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Gentoo's Bugzilla – Attachment 519138 Details for
Bug 647340
sci-biology/allpathslg-52488-r2 : /.../ld: cannot find -lieee
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sci-biology:allpathslg-52488-r2:20180211-194551.log
sci-biology:allpathslg-52488-r2:20180211-194551.log (text/plain), 414.65 KB, created by
Toralf Förster
on 2018-02-11 20:49:25 UTC
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hide
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Description:
sci-biology:allpathslg-52488-r2:20180211-194551.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2018-02-11 20:49:25 UTC
Size:
414.65 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 >>>> Unpacking allpathslg-52488-patchset.tar.bz2 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 ] > * Applying allpathslg-52488-gcc7.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/python3.5/ebuild-helpers/xattr/install -c >checking whether build environment is sane... yes >checking for a thread-safe mkdir -p... /bin/mkdir -p >checking for gawk... gawk >checking whether make sets $(MAKE)... yes >checking whether make supports nested variables... yes >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking how to print strings... printf >checking for style of include used by make... GNU >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking whether the C compiler works... yes >checking for C compiler default output file name... a.out >checking for suffix of executables... >checking whether we are cross compiling... no >checking for suffix of object files... o >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes >checking dependency style of x86_64-pc-linux-gnu-gcc... none >checking for a sed that does not truncate output... /bin/sed >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for fgrep... /bin/grep -F >checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B >checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm >checking whether ln -s works... yes >checking the maximum length of command line arguments... 1572864 >checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop >checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-dlltool... no >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok >checking for sysroot... no >checking for a working dd... /bin/dd >checking how to truncate binary pipes... /bin/dd bs=4096 count=1 >checking for x86_64-pc-linux-gnu-mt... no >checking for mt... mt >checking if mt 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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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=4.15.2 -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; > ^~~~ >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=4.15.2 -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 CorrectLongReadsTools.o `test -f 'paths/CorrectLongReadsTools.cc' || echo './'`paths/CorrectLongReadsTools.cc >paths/CorrectLongReadsTools.cc: In function âvoid ScoreGraph(const digraphE<int>&, int, const vec<std::pair<int, vec<std::pair<int, int>, std::allocator<std::pair<int, int> > > > >&, int&, int&, vec<int>&, vec<int>&)â: >paths/CorrectLongReadsTools.cc:649:16: warning: this âforâ clause does not guard... [-Wmisleading-indentation] > for ( int m = 0; m < ALIGNS[v].second.isize( ); m++ ) > ^~~ >paths/CorrectLongReadsTools.cc:651:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âforâ > for ( int m = 0; m < ALIGNS[w].second.isize( ); m++ ) > ^~~ >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=4.15.2 -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 FastaNameParser.o FastaNameParser.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=4.15.2 -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 SeqInterval.o SeqInterval.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=4.15.2 -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 AlignCollector.o `test -f 'lookup/AlignCollector.cc' || echo './'`lookup/AlignCollector.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=4.15.2 -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 FixScaffoldsCore.o `test -f 'paths/FixScaffoldsCore.cc' || echo './'`paths/FixScaffoldsCore.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=4.15.2 -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 Overlap.o Overlap.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=4.15.2 -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 Generic.o `test -f 'feudal/Generic.cc' || echo './'`feudal/Generic.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=4.15.2 -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 VerifyGapLengths.o `test -f 'paths/VerifyGapLengths.cc' || echo './'`paths/VerifyGapLengths.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/VerifyGapLengths.h:6, > from paths/VerifyGapLengths.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=4.15.2 -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 Friends.o `test -f 'paths/long/Friends.cc' || echo './'`paths/long/Friends.cc >In file included from paths/long/Friends.cc:17:0: >./feudal/HashSet.h: In member function âHopscotchHashSet<T, H, C, F>::value_type& HopscotchHashSet<T, H, C, F>::findInsertSlot(HopscotchHashSet<T, H, C, F>::size_type) [with T = KmerDictEntry<25>; H = KMer<25>::Hasher; C = std::equal_to<KMer<25> >; F = TFactory<KmerDictEntry<25> >]â: >./feudal/HashSet.h:399:14: warning: this statement may fall through [-Wimplicit-fallthrough=] > bump(pInfo); > ~~~~^~~~~~~ >./feudal/HashSet.h:401:8: note: here > case BktStatus::EMPTY: // just use the empty slot > ^~~~ >./feudal/HashSet.h: In member function âHopscotchHashSet<T, H, C, F>::value_type& HopscotchHashSet<T, H, C, F>::findInsertSlot(HopscotchHashSet<T, H, C, F>::size_type) [with T = {anonymous}::KmerFriends; H = KMer<25>::Hasher; C = std::equal_to<KMer<25> >; F = {anonymous}::KmerFriends::Factory]â: >./feudal/HashSet.h:399:14: warning: this statement may fall through [-Wimplicit-fallthrough=] > bump(pInfo); > ~~~~^~~~~~~ >./feudal/HashSet.h:401:8: note: here > case BktStatus::EMPTY: // just use the empty slot > ^~~~ >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=4.15.2 -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 FetchReadsAmb.o FetchReadsAmb.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=4.15.2 -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 RunCommand.o `test -f 'util/RunCommand.cc' || echo './'`util/RunCommand.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=4.15.2 -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 ScoreAlignment.o ScoreAlignment.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=4.15.2 -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 AssemblyCleanupTools.o `test -f 'paths/AssemblyCleanupTools.cc' || echo './'`paths/AssemblyCleanupTools.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=4.15.2 -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 SupportedHyperBasevector.o `test -f 'paths/long/SupportedHyperBasevector.cc' || echo './'`paths/long/SupportedHyperBasevector.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/SupportedHyperBasevector.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=4.15.2 -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 Placement.o `test -f 'paths/simulation/Placement.cc' || echo './'`paths/simulation/Placement.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=4.15.2 -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 DumbCall.o `test -f 'polymorphism/DumbCall.cc' || echo './'`polymorphism/DumbCall.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=4.15.2 -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 EvalCorrected.o `test -f 'paths/long/EvalCorrected.cc' || echo './'`paths/long/EvalCorrected.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/EvalCorrected.cc:22: >./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=4.15.2 -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 BuildScaffoldGraph.o `test -f 'paths/BuildScaffoldGraph.cc' || echo './'`paths/BuildScaffoldGraph.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=4.15.2 -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 KmerBaseBroker.o `test -f 'paths/KmerBaseBroker.cc' || echo './'`paths/KmerBaseBroker.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from paths/KmerBaseBroker.cc:12: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h: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=4.15.2 -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 Bernoulli.o `test -f 'random/Bernoulli.cc' || echo './'`random/Bernoulli.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=4.15.2 -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 PdfEntry.o `test -f 'paths/PdfEntry.cc' || echo './'`paths/PdfEntry.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=4.15.2 -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 Permutation.o `test -f 'math/Permutation.cc' || echo './'`math/Permutation.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=4.15.2 -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 FastaVerifier.o FastaVerifier.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=4.15.2 -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 UnibaseUtils.o `test -f 'paths/UnibaseUtils.cc' || echo './'`paths/UnibaseUtils.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=4.15.2 -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 OffsetDistributionInterface.o `test -f 'paths/OffsetDistributionInterface.cc' || echo './'`paths/OffsetDistributionInterface.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=4.15.2 -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 Edit.o `test -f 'polymorphism/Edit.cc' || echo './'`polymorphism/Edit.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=4.15.2 -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 PairedPair.o `test -f 'paths/PairedPair.cc' || echo './'`paths/PairedPair.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/FindClosures.h:15, > from paths/PairedPair.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=4.15.2 -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 ProcessGap.o `test -f 'paths/ProcessGap.cc' || echo './'`paths/ProcessGap.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=4.15.2 -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 FindCells.o `test -f 'graph/FindCells.cc' || echo './'`graph/FindCells.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=4.15.2 -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 Bases.o `test -f 'dna/Bases.cc' || echo './'`dna/Bases.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=4.15.2 -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 KmerPathMuxSearcher.o `test -f 'paths/KmerPathMuxSearcher.cc' || echo './'`paths/KmerPathMuxSearcher.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/OrientedKmerPathId.h:6, > from ./paths/Mux.h:6, > from ./paths/MuxGraph.h:12, > from ./paths/KmerPathMuxSearcher.h:7, > from paths/KmerPathMuxSearcher.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; } > ~~~~~~~~~~^~~~~ >In file included from ./paths/KmerPathMuxSearcher.h:12:0, > from paths/KmerPathMuxSearcher.cc:3: >./paths/MuxSearchAgent.h: In member function âvoid KmerPathMuxSearcher::FindClosures(int, int, int, int, MuxSearchResult&) constâ: >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::leftReadIdâ may be used uninitialized in this function [-Wmaybe-uninitialized] > class MuxSearchAgentBase { > ^~~~~~~~~~~~~~~~~~ >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::rightReadIdâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::minAcceptableExtLengthâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::maxAcceptableExtLengthâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::mp_resultâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::dist_to_hereâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::extensions_remainingâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::final_mux_subsumes_somethingâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::leftReadIdâ may be used uninitialized in this function [-Wmaybe-uninitialized] > class MuxSearchAgentBase { > ^~~~~~~~~~~~~~~~~~ >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::rightReadIdâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::minAcceptableExtLengthâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::maxAcceptableExtLengthâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::mp_resultâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::dist_to_hereâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::extensions_remainingâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:40:7: warning: âmsa.MuxSearchAgentBase::final_mux_subsumes_somethingâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./paths/MuxSearchAgent.h:294:7: warning: âmsa.MuxSearchAgentGoodReads::m_mayCloseâ may be used uninitialized in this function [-Wmaybe-uninitialized] > class MuxSearchAgentGoodReads : public MuxSearchAgentBase { > ^~~~~~~~~~~~~~~~~~~~~~~ >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=4.15.2 -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 FeudalControlBlock.o `test -f 'feudal/FeudalControlBlock.cc' || echo './'`feudal/FeudalControlBlock.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=4.15.2 -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 HTMLUtils.o `test -f 'system/HTMLUtils.cc' || echo './'`system/HTMLUtils.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=4.15.2 -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 PairsHandler.o PairsHandler.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=4.15.2 -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 HoInterval.o `test -f 'math/HoInterval.cc' || echo './'`math/HoInterval.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=4.15.2 -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 PostPatcherBridgeGap.o `test -f 'paths/PostPatcherBridgeGap.cc' || echo './'`paths/PostPatcherBridgeGap.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/PostPatcherBridgeGap.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=4.15.2 -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 MergeReads2.o MergeReads2.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=4.15.2 -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 ParseRange.o ParseRange.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=4.15.2 -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 MultipleAligner.o `test -f 'paths/long/ultra/MultipleAligner.cc' || echo './'`paths/long/ultra/MultipleAligner.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=4.15.2 -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 AgpFile.o `test -f 'agp/AgpFile.cc' || echo './'`agp/AgpFile.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=4.15.2 -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 WorklistMP.o `test -f 'system/WorklistMP.cc' || echo './'`system/WorklistMP.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=4.15.2 -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 Vec.o Vec.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=4.15.2 -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 PairsManager.o PairsManager.cc >PairsManager.cc: In function âbool operator==(const PairsManager&, const PairsManager&)â: >PairsManager.cc:218:21: warning: self-comparison always evaluates to false [-Wtautological-compare] > if ( pm1._n_reads != pm1._n_reads ) return false; > ~~~~~~~~~~~~~^~~~~~~~~~~~~~~ >PairsManager.cc:219:21: warning: self-comparison always evaluates to false [-Wtautological-compare] > if ( pm1._n_pairs != pm1._n_pairs ) return false; > ~~~~~~~~~~~~~^~~~~~~~~~~~~~~ >PairsManager.cc: In member function âvec<PM_LibraryStats> PairsManager::getLibraryStats(String) constâ: >PairsManager.cc:567:5: warning: this âforâ clause does not guard... [-Wmisleading-indentation] > for ( longlong i = 0; i < _n_pairs; i++ ) > ^~~ >PairsManager.cc:569:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âforâ > stats[stats.size() - 1].n_reads = _n_reads - (_n_pairs * 2); > ^~~~~ >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=4.15.2 -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 MakeBlocks.o `test -f 'paths/long/ultra/MakeBlocks.cc' || echo './'`paths/long/ultra/MakeBlocks.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/MakeBlocks.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=4.15.2 -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 ReadLocation.o ReadLocation.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=4.15.2 -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 FindErrorsCore.o `test -f 'paths/FindErrorsCore.cc' || echo './'`paths/FindErrorsCore.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=4.15.2 -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 FieldVec.o `test -f 'feudal/FieldVec.cc' || echo './'`feudal/FieldVec.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=4.15.2 -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 AlignReadsOnUnibases.o `test -f 'paths/AlignReadsOnUnibases.cc' || echo './'`paths/AlignReadsOnUnibases.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=4.15.2 -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 MakeAlignsMethod.o `test -f 'pairwise_aligners/MakeAlignsMethod.cc' || echo './'`pairwise_aligners/MakeAlignsMethod.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=4.15.2 -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 RemodelGapTools.o `test -f 'paths/RemodelGapTools.cc' || echo './'`paths/RemodelGapTools.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=4.15.2 -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 CAltFasta.o `test -f 'paths/CAltFasta.cc' || echo './'`paths/CAltFasta.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=4.15.2 -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 AlignAndMerge.o `test -f 'paths/AlignAndMerge.cc' || echo './'`paths/AlignAndMerge.cc >In file included from ./paths/KmerPath.h:20:0, > from paths/AlignAndMerge.cc:6: >./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=4.15.2 -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 ReadPairing.o ReadPairing.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=4.15.2 -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 PerfectAlignerLG.o `test -f 'pairwise_aligners/PerfectAlignerLG.cc' || echo './'`pairwise_aligners/PerfectAlignerLG.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=4.15.2 -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 FetchReads.o FetchReads.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=4.15.2 -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 TraceVal.o `test -f 'system/TraceVal.cc' || echo './'`system/TraceVal.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=4.15.2 -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 AnAssemblyClassUtil.o AnAssemblyClassUtil.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=4.15.2 -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 CloseUnipathGapsCore.o `test -f 'paths/CloseUnipathGapsCore.cc' || echo './'`paths/CloseUnipathGapsCore.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=4.15.2 -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 TempFile.o `test -f 'system/file/TempFile.cc' || echo './'`system/file/TempFile.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=4.15.2 -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 HostName.o `test -f 'system/HostName.cc' || echo './'`system/HostName.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=4.15.2 -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 ContigEvent.o ContigEvent.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=4.15.2 -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 CorrectPatch3.o `test -f 'paths/CorrectPatch3.cc' || echo './'`paths/CorrectPatch3.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from paths/CorrectPatch3.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=4.15.2 -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 Periodic.o `test -f 'paths/Periodic.cc' || echo './'`paths/Periodic.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=4.15.2 -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 FastIfstream.o FastIfstream.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=4.15.2 -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 Superb.o Superb.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=4.15.2 -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 PQVec.o `test -f 'feudal/PQVec.cc' || echo './'`feudal/PQVec.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=4.15.2 -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 KmerRecord.o `test -f 'kmers/KmerRecord.cc' || echo './'`kmers/KmerRecord.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=4.15.2 -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 LookupTable.o `test -f 'lookup/LookupTable.cc' || echo './'`lookup/LookupTable.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=4.15.2 -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 ReadLoc.o `test -f 'paths/ReadLoc.cc' || echo './'`paths/ReadLoc.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=4.15.2 -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 KmerSpectrumCore.o `test -f 'kmers/KmerSpectrumCore.cc' || echo './'`kmers/KmerSpectrumCore.cc >In file included from kmers/KmerSpectrumCore.cc:22:0: >./kmers/KmerSpectra.h: In constructor âKmerSpectraAffixes::KmerSpectraAffixes(unsigned int)â: >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_kf_min1â may be used uninitialized in this function [-Wmaybe-uninitialized] > class KmerSpectrum : public vec<size_t> > ^~~~~~~~~~~~ >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_kf_min2â may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_kf_min3â may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_kf_max1â may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_kf_max2â may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_kf_hiâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_kf_ave_uniqâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_nk_totalâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_nk_bad_low_kfâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_nk_good_uniqâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_nk_good_snpâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_nk_good_repâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_nk_bad_high_kfâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_ndk_totalâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_ndk_bad_low_kfâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_ndk_good_snpâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_ndk_good_uniqâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_ndk_good_repâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_ndk_bad_high_kfâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_coverageâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_genome_size_uniqueâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_genome_size_repetitiveâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_genome_sizeâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_stddev_biasâ may be used uninitialized in this function [-Wmaybe-uninitialized] >./kmers/KmerSpectra.h:15:7: warning: â<anonymous>.KmerSpectrum::_d_SNPâ 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=4.15.2 -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 EvalByReads.o `test -f 'paths/long/EvalByReads.cc' || echo './'`paths/long/EvalByReads.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.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=4.15.2 -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 AssessBestAlignCore.o `test -f 'paths/long/AssessBestAlignCore.cc' || echo './'`paths/long/AssessBestAlignCore.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=4.15.2 -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 IntDistribution.o `test -f 'math/IntDistribution.cc' || echo './'`math/IntDistribution.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=4.15.2 -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 SquashHyperFastavector.o `test -f 'paths/SquashHyperFastavector.cc' || echo './'`paths/SquashHyperFastavector.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/SquashHyperFastavector.h:12, > from paths/SquashHyperFastavector.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=4.15.2 -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 RNGen.o `test -f 'random/RNGen.cc' || echo './'`random/RNGen.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=4.15.2 -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 ScaffoldsUtils.o `test -f 'paths/ScaffoldsUtils.cc' || echo './'`paths/ScaffoldsUtils.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=4.15.2 -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 Fosmids.o `test -f 'paths/long/fosmid/Fosmids.cc' || echo './'`paths/long/fosmid/Fosmids.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=4.15.2 -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 PseudoUnipathGapCloser.o `test -f 'paths/PseudoUnipathGapCloser.cc' || echo './'`paths/PseudoUnipathGapCloser.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/PseudoUnipathGapCloser.h:17, > from paths/PseudoUnipathGapCloser.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=4.15.2 -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 MakeScaffoldsCloseBest.o `test -f 'paths/MakeScaffoldsCloseBest.cc' || echo './'`paths/MakeScaffoldsCloseBest.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/MakeScaffoldsCloseBest.cc:22: >./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=4.15.2 -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 QualNibbleVec.o `test -f 'feudal/QualNibbleVec.cc' || echo './'`feudal/QualNibbleVec.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=4.15.2 -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 HashSimple.o HashSimple.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=4.15.2 -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 BigMapTools.o `test -f 'paths/BigMapTools.cc' || echo './'`paths/BigMapTools.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=4.15.2 -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 GetFriendsAndAlignsInitial.o `test -f 'paths/long/ultra/GetFriendsAndAlignsInitial.cc' || echo './'`paths/long/ultra/GetFriendsAndAlignsInitial.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/GetFriendsAndAlignsInitial.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=4.15.2 -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 Fastavector.o Fastavector.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=4.15.2 -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 OffsetDistribution.o `test -f 'paths/OffsetDistribution.cc' || echo './'`paths/OffsetDistribution.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=4.15.2 -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 UseGDB.o `test -f 'system/UseGDB.cc' || echo './'`system/UseGDB.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=4.15.2 -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 ImperfectLookup.o `test -f 'lookup/ImperfectLookup.cc' || echo './'`lookup/ImperfectLookup.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=4.15.2 -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 MakeScaffoldsScoredBest.o `test -f 'paths/MakeScaffoldsScoredBest.cc' || echo './'`paths/MakeScaffoldsScoredBest.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/MakeScaffoldsScoredBest.cc:22: >./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=4.15.2 -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 SInsertion.o `test -f 'paths/SInsertion.cc' || echo './'`paths/SInsertion.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=4.15.2 -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 LookupTableBuilder.o `test -f 'lookup/LookupTableBuilder.cc' || echo './'`lookup/LookupTableBuilder.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=4.15.2 -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 ReadLocationUtil.o ReadLocationUtil.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=4.15.2 -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 VecString.o VecString.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=4.15.2 -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 UnipathNhoodLG.o `test -f 'paths/UnipathNhoodLG.cc' || echo './'`paths/UnipathNhoodLG.cc >In file included from ./paths/KmerPath.h:20:0, > from ./LocsHandlerLG.h:14, > from paths/UnipathNhoodLG.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=4.15.2 -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 MapUnibasesToContigs.o `test -f 'paths/MapUnibasesToContigs.cc' || echo './'`paths/MapUnibasesToContigs.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=4.15.2 -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 ProcBuf.o `test -f 'system/ProcBuf.cc' || echo './'`system/ProcBuf.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=4.15.2 -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 SimpleWalk.o `test -f 'paths/SimpleWalk.cc' || echo './'`paths/SimpleWalk.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=4.15.2 -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 VariantPostProcess.o `test -f 'paths/long/VariantPostProcess.cc' || echo './'`paths/long/VariantPostProcess.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=4.15.2 -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 KmerPathInterval.o `test -f 'paths/KmerPathInterval.cc' || echo './'`paths/KmerPathInterval.cc >In file included from paths/KmerPathInterval.cc:3:0: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h: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=4.15.2 -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 UnipathSeq.o `test -f 'paths/UnipathSeq.cc' || echo './'`paths/UnipathSeq.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/UnipathSeq.h:13, > from paths/UnipathSeq.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=4.15.2 -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 FounderAlignment.o `test -f 'paths/long/ultra/FounderAlignment.cc' || echo './'`paths/long/ultra/FounderAlignment.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=4.15.2 -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 Charvector.o Charvector.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=4.15.2 -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 MuxSearchAgent.o `test -f 'paths/MuxSearchAgent.cc' || echo './'`paths/MuxSearchAgent.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/OrientedKmerPathId.h:6, > from ./paths/Mux.h:6, > from ./paths/MuxSearchAgent.h:8, > from paths/MuxSearchAgent.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=4.15.2 -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 GetNextKmerPair.o `test -f 'kmers/GetNextKmerPair.cc' || echo './'`kmers/GetNextKmerPair.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=4.15.2 -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 VCF.o `test -f 'paths/simulation/VCF.cc' || echo './'`paths/simulation/VCF.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=4.15.2 -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 FastaFilestream.o FastaFilestream.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=4.15.2 -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 KmerAlign.o `test -f 'paths/long/KmerAlign.cc' || echo './'`paths/long/KmerAlign.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=4.15.2 -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 LocsHandlerLG.o LocsHandlerLG.cc >In file included from paths/KmerPath.h:20:0, > from LocsHandlerLG.h:14, > from LocsHandlerLG.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=4.15.2 -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 FeudalFileReader.o `test -f 'feudal/FeudalFileReader.cc' || echo './'`feudal/FeudalFileReader.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=4.15.2 -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 ReadFillDatabase.o `test -f 'paths/ReadFillDatabase.cc' || echo './'`paths/ReadFillDatabase.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=4.15.2 -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 Ulink.o `test -f 'paths/Ulink.cc' || echo './'`paths/Ulink.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=4.15.2 -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 SAM.o `test -f 'lookup/SAM.cc' || echo './'`lookup/SAM.cc >lookup/SAM.cc: In function âbool {anonymous}::parseDate8601(const char*, time_t&)â: >lookup/SAM.cc:120:24: warning: this statement may fall through [-Wimplicit-fallthrough=] > tm.tm_year /= 100; > ~~~~~~~~~~~^~~~~~ >lookup/SAM.cc:122:9: note: here > case 6: > ^~~~ >lookup/SAM.cc:176:13: warning: this statement may fall through [-Wimplicit-fallthrough=] > if ( *ptr == '.' ) > ^~ >lookup/SAM.cc:181:9: note: here > case 4: > ^~~~ >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=4.15.2 -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 FlowAlignSummary.o `test -f 'lookup/FlowAlignSummary.cc' || echo './'`lookup/FlowAlignSummary.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=4.15.2 -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 PrettyPrintTable.o PrettyPrintTable.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=4.15.2 -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 PrintAlignment.o PrintAlignment.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=4.15.2 -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 DigraphVTripleIIB.o `test -f 'paths/DigraphVTripleIIB.cc' || echo './'`paths/DigraphVTripleIIB.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=4.15.2 -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 CompressedSequence.o CompressedSequence.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=4.15.2 -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 OffsetTracker.o `test -f 'paths/OffsetTracker.cc' || echo './'`paths/OffsetTracker.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/UnipathSeq.h:13, > from ./paths/OffsetTracker.h:15, > from paths/OffsetTracker.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=4.15.2 -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 HitReceiver.o `test -f 'lookup/HitReceiver.cc' || echo './'`lookup/HitReceiver.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=4.15.2 -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 SuperMap.o SuperMap.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=4.15.2 -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 UnibaseCopyNumberCommon.o `test -f 'paths/UnibaseCopyNumberCommon.cc' || echo './'`paths/UnibaseCopyNumberCommon.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=4.15.2 -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 ProcessFrequentKmers.o `test -f 'pairwise_aligners/ProcessFrequentKmers.cc' || echo './'`pairwise_aligners/ProcessFrequentKmers.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=4.15.2 -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 AlignConsecutiveContigs.o `test -f 'pairwise_aligners/AlignConsecutiveContigs.cc' || echo './'`pairwise_aligners/AlignConsecutiveContigs.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=4.15.2 -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 ReftigUtils.o `test -f 'paths/reporting/ReftigUtils.cc' || echo './'`paths/reporting/ReftigUtils.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/reporting/ReftigUtils.h:15, > from paths/reporting/ReftigUtils.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=4.15.2 -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 PairDistModels.o `test -f 'paths/PairDistModels.cc' || echo './'`paths/PairDistModels.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=4.15.2 -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 SupportedHyperBasevector5.o `test -f 'paths/long/SupportedHyperBasevector5.cc' || echo './'`paths/long/SupportedHyperBasevector5.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/SupportedHyperBasevector5.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=4.15.2 -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 MaxMutmerFromMer.o `test -f 'pairwise_aligners/MaxMutmerFromMer.cc' || echo './'`pairwise_aligners/MaxMutmerFromMer.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=4.15.2 -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 Functions.o `test -f 'math/Functions.cc' || echo './'`math/Functions.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=4.15.2 -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 VecInserts.o VecInserts.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=4.15.2 -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 FastgTools.o `test -f 'fastg/FastgTools.cc' || echo './'`fastg/FastgTools.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=4.15.2 -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 ParallelVecUtilities.o ParallelVecUtilities.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=4.15.2 -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 VariantFilters.o `test -f 'paths/long/VariantFilters.cc' || echo './'`paths/long/VariantFilters.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/VariantFilters.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=4.15.2 -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 SequenceEntropy.o `test -f 'random/SequenceEntropy.cc' || echo './'`random/SequenceEntropy.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=4.15.2 -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 Utils.o `test -f 'system/Utils.cc' || echo './'`system/Utils.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=4.15.2 -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 BitVec.o `test -f 'feudal/BitVec.cc' || echo './'`feudal/BitVec.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=4.15.2 -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 Oob.o `test -f 'feudal/Oob.cc' || echo './'`feudal/Oob.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=4.15.2 -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 RunAllPathsCommonRules.o `test -f 'paths/RunAllPathsCommonRules.cc' || echo './'`paths/RunAllPathsCommonRules.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=4.15.2 -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 SmithWatBandedA.o `test -f 'pairwise_aligners/SmithWatBandedA.cc' || echo './'`pairwise_aligners/SmithWatBandedA.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=4.15.2 -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 SmithWatAffine.o `test -f 'pairwise_aligners/SmithWatAffine.cc' || echo './'`pairwise_aligners/SmithWatAffine.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=4.15.2 -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 Alignment.o Alignment.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=4.15.2 -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 Hit.o `test -f 'lookup/Hit.cc' || echo './'`lookup/Hit.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=4.15.2 -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 CharString.o `test -f 'feudal/CharString.cc' || echo './'`feudal/CharString.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=4.15.2 -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 MiscUtil.o `test -f 'system/MiscUtil.cc' || echo './'`system/MiscUtil.cc >system/MiscUtil.cc: In member function âvoid MakeMgr::WriteDependencyGraph(filename_t, Bool, const vec<FeudalString<char> >*, const vec<int>*, const std::map<FeudalString<char>, FeudalString<char> >*, const std::map<int, FeudalString<char> >*, String) constâ: >system/MiscUtil.cc:1193:5: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > if ( limitToTheseRules && !BinMember( *limitToTheseRules, ruleIdx ) ) > ^~ >system/MiscUtil.cc:1196:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âifâ > const MakeRule& r = rules[ ruleIdx ]; > ^~~~~ >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=4.15.2 -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 SmithWatFree.o `test -f 'pairwise_aligners/SmithWatFree.cc' || echo './'`pairwise_aligners/SmithWatFree.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=4.15.2 -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 SearchFastb2Core.o `test -f 'util/SearchFastb2Core.cc' || echo './'`util/SearchFastb2Core.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=4.15.2 -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 FastaFilestreamPreview.o FastaFilestreamPreview.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=4.15.2 -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 SupportedHyperBasevector8.o `test -f 'paths/long/SupportedHyperBasevector8.cc' || echo './'`paths/long/SupportedHyperBasevector8.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/SupportedHyperBasevector8.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=4.15.2 -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 KmerSpectra.o `test -f 'kmers/KmerSpectra.cc' || echo './'`kmers/KmerSpectra.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=4.15.2 -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 Matrix.o `test -f 'math/Matrix.cc' || echo './'`math/Matrix.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=4.15.2 -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 CRefMerger.o `test -f 'pairwise_aligners/CRefMerger.cc' || echo './'`pairwise_aligners/CRefMerger.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=4.15.2 -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 HyperFastavector.o `test -f 'paths/HyperFastavector.cc' || echo './'`paths/HyperFastavector.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/HyperFastavector.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=4.15.2 -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 WorklistUtils.o `test -f 'system/WorklistUtils.cc' || echo './'`system/WorklistUtils.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=4.15.2 -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 UnipathFixerTools.o `test -f 'paths/UnipathFixerTools.cc' || echo './'`paths/UnipathFixerTools.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=4.15.2 -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 ReadPather.o `test -f 'kmers/ReadPather.cc' || echo './'`kmers/ReadPather.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=4.15.2 -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 OverlapReads.o `test -f 'paths/long/OverlapReads.cc' || echo './'`paths/long/OverlapReads.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=4.15.2 -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 InternalMerge.o `test -f 'paths/InternalMerge.cc' || echo './'`paths/InternalMerge.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/InternalMerge.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=4.15.2 -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 MD5.o `test -f 'util/MD5.cc' || echo './'`util/MD5.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=4.15.2 -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 Unipath.o `test -f 'paths/Unipath.cc' || echo './'`paths/Unipath.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperBasevector.h:20, > from paths/Unipath.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=4.15.2 -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 NegativeGapValidator.o `test -f 'paths/NegativeGapValidator.cc' || echo './'`paths/NegativeGapValidator.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/NegativeGapValidator.h:11, > from paths/NegativeGapValidator.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=4.15.2 -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 KmerCount.o `test -f 'paths/long/KmerCount.cc' || echo './'`paths/long/KmerCount.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=4.15.2 -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 VariantReadSupport.o `test -f 'paths/long/VariantReadSupport.cc' || echo './'`paths/long/VariantReadSupport.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/VariantReadSupport.h:6, > from paths/long/VariantReadSupport.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/VariantReadSupport.cc: In function âvoid FindReadHomesBest(const vecbasevector&, const vecqualvector&, const HyperBasevector&, vec<vec<std::pair<int, int>, std::allocator<std::pair<int, int> > > >*, vec<int>, vec<std::tuple<int, int, read_place> >*, int, bool)â: >paths/long/VariantReadSupport.cc:1556:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] > for (size_t id = 0; id < places2size; id++) > ~~~^~~~~~~~~~~~~ >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=4.15.2 -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 UnipathNhoodCommon.o `test -f 'paths/UnipathNhoodCommon.cc' || echo './'`paths/UnipathNhoodCommon.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=4.15.2 -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 Intvector.o Intvector.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=4.15.2 -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 AlignFromMutmersAndSW.o `test -f 'pairwise_aligners/AlignFromMutmersAndSW.cc' || echo './'`pairwise_aligners/AlignFromMutmersAndSW.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=4.15.2 -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 Types.o `test -f 'system/Types.cc' || echo './'`system/Types.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=4.15.2 -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 FirstLookupFinder.o `test -f 'lookup/FirstLookupFinder.cc' || echo './'`lookup/FirstLookupFinder.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=4.15.2 -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 LookupTab.o `test -f 'lookup/LookupTab.cc' || echo './'`lookup/LookupTab.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=4.15.2 -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 CLinFastavec.o `test -f 'paths/CLinFastavec.cc' || echo './'`paths/CLinFastavec.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.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=4.15.2 -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 BlockAlign.o BlockAlign.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=4.15.2 -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 Sepdev.o `test -f 'paths/Sepdev.cc' || echo './'`paths/Sepdev.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=4.15.2 -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 Thread.o `test -f 'system/Thread.cc' || echo './'`system/Thread.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=4.15.2 -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 DotUtils.o `test -f 'graph/DotUtils.cc' || echo './'`graph/DotUtils.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=4.15.2 -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 EfastaTools.o `test -f 'efasta/EfastaTools.cc' || echo './'`efasta/EfastaTools.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=4.15.2 -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 AnnotatedContig.o AnnotatedContig.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=4.15.2 -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 BinsVec.o BinsVec.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=4.15.2 -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 MakeAlignsPathsParallelX.o `test -f 'paths/MakeAlignsPathsParallelX.cc' || echo './'`paths/MakeAlignsPathsParallelX.cc >In file included from ./paths/KmerPath.h:20:0, > from paths/MakeAlignsPathsParallelX.cc:17: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h: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=4.15.2 -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 ConsensusScoreModel.o `test -f 'paths/long/ultra/ConsensusScoreModel.cc' || echo './'`paths/long/ultra/ConsensusScoreModel.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=4.15.2 -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 KMerContext.o `test -f 'kmers/KMerContext.cc' || echo './'`kmers/KMerContext.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=4.15.2 -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 LargeKDispatcher.o `test -f 'paths/long/LargeKDispatcher.cc' || echo './'`paths/long/LargeKDispatcher.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=4.15.2 -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 SortKmersD.o `test -f 'sort_kmers/SortKmersD.cc' || echo './'`sort_kmers/SortKmersD.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=4.15.2 -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 COffset.o `test -f 'paths/reporting/COffset.cc' || echo './'`paths/reporting/COffset.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=4.15.2 -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 LongReadPatchOptimizer.o `test -f 'paths/LongReadPatchOptimizer.cc' || echo './'`paths/LongReadPatchOptimizer.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=4.15.2 -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 LinkingPairs.o `test -f 'paths/LinkingPairs.cc' || echo './'`paths/LinkingPairs.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=4.15.2 -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 MuxToPath.o `test -f 'paths/MuxToPath.cc' || echo './'`paths/MuxToPath.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/OrientedKmerPathId.h:6, > from ./paths/Mux.h:6, > from ./paths/MuxToPath.h:6, > from paths/MuxToPath.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=4.15.2 -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 AlignHyperKmerPath.o `test -f 'paths/AlignHyperKmerPath.cc' || echo './'`paths/AlignHyperKmerPath.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/AlignHyperKmerPath.h:44, > from paths/AlignHyperKmerPath.cc:20: >./paths/KmerPathInterval.h: In member function âvoid tagged_rpint::SetLookback(int)â: >./paths/KmerPathInterval.h: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/AlignHyperKmerPath.cc: In function âvoid ReorderToFollowReference(HyperKmerPath&, vec<look_align>&, const vec<vec<int> >&)â: >paths/AlignHyperKmerPath.cc:229:26: warning: this âifâ clause does not guard... [-Wmisleading-indentation] > { if ( la.a.pos2( ) < min_pos ) > ^~ >paths/AlignHyperKmerPath.cc:231:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the âifâ > min_rc = la.rc1; } } } > ^~~~~~ >x86_64-pc-linux-gnu-g++ -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=4.15.2 -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 RegapSupers.o `test -f 'paths/RegapSupers.cc' || echo './'`paths/RegapSupers.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=4.15.2 -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 SortKmersC.o `test -f 'sort_kmers/SortKmersC.cc' || echo './'`sort_kmers/SortKmersC.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=4.15.2 -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 DiscovarTools.o `test -f 'paths/long/DiscovarTools.cc' || echo './'`paths/long/DiscovarTools.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/DiscovarTools.h:18, > from paths/long/DiscovarTools.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=4.15.2 -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 Fastq.o `test -f 'util/Fastq.cc' || echo './'`util/Fastq.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=4.15.2 -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 Parallel.o `test -f 'system/Parallel.cc' || echo './'`system/Parallel.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=4.15.2 -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 FeudalTools.o `test -f 'feudal/FeudalTools.cc' || echo './'`feudal/FeudalTools.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=4.15.2 -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 FosmidPool.o `test -f 'paths/long/fosmid/FosmidPool.cc' || echo './'`paths/long/fosmid/FosmidPool.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=4.15.2 -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 Directory.o `test -f 'system/file/Directory.cc' || echo './'`system/file/Directory.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=4.15.2 -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 MuxGraph.o `test -f 'paths/MuxGraph.cc' || echo './'`paths/MuxGraph.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/OrientedKmerPathId.h:6, > from ./paths/Mux.h:6, > from ./paths/MuxGraph.h:12, > from paths/MuxGraph.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=4.15.2 -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 CorrectLongReads1.o `test -f 'paths/CorrectLongReads1.cc' || echo './'`paths/CorrectLongReads1.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=4.15.2 -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 HyperKmerPathCleaner.o `test -f 'paths/HyperKmerPathCleaner.cc' || echo './'`paths/HyperKmerPathCleaner.cc >In file included from ./paths/KmerPath.h:20:0, > from ./paths/KmerBaseBroker.h:16, > from ./paths/HyperKmerPath.h:17, > from ./paths/HyperKmerPathCleaner.h:13, > from paths/HyperKmerPathCleaner.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=4.15.2 -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 CreateGenome.o `test -f 'paths/long/CreateGenome.cc' || echo './'`paths/long/CreateGenome.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.cc:22: >./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; } > ~~~~~~~~~~^~~~~ >rm -f libAllPathsLG.a >x86_64-pc-linux-gnu-ar cru libAllPathsLG.a CleanEfasta.o HyperBasevector.o AllOfOutput.o ScaffoldGraphIntegrity.o ErrNo.o Combinatorics.o Mutmer.o EvalScaffoldsUtils.o EvalUtils.o Floatvector.o Mempool.o SupportedHyperBasevector4.o CorrectPatch.o Basevector.o VecOverlap.o HKPMerger.o PerfStat.o FindUnipathSeedsLG.o AffineRefiner.o ExtendUnipathSeqs.o FastgGraph.o ParsedArgs.o FeudalFileWriter.o RefTraceControl.o Jumpster.o TextTable.o PerfectLookup.o AddSuperReads.o TrackingAllocator.o PseudoUnipatherLib.o RefTrace.o Array.o Digraph.o FileReader.o Equiv.o FirstLookup.o IndexedAlignmentPlusVector.o CLinkBundle.o PerfectCount.o SupersHandler.o LookAlign.o CSublink.o SupportedHyperBasevector2.o PatcherCottageCore.o LongReadUnipathPatcherUtils.o Eps.o Quality.o FileWriter.o LookupTabBuilder.o CorrectLongReadsTools2.o MuxSearchPolicy.o BigMapDot.o Misc.o Logger.o AnAssemblyClass.o UnibaseCopyNumber3Core.o AlignTwoBasevectors.o UnipathSeqBuilder.o RemoveDuplicateAligns.o LongReadTools.o GetHomes.o Color.o SortKmersB.o SortKmers.o ReportWalkingRatesCore.o ThreadsafeIO.o Shuffle.o ScaffoldAccuracyCore.o Assert.o FastaConverter.o NormalRandom.o LongProtoTools.o File.o HyperEfasta.o ContigsManager.o SysConf.o SeqOnHyper.o MakeAlignsStatic.o SupportedHyperBasevector6.o SymLink.o SaveScaffoldGraph.o ScaffoldContigsOnRef.o FastaFileset.o HyperKmerPath.o PowerOf2.o Calculator.o KmerParcels.o Variants.o UnibaseCopyNumber3LowerCN.o ReadTracker.o TokenizeString.o KmerParcelsBuilder.o Crash.o SupportedHyperBasevector7.o Useq.o QueryLookupTableCore.o FindGaps.o FixSomeIndelsUtils.o KmerShape.o CGraphMass.o UnipathScaffold.o Arith.o ClusterAligner.o BasevectorTools.o GapSkip.o VecAlignmentPlus.o UnibaseCopyNumber2Core.o NStatsTools.o PairDistCorrection.o Exit.o ContigActualloc.o PolymorphismRemoveCore.o FirstLookupFinderECJ.o SuckScaffolds.o PackAlign.o MuxWalkGraph.o ReadsToPathsCoreX.o SortKmersA.o DigraphFromWords.o RunTime.o SupportedHyperBasevector3.o SeedNeighborhoodAnnex.o IdentifyCircularScaffolds.o ParseSet.o AmbiguityScore.o CommonPatherCore.o ImproperMerge.o MergeReadSetsCore.o SeedNeighborhood.o FastaParser.o LinkTimestamp.o NormalDistribution.o MemTracker.o PathEmbedding.o Qualvector.o FlattenHyperFastavector.o FirstLookupPerfect.o ReadHBVs.o InsertWalker.o ReadOriginTracker.o IntPairVec.o FindClosures.o CSuperLinks.o MapAligns.o KmerPathDatabase.o Prefab.o MemberOf.o System.o SubsumptionList.o InternalMergeImpl.o RefDesc.o ThreadedBlocks.o RefTraceTools.o BreakBadScaffolds.o MatchList.o AgpMods.o RunAllPathsCommon.o BinaryStream.o KmerAlignSet.o BaseVec.o Uniseq.o MersenneTwister.o SimpleLoop.o KmerPath.o VariantCallTools.o CorrectLongReadsTools.o FastaNameParser.o SeqInterval.o AlignCollector.o FixScaffoldsCore.o Overlap.o Generic.o VerifyGapLengths.o Friends.o FetchReadsAmb.o RunCommand.o ScoreAlignment.o AssemblyCleanupTools.o SupportedHyperBasevector.o Placement.o DumbCall.o EvalCorrected.o BuildScaffoldGraph.o KmerBaseBroker.o Bernoulli.o PdfEntry.o Permutation.o FastaVerifier.o UnibaseUtils.o OffsetDistributionInterface.o Edit.o PairedPair.o ProcessGap.o FindCells.o Bases.o KmerPathMuxSearcher.o FeudalControlBlock.o HTMLUtils.o PairsHandler.o HoInterval.o PostPatcherBridgeGap.o MergeReads2.o ParseRange.o MultipleAligner.o AgpFile.o WorklistMP.o Vec.o PairsManager.o MakeBlocks.o ReadLocation.o FindErrorsCore.o FieldVec.o AlignReadsOnUnibases.o MakeAlignsMethod.o RemodelGapTools.o CAltFasta.o AlignAndMerge.o ReadPairing.o PerfectAlignerLG.o FetchReads.o TraceVal.o AnAssemblyClassUtil.o CloseUnipathGapsCore.o TempFile.o HostName.o ContigEvent.o CorrectPatch3.o Periodic.o FastIfstream.o Superb.o PQVec.o KmerRecord.o LookupTable.o ReadLoc.o KmerSpectrumCore.o EvalByReads.o AssessBestAlignCore.o IntDistribution.o SquashHyperFastavector.o RNGen.o ScaffoldsUtils.o Fosmids.o PseudoUnipathGapCloser.o MakeScaffoldsCloseBest.o QualNibbleVec.o HashSimple.o BigMapTools.o GetFriendsAndAlignsInitial.o Fastavector.o OffsetDistribution.o UseGDB.o ImperfectLookup.o MakeScaffoldsScoredBest.o SInsertion.o LookupTableBuilder.o ReadLocationUtil.o VecString.o UnipathNhoodLG.o MapUnibasesToContigs.o ProcBuf.o SimpleWalk.o VariantPostProcess.o KmerPathInterval.o UnipathSeq.o FounderAlignment.o Charvector.o MuxSearchAgent.o GetNextKmerPair.o VCF.o FastaFilestream.o KmerAlign.o LocsHandlerLG.o FeudalFileReader.o ReadFillDatabase.o Ulink.o SAM.o FlowAlignSummary.o PrettyPrintTable.o PrintAlignment.o DigraphVTripleIIB.o CompressedSequence.o OffsetTracker.o HitReceiver.o SuperMap.o UnibaseCopyNumberCommon.o ProcessFrequentKmers.o AlignConsecutiveContigs.o ReftigUtils.o PairDistModels.o SupportedHyperBasevector5.o MaxMutmerFromMer.o Functions.o VecInserts.o FastgTools.o ParallelVecUtilities.o VariantFilters.o SequenceEntropy.o Utils.o BitVec.o Oob.o RunAllPathsCommonRules.o SmithWatBandedA.o SmithWatAffine.o Alignment.o Hit.o CharString.o MiscUtil.o SmithWatFree.o SearchFastb2Core.o FastaFilestreamPreview.o SupportedHyperBasevector8.o KmerSpectra.o Matrix.o CRefMerger.o HyperFastavector.o WorklistUtils.o UnipathFixerTools.o ReadPather.o OverlapReads.o InternalMerge.o MD5.o Unipath.o NegativeGapValidator.o KmerCount.o VariantReadSupport.o UnipathNhoodCommon.o Intvector.o AlignFromMutmersAndSW.o Types.o FirstLookupFinder.o LookupTab.o CLinFastavec.o BlockAlign.o Sepdev.o Thread.o DotUtils.o EfastaTools.o AnnotatedContig.o BinsVec.o MakeAlignsPathsParallelX.o ConsensusScoreModel.o KMerContext.o LargeKDispatcher.o SortKmersD.o COffset.o LongReadPatchOptimizer.o LinkingPairs.o MuxToPath.o AlignHyperKmerPath.o RegapSupers.o SortKmersC.o DiscovarTools.o Fastq.o Parallel.o FeudalTools.o FosmidPool.o Directory.o MuxGraph.o CorrectLongReads1.o HyperKmerPathCleaner.o CreateGenome.o >x86_64-pc-linux-gnu-ranlib libAllPathsLG.a >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=4.15.2 -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 RemodelGaps.o `test -f 'paths/RemodelGaps.cc' || echo './'`paths/RemodelGaps.cc >/bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -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 -Wl,-O1 -Wl,--as-needed -o RemodelGaps RemodelGaps.o libAllPathsLG.a >libtool: link: x86_64-pc-linux-gnu-g++ -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 -Wl,-O1 -o RemodelGaps RemodelGaps.o -Wl,--as-needed libAllPathsLG.a -fopenmp -pthread >/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lieee >collect2: error: ld returned 1 exit status >make[1]: *** [Makefile:2252: RemodelGaps] 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-r2:20180211-194551.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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