'system/SysConf.cc' || echo './'`system/SysConf.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SeqOnHyper.o `test -f 'paths/SeqOnHyper.cc' || echo './'`paths/SeqOnHyper.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:19, > from ./paths/SeqOnHyper.h:22, > from paths/SeqOnHyper.cc:10: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o RNGen.o `test -f 'random/RNGen.cc' || echo './'`random/RNGen.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SymLink.o `test -f 'system/file/SymLink.cc' || echo './'`system/file/SymLink.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CharString.o `test -f 'feudal/CharString.cc' || echo './'`feudal/CharString.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastaFileset.o FastaFileset.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o HyperKmerPath.o `test -f 'paths/HyperKmerPath.cc' || echo './'`paths/HyperKmerPath.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from paths/HyperKmerPath.cc:19: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o QualNibbleVec.o `test -f 'feudal/QualNibbleVec.cc' || echo './'`feudal/QualNibbleVec.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PowerOf2.o `test -f 'math/PowerOf2.cc' || echo './'`math/PowerOf2.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o KmerParcels.o `test -f 'kmers/KmerParcels.cc' || echo './'`kmers/KmerParcels.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SuffixTree.o `test -f 'pairwise_aligners/SuffixTree.cc' || echo './'`pairwise_aligners/SuffixTree.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Fastavector.o Fastavector.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o TruePolyCore.o `test -f 'polymorphism/TruePolyCore.cc' || echo './'`polymorphism/TruePolyCore.cc >In file included from ./paths/KmerPath.h:20:0, > from polymorphism/TruePolyCore.cc:22: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o TokenizeString.o TokenizeString.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o KmerParcelsBuilder.o `test -f 'kmers/kmer_parcels/KmerParcelsBuilder.cc' || echo './'`kmers/kmer_parcels/KmerParcelsBuilder.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FourBase2.o `test -f 'solexa/FourBase2.cc' || echo './'`solexa/FourBase2.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Crash.o `test -f 'system/Crash.cc' || echo './'`system/Crash.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o UseGDB.o `test -f 'system/UseGDB.cc' || echo './'`system/UseGDB.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ImperfectLookup.o `test -f 'lookup/ImperfectLookup.cc' || echo './'`lookup/ImperfectLookup.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o VecString.o VecString.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o KmerShape.o `test -f 'kmers/KmerShape.cc' || echo './'`kmers/KmerShape.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LockedData.o `test -f 'system/LockedData.cc' || echo './'`system/LockedData.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Arith.o `test -f 'math/Arith.cc' || echo './'`math/Arith.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o BasevectorTools.o BasevectorTools.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o VecAlignmentPlus.o VecAlignmentPlus.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastaFilestream.o FastaFilestream.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FeudalFileReader.o `test -f 'feudal/FeudalFileReader.cc' || echo './'`feudal/FeudalFileReader.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Exit.o `test -f 'system/Exit.cc' || echo './'`system/Exit.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SmithWatBandedA.o `test -f 'pairwise_aligners/SmithWatBandedA.cc' || echo './'`pairwise_aligners/SmithWatBandedA.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FlowAlignSummary.o `test -f 'lookup/FlowAlignSummary.cc' || echo './'`lookup/FlowAlignSummary.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SmithWatFree.o `test -f 'pairwise_aligners/SmithWatFree.cc' || echo './'`pairwise_aligners/SmithWatFree.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ContigActualloc.o `test -f 'layout/ContigActualloc.cc' || echo './'`layout/ContigActualloc.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PrintAlignment.o PrintAlignment.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MakeAlignsMethod.o `test -f 'pairwise_aligners/MakeAlignsMethod.cc' || echo './'`pairwise_aligners/MakeAlignsMethod.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CompressedSequence.o CompressedSequence.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PackAlign.o PackAlign.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o BlockAlign.o BlockAlign.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ReadsToPathsCoreX.o `test -f 'paths/ReadsToPathsCoreX.cc' || echo './'`paths/ReadsToPathsCoreX.cc >In file included from ./paths/KmerPath.h:20:0, > from paths/ReadsToPathsCoreX.cc:19: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SortKmersA.o `test -f 'sort_kmers/SortKmersA.cc' || echo './'`sort_kmers/SortKmersA.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SortKmersC.o `test -f 'sort_kmers/SortKmersC.cc' || echo './'`sort_kmers/SortKmersC.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o HashSimple.o HashSimple.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o RunTime.o `test -f 'system/RunTime.cc' || echo './'`system/RunTime.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o HyperBasevector.o `test -f 'paths/HyperBasevector.cc' || echo './'`paths/HyperBasevector.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:19, > from paths/HyperBasevector.cc:16: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ParseSet.o ParseSet.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MaxMutmerFromMer.o `test -f 'pairwise_aligners/MaxMutmerFromMer.cc' || echo './'`pairwise_aligners/MaxMutmerFromMer.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Solid.o `test -f 'solid/Solid.cc' || echo './'`solid/Solid.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SequenceEntropy.o `test -f 'random/SequenceEntropy.cc' || echo './'`random/SequenceEntropy.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Calculator.o `test -f 'math/Calculator.cc' || echo './'`math/Calculator.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o BitVec.o `test -f 'feudal/BitVec.cc' || echo './'`feudal/BitVec.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Oob.o `test -f 'feudal/Oob.cc' || echo './'`feudal/Oob.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o BaseVec.o `test -f 'feudal/BaseVec.cc' || echo './'`feudal/BaseVec.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o VAALTools.o `test -f 'polymorphism/VAALTools.cc' || echo './'`polymorphism/VAALTools.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from polymorphism/VAALTools.cc:13: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Intvector.o Intvector.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Hit.o `test -f 'lookup/Hit.cc' || echo './'`lookup/Hit.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastaVerifier.o FastaVerifier.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LinkTimestamp.o LinkTimestamp.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MemTracker.o `test -f 'system/MemTracker.cc' || echo './'`system/MemTracker.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PathEmbedding.o `test -f 'paths/PathEmbedding.cc' || echo './'`paths/PathEmbedding.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/PathEmbedding.h:9, > from paths/PathEmbedding.cc:3: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o EvalUtils.o `test -f 'paths/EvalUtils.cc' || echo './'`paths/EvalUtils.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/AlignHyperKmerPath.h:44, > from paths/EvalUtils.cc:19: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PerfectLookup.o `test -f 'lookup/PerfectLookup.cc' || echo './'`lookup/PerfectLookup.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Matrix.o `test -f 'math/Matrix.cc' || echo './'`math/Matrix.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastaFilestreamPreview.o FastaFilestreamPreview.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o WorklistUtils.o `test -f 'system/WorklistUtils.cc' || echo './'`system/WorklistUtils.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o DotUtils.o `test -f 'graph/DotUtils.cc' || echo './'`graph/DotUtils.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MemberOf.o MemberOf.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MersenneTwister.o `test -f 'random/MersenneTwister.cc' || echo './'`random/MersenneTwister.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o System.o `test -f 'system/System.cc' || echo './'`system/System.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Unipath.o `test -f 'paths/Unipath.cc' || echo './'`paths/Unipath.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:19, > from paths/Unipath.cc:17: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastaNameParser.o FastaNameParser.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o VectorTrimmer.o `test -f 'micro/VectorTrimmer.cc' || echo './'`micro/VectorTrimmer.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AlignFromMutmersAndSW.o `test -f 'pairwise_aligners/AlignFromMutmersAndSW.cc' || echo './'`pairwise_aligners/AlignFromMutmersAndSW.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Types.o `test -f 'system/Types.cc' || echo './'`system/Types.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o HostName.o `test -f 'system/HostName.cc' || echo './'`system/HostName.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AnnotatedContig.o AnnotatedContig.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MakeAlignsPathsParallelX.o `test -f 'paths/MakeAlignsPathsParallelX.cc' || echo './'`paths/MakeAlignsPathsParallelX.cc >In file included from ./paths/KmerPath.h:20:0, > from paths/MakeAlignsPathsParallelX.cc:17: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MatchList.o `test -f 'pairwise_aligners/MatchList.cc' || echo './'`pairwise_aligners/MatchList.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o BinaryStream.o `test -f 'feudal/BinaryStream.cc' || echo './'`feudal/BinaryStream.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o EfastaTools.o `test -f 'efasta/EfastaTools.cc' || echo './'`efasta/EfastaTools.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SortKmersD.o `test -f 'sort_kmers/SortKmersD.cc' || echo './'`sort_kmers/SortKmersD.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LookupTableBuilder.o `test -f 'lookup/LookupTableBuilder.cc' || echo './'`lookup/LookupTableBuilder.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Charvector.o Charvector.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AlignHyperKmerPath.o `test -f 'paths/AlignHyperKmerPath.cc' || echo './'`paths/AlignHyperKmerPath.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/AlignHyperKmerPath.h:44, > from paths/AlignHyperKmerPath.cc:20: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >paths/AlignHyperKmerPath.cc: In function âvoid ReorderToFollowReference(HyperKmerPath&, vec<look_align>&, const vec<vec<int> >&)â: >paths/AlignHyperKmerPath.cc:229:26: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > { if ( la.a.pos2( ) < min_pos ) > ^~ >paths/AlignHyperKmerPath.cc:231:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âifâ > min_rc = la.rc1; } } } > ^~~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o HitReceiver.o `test -f 'lookup/HitReceiver.cc' || echo './'`lookup/HitReceiver.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SolexaMetrics.o `test -f 'solexa/SolexaMetrics.cc' || echo './'`solexa/SolexaMetrics.cc >solexa/SolexaMetrics.cc: In member function âvoid solexa_metric_db::WriteMetrics(const filename_t&, Bool) constâ: >solexa/SolexaMetrics.cc:162:9: warning: ignoring return value of âint system(const char*)â, declared with attribute warn_unused_result [-Wunused-result] > system(theCommand.c_str()); > ~~~~~~^~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Functions.o `test -f 'math/Functions.cc' || echo './'`math/Functions.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o KmerPath.o `test -f 'paths/KmerPath.cc' || echo './'`paths/KmerPath.cc >In file included from ./paths/KmerPath.h:20:0, > from paths/KmerPath.cc:12: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Directory.o `test -f 'system/file/Directory.cc' || echo './'`system/file/Directory.cc >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SeqInterval.o SeqInterval.cc >rm -f libVAAL.a >x86_64-pc-linux-gnu-ar cru libVAAL.a ErrNo.o Mutmer.o LookAlignSort.o FetchReadsAmb.o Floatvector.o ScoreAlignment.o Mempool.o SolexaTools.o Basevector.o KmerBaseBroker.o AffineRefiner.o QueryLookupTableCore.o Permutation.o ParsedArgs.o FeudalFileWriter.o Qualvector.o FileReader.o Bases.o FeudalControlBlock.o AlignCollector.o HoInterval.o LookAlignFinder.o Generic.o Array.o Digraph.o Equiv.o ParseRange.o Vec.o IndexedAlignmentPlusVector.o PerfectCount.o FourBase.o LookAlign.o ProcBuf.o FieldVec.o FileWriter.o SmithWatAffine.o ScaffoldAccuracyCore.o ReadPairing.o Misc.o PerfStat.o BaitMap.o FeudalTools.o PerfectAlignerLG.o FetchReads.o TraceVal.o SortKmersB.o SortKmers.o Alignment.o TempFile.o ThreadsafeIO.o Shuffle.o AlignSeqsToHyper.o KmerPathInterval.o FastIfstream.o Assert.o FastaConverter.o Superb.o ArtifactualSequenceDetector.o KmerRecord.o LookupTable.o File.o SysConf.o SeqOnHyper.o RNGen.o SymLink.o CharString.o FastaFileset.o HyperKmerPath.o QualNibbleVec.o PowerOf2.o KmerParcels.o SuffixTree.o Fastavector.o TruePolyCore.o TokenizeString.o KmerParcelsBuilder.o FourBase2.o Crash.o UseGDB.o ImperfectLookup.o VecString.o KmerShape.o LockedData.o Arith.o BasevectorTools.o VecAlignmentPlus.o FastaFilestream.o FeudalFileReader.o Exit.o SmithWatBandedA.o FlowAlignSummary.o SmithWatFree.o ContigActualloc.o PrintAlignment.o MakeAlignsMethod.o CompressedSequence.o PackAlign.o BlockAlign.o ReadsToPathsCoreX.o SortKmersA.o SortKmersC.o HashSimple.o RunTime.o HyperBasevector.o ParseSet.o MaxMutmerFromMer.o Solid.o SequenceEntropy.o Calculator.o BitVec.o Oob.o BaseVec.o VAALTools.o Intvector.o Hit.o FastaVerifier.o LinkTimestamp.o MemTracker.o PathEmbedding.o EvalUtils.o PerfectLookup.o Matrix.o FastaFilestreamPreview.o WorklistUtils.o DotUtils.o MemberOf.o MersenneTwister.o System.o Unipath.o FastaNameParser.o VectorTrimmer.o AlignFromMutmersAndSW.o Types.o HostName.o AnnotatedContig.o MakeAlignsPathsParallelX.o MatchList.o BinaryStream.o EfastaTools.o SortKmersD.o LookupTableBuilder.o Charvector.o AlignHyperKmerPath.o HitReceiver.o SolexaMetrics.o Functions.o KmerPath.o Directory.o SeqInterval.o >x86_64-pc-linux-gnu-ranlib libVAAL.a >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.15.3 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o VAAL0_5.o `test -f 'polymorphism/VAAL0_5.cc' || echo './'`polymorphism/VAAL0_5.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./polymorphism/VAALTools.h:17, > from polymorphism/VAAL0_5.cc:34: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:359:50: warning: result of â(511 << 24)â requires 34 bits to represent, but âintâ only has 32 bits [-Wshift-overflow=] > { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } > ~~~~~~~~~~^~~~~ >/bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -pthread -Wl,-O1 -Wl,--as-needed -o VAAL0_5 VAAL0_5.o libVAAL.a >libtool: link: x86_64-pc-linux-gnu-g++ -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -pthread -Wl,-O1 -o VAAL0_5 VAAL0_5.o -Wl,--as-needed libVAAL.a -pthread -fopenmp >/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lieee >collect2: error: ld returned 1 exit status >make[2]: *** [Makefile:891: VAAL0_5] Error 1 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233/src' >make[1]: *** [Makefile:739: all] Error 2 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233/src' >make: *** [Makefile:389: all-recursive] Error 1 > * ERROR: sci-biology/vaal-46233-r2::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/vaal-46233-r2::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/vaal-46233-r2::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:vaal-46233-r2:20180216-114706.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/vaal-46233-r2/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/vaal-46233-r2/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233' > * S: '/var/tmp/portage/sci-biology/vaal-46233-r2/work/vaal-46233'
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