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Gentoo's Bugzilla – Attachment 506414 Details for
Bug 638724
sci-biology/allpathslg-52488-r2 : paths/.../VariantCallTools.cc:1874:47: error: call of overloaded abs(FeudalString<char>::size_type) is ambiguous
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sci-biology:allpathslg-52488-r2:20171124-140832.log
sci-biology:allpathslg-52488-r2:20171124-140832.log (text/plain), 196.89 KB, created by
Toralf Förster
on 2017-11-24 17:01:30 UTC
(
hide
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Description:
sci-biology:allpathslg-52488-r2:20171124-140832.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2017-11-24 17:01:30 UTC
Size:
196.89 KB
patch
obsolete
> * Package: sci-biology/allpathslg-52488-r2 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking allpathslg-52488.tar.gz to /var/tmp/portage/sci-biology/allpathslg-52488-r2/work >>>> Source unpacked in /var/tmp/portage/sci-biology/allpathslg-52488-r2/work >>>> Preparing source in /var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488 ... > * Applying allpathslg-52488_fix-buildsystem.patch ... > [ ok ] > * Applying allpathslg-52488_remove-namespace-std.patch ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488' ... > * Running libtoolize --install --copy --force --automake ... > [ ok ] > * Running aclocal -I m4 ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running automake --add-missing --copy --foreign --force-missing ... > [ ok ] > * Running elibtoolize in: allpathslg-52488/ > * Applying portage/1.2.0 patch ... > * Applying sed/1.5.6 patch ... > * Applying as-needed/2.4.3 patch ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488 ... > * econf: updating allpathslg-52488/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating allpathslg-52488/config.guess with /usr/share/gnuconfig/config.guess >./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/allpathslg-52488-r2 --htmldir=/usr/share/doc/allpathslg-52488-r2/html --libdir=/usr/lib64 >checking for a BSD-compatible install... /usr/lib/portage/python3.4/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 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 validity of OpenMP configuation.... checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating src/Makefile >config.status: executing depfiles commands >config.status: executing libtool commands >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488 ... >make -j1 >Making all in src >make[1]: Entering directory '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488/src' >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CleanEfasta.o `test -f 'paths/long/CleanEfasta.cc' || echo './'`paths/long/CleanEfasta.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/HyperEfasta.h:19, > from paths/long/CleanEfasta.cc:14: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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:20, > from paths/HyperBasevector.cc:21: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AllOfOutput.o `test -f 'system/AllOfOutput.cc' || echo './'`system/AllOfOutput.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ScaffoldGraphIntegrity.o `test -f 'paths/ScaffoldGraphIntegrity.cc' || echo './'`paths/ScaffoldGraphIntegrity.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Combinatorics.o `test -f 'math/Combinatorics.cc' || echo './'`math/Combinatorics.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o EvalScaffoldsUtils.o `test -f 'paths/reporting/EvalScaffoldsUtils.cc' || echo './'`paths/reporting/EvalScaffoldsUtils.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Floatvector.o Floatvector.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SupportedHyperBasevector4.o `test -f 'paths/long/SupportedHyperBasevector4.cc' || echo './'`paths/long/SupportedHyperBasevector4.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/long/EvalByReads.h:16, > from paths/long/SupportedHyperBasevector4.cc:15: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CorrectPatch.o `test -f 'paths/CorrectPatch.cc' || echo './'`paths/CorrectPatch.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Basevector.o Basevector.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o VecOverlap.o VecOverlap.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o HKPMerger.o `test -f 'paths/HKPMerger.cc' || echo './'`paths/HKPMerger.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HKPMerger.h:21, > from paths/HKPMerger.cc:16: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FindUnipathSeedsLG.o `test -f 'paths/FindUnipathSeedsLG.cc' || echo './'`paths/FindUnipathSeedsLG.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/FindUnipathSeedsLG.h:17, > from paths/FindUnipathSeedsLG.cc:14: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ExtendUnipathSeqs.o `test -f 'paths/ExtendUnipathSeqs.cc' || echo './'`paths/ExtendUnipathSeqs.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/ExtendUnipathSeqs.h:13, > from paths/ExtendUnipathSeqs.cc:10: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastgGraph.o `test -f 'fastg/FastgGraph.cc' || echo './'`fastg/FastgGraph.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./fastg/FastgGraph.h:19, > from fastg/FastgGraph.cc:15: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o RefTraceControl.o `test -f 'paths/long/RefTraceControl.cc' || echo './'`paths/long/RefTraceControl.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Jumpster.o `test -f 'paths/Jumpster.cc' || echo './'`paths/Jumpster.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o TextTable.o `test -f 'util/TextTable.cc' || echo './'`util/TextTable.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AddSuperReads.o `test -f 'paths/AddSuperReads.cc' || echo './'`paths/AddSuperReads.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/AddSuperReads.h:27, > from paths/AddSuperReads.cc:10: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o TrackingAllocator.o `test -f 'feudal/TrackingAllocator.cc' || echo './'`feudal/TrackingAllocator.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PseudoUnipatherLib.o `test -f 'paths/PseudoUnipatherLib.cc' || echo './'`paths/PseudoUnipatherLib.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/PseudoUnipatherLib.h:29, > from paths/PseudoUnipatherLib.cc:20: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o RefTrace.o `test -f 'paths/long/RefTrace.cc' || echo './'`paths/long/RefTrace.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/long/RefTrace.h:13, > from paths/long/RefTrace.cc:62: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Equiv.o Equiv.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FirstLookup.o `test -f 'lookup/FirstLookup.cc' || echo './'`lookup/FirstLookup.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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:144:7: warning: â<anonymous>.alignment_plus::scoreâ may be used uninitialized in this function [-Wmaybe-uninitialized] > class alignment_plus { > ^~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CLinkBundle.o `test -f 'paths/reporting/CLinkBundle.cc' || echo './'`paths/reporting/CLinkBundle.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SupersHandler.o SupersHandler.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CSublink.o `test -f 'paths/CSublink.cc' || echo './'`paths/CSublink.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SupportedHyperBasevector2.o `test -f 'paths/long/SupportedHyperBasevector2.cc' || echo './'`paths/long/SupportedHyperBasevector2.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from paths/long/SupportedHyperBasevector2.cc:16: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PatcherCottageCore.o `test -f 'paths/PatcherCottageCore.cc' || echo './'`paths/PatcherCottageCore.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LongReadUnipathPatcherUtils.o `test -f 'paths/LongReadUnipathPatcherUtils.cc' || echo './'`paths/LongReadUnipathPatcherUtils.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Eps.o `test -f 'graphics/Eps.cc' || echo './'`graphics/Eps.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Quality.o Quality.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LookupTabBuilder.o `test -f 'lookup/LookupTabBuilder.cc' || echo './'`lookup/LookupTabBuilder.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CorrectLongReadsTools2.o `test -f 'paths/CorrectLongReadsTools2.cc' || echo './'`paths/CorrectLongReadsTools2.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MuxSearchPolicy.o `test -f 'paths/MuxSearchPolicy.cc' || echo './'`paths/MuxSearchPolicy.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/OrientedKmerPathId.h:6, > from ./paths/Mux.h:6, > from ./paths/MuxSearchPolicy.h:16, > from paths/MuxSearchPolicy.cc:9: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o BigMapDot.o `test -f 'paths/BigMapDot.cc' || echo './'`paths/BigMapDot.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Misc.o Misc.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Logger.o `test -f 'util/Logger.cc' || echo './'`util/Logger.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AnAssemblyClass.o AnAssemblyClass.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o UnibaseCopyNumber3Core.o `test -f 'paths/UnibaseCopyNumber3Core.cc' || echo './'`paths/UnibaseCopyNumber3Core.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AlignTwoBasevectors.o `test -f 'pairwise_aligners/AlignTwoBasevectors.cc' || echo './'`pairwise_aligners/AlignTwoBasevectors.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o UnipathSeqBuilder.o `test -f 'paths/UnipathSeqBuilder.cc' || echo './'`paths/UnipathSeqBuilder.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/UnipathSeqBuilder.h:15, > from paths/UnipathSeqBuilder.cc:10: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o RemoveDuplicateAligns.o `test -f 'paths/RemoveDuplicateAligns.cc' || echo './'`paths/RemoveDuplicateAligns.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LongReadTools.o `test -f 'paths/LongReadTools.cc' || echo './'`paths/LongReadTools.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o GetHomes.o `test -f 'paths/GetHomes.cc' || echo './'`paths/GetHomes.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Color.o `test -f 'graphics/Color.cc' || echo './'`graphics/Color.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ReportWalkingRatesCore.o `test -f 'paths/reporting/ReportWalkingRatesCore.cc' || echo './'`paths/reporting/ReportWalkingRatesCore.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastaConverter.o FastaConverter.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o NormalRandom.o `test -f 'random/NormalRandom.cc' || echo './'`random/NormalRandom.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LongProtoTools.o `test -f 'paths/long/LongProtoTools.cc' || echo './'`paths/long/LongProtoTools.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/long/CreateGenome.h:15, > from paths/long/LongProtoTools.cc:24: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o HyperEfasta.o `test -f 'paths/HyperEfasta.cc' || echo './'`paths/HyperEfasta.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/HyperEfasta.h:19, > from paths/HyperEfasta.cc:12: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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/HyperEfasta.cc: In function âvec<FeudalString<char> > SpecialEfastaTag2Graph(digraphE<BaseVec>&, efasta)â: >paths/HyperEfasta.cc:28:15: warning: self-comparison always evaluates to false [-Wtautological-compare] > if( nClose!=nClose || nOpen!=1 || nClose!=1 || in.front()!='{' || in.back()!='}' > ~~~~~~^~~~~~~~ >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ContigsManager.o `test -f 'paths/ContigsManager.cc' || echo './'`paths/ContigsManager.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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:20, > 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:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MakeAlignsStatic.o `test -f 'pairwise_aligners/MakeAlignsStatic.cc' || echo './'`pairwise_aligners/MakeAlignsStatic.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SupportedHyperBasevector6.o `test -f 'paths/long/SupportedHyperBasevector6.cc' || echo './'`paths/long/SupportedHyperBasevector6.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/long/CreateGenome.h:15, > from paths/long/SupportedHyperBasevector6.cc:23: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SaveScaffoldGraph.o `test -f 'paths/SaveScaffoldGraph.cc' || echo './'`paths/SaveScaffoldGraph.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ScaffoldContigsOnRef.o `test -f 'util/ScaffoldContigsOnRef.cc' || echo './'`util/ScaffoldContigsOnRef.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastaFileset.o FastaFileset.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Variants.o `test -f 'paths/long/Variants.cc' || echo './'`paths/long/Variants.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/HyperEfasta.h:19, > from ./paths/long/Variants.h:14, > from paths/long/Variants.cc:11: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o UnibaseCopyNumber3LowerCN.o `test -f 'paths/UnibaseCopyNumber3LowerCN.cc' || echo './'`paths/UnibaseCopyNumber3LowerCN.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ReadTracker.o `test -f 'util/ReadTracker.cc' || echo './'`util/ReadTracker.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o TokenizeString.o TokenizeString.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SupportedHyperBasevector7.o `test -f 'paths/long/SupportedHyperBasevector7.cc' || echo './'`paths/long/SupportedHyperBasevector7.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./fastg/FastgGraph.h:19, > from paths/long/SupportedHyperBasevector7.cc:14: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Useq.o `test -f 'paths/Useq.cc' || echo './'`paths/Useq.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FindGaps.o FindGaps.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FixSomeIndelsUtils.o `test -f 'paths/FixSomeIndelsUtils.cc' || echo './'`paths/FixSomeIndelsUtils.cc >In file included from ./Vec.h:44:0, > from ./CoreTools.h:20, > from ./feudal/FieldVec.h:21, > from ./feudal/BaseVec.h:13, > from ./Basevector.h:12, > from ./Alignment.h:30, > from paths/FixSomeIndelsUtils.cc:9: >./STLExtensions.h: In function âvoid std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<triple<BaseVec, int, int>*, std::vector<triple<BaseVec, int, int>, std::allocator<triple<BaseVec, int, int> > > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]â: >./STLExtensions.h:425:8: warning: â#âtarget_mem_refâ not supported by dump_expr#<expression error>â may be used uninitialized in this function [-Wmaybe-uninitialized] > struct triple { > ^~~~~~ >./STLExtensions.h:425:8: warning: â#âtarget_mem_refâ not supported by dump_expr#<expression error>â may be used uninitialized in this function [-Wmaybe-uninitialized] >./STLExtensions.h: In function âvoid std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<triple<BaseVec, int, int>*, std::vector<triple<BaseVec, int, int>, std::allocator<triple<BaseVec, int, int> > > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<triple<BaseVec, int, int> > >]â: >./STLExtensions.h:425:8: warning: â#âtarget_mem_refâ not supported by dump_expr#<expression error>â may be used uninitialized in this function [-Wmaybe-uninitialized] > struct triple { > ^~~~~~ >./STLExtensions.h:425:8: warning: â#âtarget_mem_refâ not supported by dump_expr#<expression error>â may be used uninitialized in this function [-Wmaybe-uninitialized] >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CGraphMass.o `test -f 'graph/CGraphMass.cc' || echo './'`graph/CGraphMass.cc >In file included from ./paths/KmerPath.h:20:0, > from graph/CGraphMass.cc:12: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o UnipathScaffold.o `test -f 'paths/UnipathScaffold.cc' || echo './'`paths/UnipathScaffold.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ClusterAligner.o `test -f 'pairwise_aligners/ClusterAligner.cc' || echo './'`pairwise_aligners/ClusterAligner.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o BasevectorTools.o BasevectorTools.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o GapSkip.o `test -f 'paths/GapSkip.cc' || echo './'`paths/GapSkip.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/GapSkip.h:7, > from paths/GapSkip.cc:4: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o VecAlignmentPlus.o VecAlignmentPlus.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o UnibaseCopyNumber2Core.o `test -f 'paths/UnibaseCopyNumber2Core.cc' || echo './'`paths/UnibaseCopyNumber2Core.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o NStatsTools.o `test -f 'math/NStatsTools.cc' || echo './'`math/NStatsTools.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PairDistCorrection.o `test -f 'paths/PairDistCorrection.cc' || echo './'`paths/PairDistCorrection.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PolymorphismRemoveCore.o `test -f 'paths/PolymorphismRemoveCore.cc' || echo './'`paths/PolymorphismRemoveCore.cc >In file included from ./paths/PolymorphismRemoveCore.h:20:0, > from paths/PolymorphismRemoveCore.cc:10: >./kmers/naif_kmer/KmerFreqAffixesMap.h: In member function âunsigned int FreqAffixes::_base(unsigned int, unsigned int) constâ: >./kmers/naif_kmer/KmerFreqAffixesMap.h:39:5: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > if (bit4 & 1u) n++; if (n > i) return 0u; > ^~ >./kmers/naif_kmer/KmerFreqAffixesMap.h:39:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âifâ > if (bit4 & 1u) n++; if (n > i) return 0u; > ^~ >./kmers/naif_kmer/KmerFreqAffixesMap.h:40:5: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > if (bit4 & 2u) n++; if (n > i) return 1u; > ^~ >./kmers/naif_kmer/KmerFreqAffixesMap.h:40:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âifâ > if (bit4 & 2u) n++; if (n > i) return 1u; > ^~ >./kmers/naif_kmer/KmerFreqAffixesMap.h:41:5: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > if (bit4 & 4u) n++; if (n > i) return 2u; > ^~ >./kmers/naif_kmer/KmerFreqAffixesMap.h:41:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âifâ > if (bit4 & 4u) n++; if (n > i) return 2u; > ^~ >./kmers/naif_kmer/KmerFreqAffixesMap.h:42:5: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > if (bit4 & 8u) n++; if (n > i) return 3u; > ^~ >./kmers/naif_kmer/KmerFreqAffixesMap.h:42:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âifâ > if (bit4 & 8u) n++; if (n > i) return 3u; > ^~ >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FirstLookupFinderECJ.o `test -f 'lookup/FirstLookupFinderECJ.cc' || echo './'`lookup/FirstLookupFinderECJ.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SuckScaffolds.o `test -f 'paths/SuckScaffolds.cc' || echo './'`paths/SuckScaffolds.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/HyperFastavector.h:18, > from ./paths/SuckScaffolds.h:15, > from paths/SuckScaffolds.cc:17: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o PackAlign.o PackAlign.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MuxWalkGraph.o `test -f 'paths/MuxWalkGraph.cc' || echo './'`paths/MuxWalkGraph.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/OrientedKmerPathId.h:6, > from ./paths/MuxWalkGraph.h:13, > from paths/MuxWalkGraph.cc:10: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o DigraphFromWords.o `test -f 'paths/long/DigraphFromWords.cc' || echo './'`paths/long/DigraphFromWords.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/HyperEfasta.h:19, > from ./paths/long/LongProtoTools.h:25, > from ./paths/long/DigraphFromWords.h:15, > from paths/long/DigraphFromWords.cc:16: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SupportedHyperBasevector3.o `test -f 'paths/long/SupportedHyperBasevector3.cc' || echo './'`paths/long/SupportedHyperBasevector3.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/long/CreateGenome.h:15, > from paths/long/SupportedHyperBasevector3.cc:18: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SeedNeighborhoodAnnex.o `test -f 'paths/SeedNeighborhoodAnnex.cc' || echo './'`paths/SeedNeighborhoodAnnex.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from paths/SeedNeighborhoodAnnex.cc:35: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o IdentifyCircularScaffolds.o `test -f 'paths/IdentifyCircularScaffolds.cc' || echo './'`paths/IdentifyCircularScaffolds.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ParseSet.o ParseSet.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AmbiguityScore.o `test -f 'efasta/AmbiguityScore.cc' || echo './'`efasta/AmbiguityScore.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CommonPatherCore.o `test -f 'paths/CommonPatherCore.cc' || echo './'`paths/CommonPatherCore.cc >In file included from ./paths/KmerPath.h:20:0, > from paths/CommonPatherCore.cc:10: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ImproperMerge.o `test -f 'paths/ImproperMerge.cc' || echo './'`paths/ImproperMerge.cc >In file included from ./paths/KmerPath.h:20:0, > from paths/ImproperMerge.cc:4: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MergeReadSetsCore.o `test -f 'paths/MergeReadSetsCore.cc' || echo './'`paths/MergeReadSetsCore.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SeedNeighborhood.o `test -f 'paths/SeedNeighborhood.cc' || echo './'`paths/SeedNeighborhood.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/ReadsToPathsCoreX.h:36, > from paths/SeedNeighborhood.cc:13: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FastaParser.o `test -f 'util/FastaParser.cc' || echo './'`util/FastaParser.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o LinkTimestamp.o LinkTimestamp.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o NormalDistribution.o `test -f 'random/NormalDistribution.cc' || echo './'`random/NormalDistribution.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Qualvector.o Qualvector.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FlattenHyperFastavector.o `test -f 'paths/FlattenHyperFastavector.cc' || echo './'`paths/FlattenHyperFastavector.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/HyperFastavector.h:18, > from ./paths/CLinFastavec.h:14, > from paths/FlattenHyperFastavector.cc:9: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FirstLookupPerfect.o `test -f 'lookup/FirstLookupPerfect.cc' || echo './'`lookup/FirstLookupPerfect.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ReadHBVs.o `test -f 'paths/ReadHBVs.cc' || echo './'`paths/ReadHBVs.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/ReadHBVs.h:20, > from paths/ReadHBVs.cc:15: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o InsertWalker.o `test -f 'paths/InsertWalker.cc' || echo './'`paths/InsertWalker.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/InsertWalker.h:33, > from paths/InsertWalker.cc:13: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ReadOriginTracker.o `test -f 'paths/long/ReadOriginTracker.cc' || echo './'`paths/long/ReadOriginTracker.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/long/RefTrace.h:13, > from paths/long/ReadOriginTracker.cc:10: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o IntPairVec.o IntPairVec.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o FindClosures.o `test -f 'paths/FindClosures.cc' || echo './'`paths/FindClosures.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/AddSuperReads.h:27, > from paths/FindClosures.cc:14: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o CSuperLinks.o `test -f 'paths/reporting/CSuperLinks.cc' || echo './'`paths/reporting/CSuperLinks.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MapAligns.o `test -f 'paths/MapAligns.cc' || echo './'`paths/MapAligns.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o KmerPathDatabase.o `test -f 'paths/KmerPathDatabase.cc' || echo './'`paths/KmerPathDatabase.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerPathDatabase.h:6, > from paths/KmerPathDatabase.cc:3: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Prefab.o `test -f 'paths/long/ultra/Prefab.cc' || echo './'`paths/long/ultra/Prefab.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/long/CreateGenome.h:15, > from paths/long/ultra/Prefab.cc:20: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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/long/ultra/Prefab.cc: In function âint {anonymous}::FindEdits(const vec<BaseVec>&, const basevector&, vec<vec<edit0> >&, std::ostream&)â: >paths/long/ultra/Prefab.cc:327:21: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > if ( threads[i][p2] != t[p1] ) > ^~ >paths/long/ultra/Prefab.cc:329:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âifâ > p1++, p2++; > ^~ >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o MemberOf.o MemberOf.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SubsumptionList.o `test -f 'paths/SubsumptionList.cc' || echo './'`paths/SubsumptionList.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/OrientedKmerPathId.h:6, > from ./paths/SubsumptionList.h:6, > from paths/SubsumptionList.cc:3: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o InternalMergeImpl.o `test -f 'paths/InternalMergeImpl.cc' || echo './'`paths/InternalMergeImpl.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/ImproperMerge.h:9, > from paths/InternalMergeImpl.cc:16: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o RefDesc.o `test -f 'util/RefDesc.cc' || echo './'`util/RefDesc.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o ThreadedBlocks.o `test -f 'paths/long/ultra/ThreadedBlocks.cc' || echo './'`paths/long/ultra/ThreadedBlocks.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/HyperEfasta.h:19, > from ./paths/long/LongProtoTools.h:25, > from paths/long/ultra/ThreadedBlocks.cc:19: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o RefTraceTools.o `test -f 'paths/long/RefTraceTools.cc' || echo './'`paths/long/RefTraceTools.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/long/RefTraceTools.h:15, > from paths/long/RefTraceTools.cc:8: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o BreakBadScaffolds.o `test -f 'paths/BreakBadScaffolds.cc' || echo './'`paths/BreakBadScaffolds.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o AgpMods.o `test -f 'agp/AgpMods.cc' || echo './'`agp/AgpMods.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o RunAllPathsCommon.o `test -f 'paths/RunAllPathsCommon.cc' || echo './'`paths/RunAllPathsCommon.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o KmerAlignSet.o `test -f 'paths/KmerAlignSet.cc' || echo './'`paths/KmerAlignSet.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o Uniseq.o `test -f 'paths/Uniseq.cc' || echo './'`paths/Uniseq.cc >x86_64-pc-linux-gnu-g++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o SimpleLoop.o `test -f 'paths/SimpleLoop.cc' || echo './'`paths/SimpleLoop.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from paths/SimpleLoop.cc:14: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -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:364:50: 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++ -DPACKAGE_NAME=\"AllPathsLG\" -DPACKAGE_TARNAME=\"allpathslg\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"AllPathsLG\ 52488\" -DPACKAGE_BUGREPORT=\"crdhelp@broadinstitute.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"allpathslg\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1 -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=4.13.15 -DMAKE_RELEASE=3.0 -DSVN_VERSION=52488 -pthread -fopenmp -O2 -pipe -march=native -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG -c -o VariantCallTools.o `test -f 'paths/long/VariantCallTools.cc' || echo './'`paths/long/VariantCallTools.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from ./paths/long/SupportedHyperBasevector.h:35, > from ./paths/long/VariantCallTools.h:12, > from paths/long/VariantCallTools.cc:12: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h:364:50: 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/long/VariantCallTools.cc: In member function âbool EdgesOnRef::FindAlternativePath(int, vec<std::pair<int, int>, std::allocator<std::pair<int, int> > >*, int*, const vec<vec<std::pair<int, int>, std::allocator<std::pair<int, int> > > >&, int, int, int)â: >paths/long/VariantCallTools.cc:1342:17: warning: this âforâ clause does not guard... [-Wmisleading-indentation] > for (const auto& x : starts) cout << x.first << " "; cout << endl; > ^~~ >paths/long/VariantCallTools.cc:1342:70: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âforâ > for (const auto& x : starts) cout << x.first << " "; cout << endl; > ^~~~ >paths/long/VariantCallTools.cc: In member function âvoid EdgesOnRef::FilterAndModifyEdits(vec<triple<int, int, FeudalString<char> > >&, vec<std::pair<FeudalString<char>, FeudalString<char> > >&)â: >paths/long/VariantCallTools.cc:1874:47: error: call of overloaded âabs(FeudalString<char>::size_type)â is ambiguous > - change[j-1].first.size()) < MinClumpSep) { > ^ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/cstdlib:75:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/ext/string_conversions.h:41, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/basic_string.h:6159, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/string:52, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/locale_classes.h:40, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/ios_base.h:41, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/iomanip:40, > from ./system/System.h:13, > from ./CoreTools.h:17, > from ./paths/long/VariantCallTools.h:11, > from paths/long/VariantCallTools.cc:12: >/usr/include/stdlib.h:722:12: note: candidate: int abs(int) > extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur; > ^~~ >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/cstdlib:77:0, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/ext/string_conversions.h:41, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/basic_string.h:6159, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/string:52, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/locale_classes.h:40, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/ios_base.h:41, > from /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/iomanip:40, > from ./system/System.h:13, > from ./CoreTools.h:17, > from ./paths/long/VariantCallTools.h:11, > from paths/long/VariantCallTools.cc:12: >/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/std_abs.h:56:3: note: candidate: long int std::abs(long int) > abs(long __i) { return __builtin_labs(__i); } > ^~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/std_abs.h:61:3: note: candidate: long long int std::abs(long long int) > abs(long long __x) { return __builtin_llabs (__x); } > ^~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/std_abs.h:70:3: note: candidate: constexpr double std::abs(double) > abs(double __x) > ^~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/std_abs.h:74:3: note: candidate: constexpr float std::abs(float) > abs(float __x) > ^~~ >/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/include/g++-v7/bits/std_abs.h:78:3: note: candidate: constexpr long double std::abs(long double) > abs(long double __x) > ^~~ >make[1]: *** [Makefile:4917: VariantCallTools.o] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488/src' >make: *** [Makefile:388: all-recursive] Error 1 > * ERROR: sci-biology/allpathslg-52488-r2::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/allpathslg-52488-r2::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/allpathslg-52488-r2::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:allpathslg-52488-r2:20171124-140832.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/allpathslg-52488-r2/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/allpathslg-52488-r2/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488' > * S: '/var/tmp/portage/sci-biology/allpathslg-52488-r2/work/allpathslg-52488'
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