* 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void VecAlignmentPlusReader::ReadHalf(vec&, vec&, vec&)’: Alignment.h:144:7: warning: ‘.alignment_plus::score’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ only has 32 bits [-Wshift-overflow=] { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } ~~~~~~~~~~^~~~~ paths/HyperEfasta.cc: In function ‘vec > SpecialEfastaTag2Graph(digraphE&, efasta)’: 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: ./STLExtensions.h:425:8: warning: ‘#‘target_mem_ref’ not supported by dump_expr#’ may be used uninitialized in this function [-Wmaybe-uninitialized] struct triple { ^~~~~~ ./STLExtensions.h:425:8: warning: ‘#‘target_mem_ref’ not supported by dump_expr#’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./STLExtensions.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter > >]’: ./STLExtensions.h:425:8: warning: ‘#‘target_mem_ref’ not supported by dump_expr#’ may be used uninitialized in this function [-Wmaybe-uninitialized] struct triple { ^~~~~~ ./STLExtensions.h:425:8: warning: ‘#‘target_mem_ref’ not supported by dump_expr#’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘unsigned int FreqAffixes::_base(unsigned int, unsigned int) const’: ./kmers/naif_kmer/KmerFreqAffixesMap.h:39:5: warning: this ‘if’ 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 ‘if’ if (bit4 & 1u) n++; if (n > i) return 0u; ^~ ./kmers/naif_kmer/KmerFreqAffixesMap.h:40:5: warning: this ‘if’ 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 ‘if’ if (bit4 & 2u) n++; if (n > i) return 1u; ^~ ./kmers/naif_kmer/KmerFreqAffixesMap.h:41:5: warning: this ‘if’ 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 ‘if’ if (bit4 & 4u) n++; if (n > i) return 2u; ^~ ./kmers/naif_kmer/KmerFreqAffixesMap.h:42:5: warning: this ‘if’ 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 ‘if’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ only has 32 bits [-Wshift-overflow=] { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } ~~~~~~~~~~^~~~~ paths/long/ultra/Prefab.cc: In function ‘int {anonymous}::FindEdits(const vec&, const basevector&, vec >&, std::ostream&)’: paths/long/ultra/Prefab.cc:327:21: warning: this ‘if’ 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 ‘if’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ only has 32 bits [-Wshift-overflow=] { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } ~~~~~~~~~~^~~~~ paths/long/VariantCallTools.cc: In member function ‘bool EdgesOnRef::FindAlternativePath(int, vec, std::allocator > >*, int*, const vec, std::allocator > > >&, int, int, int)’: paths/long/VariantCallTools.cc:1342:17: warning: this ‘for’ 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 ‘for’ 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 ‘void ScoreGraph(const digraphE&, int, const vec, std::allocator > > > >&, int&, int&, vec&, vec&)’: paths/CorrectLongReadsTools.cc:649:16: warning: this ‘for’ 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 ‘for’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘HopscotchHashSet::value_type& HopscotchHashSet::findInsertSlot(HopscotchHashSet::size_type) [with T = KmerDictEntry<25>; H = KMer<25>::Hasher; C = std::equal_to >; F = TFactory >]’: ./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 ‘HopscotchHashSet::value_type& HopscotchHashSet::findInsertSlot(HopscotchHashSet::size_type) [with T = {anonymous}::KmerFriends; H = KMer<25>::Hasher; C = std::equal_to >; F = {anonymous}::KmerFriends::Factory]’: ./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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void KmerPathMuxSearcher::FindClosures(int, int, int, int, MuxSearchResult&) const’: ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::leftReadId’ may be used uninitialized in this function [-Wmaybe-uninitialized] class MuxSearchAgentBase { ^~~~~~~~~~~~~~~~~~ ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::rightReadId’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::minAcceptableExtLength’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::maxAcceptableExtLength’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::mp_result’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::dist_to_here’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::extensions_remaining’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::final_mux_subsumes_something’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::leftReadId’ may be used uninitialized in this function [-Wmaybe-uninitialized] class MuxSearchAgentBase { ^~~~~~~~~~~~~~~~~~ ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::rightReadId’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::minAcceptableExtLength’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::maxAcceptableExtLength’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::mp_result’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::dist_to_here’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::extensions_remaining’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:40:7: warning: ‘msa.MuxSearchAgentBase::final_mux_subsumes_something’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./paths/MuxSearchAgent.h:294:7: warning: ‘msa.MuxSearchAgentGoodReads::m_mayClose’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘bool operator==(const PairsManager&, const PairsManager&)’: 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 ‘vec PairsManager::getLibraryStats(String) const’: PairsManager.cc:567:5: warning: this ‘for’ 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 ‘for’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘KmerSpectraAffixes::KmerSpectraAffixes(unsigned int)’: ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_kf_min1’ may be used uninitialized in this function [-Wmaybe-uninitialized] class KmerSpectrum : public vec ^~~~~~~~~~~~ ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_kf_min2’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_kf_min3’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_kf_max1’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_kf_max2’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_kf_hi’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_kf_ave_uniq’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_nk_total’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_nk_bad_low_kf’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_nk_good_uniq’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_nk_good_snp’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_nk_good_rep’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_nk_bad_high_kf’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_ndk_total’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_ndk_bad_low_kf’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_ndk_good_snp’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_ndk_good_uniq’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_ndk_good_rep’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_ndk_bad_high_kf’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_coverage’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_genome_size_unique’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_genome_size_repetitive’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_genome_size’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_stddev_bias’ may be used uninitialized in this function [-Wmaybe-uninitialized] ./kmers/KmerSpectra.h:15:7: warning: ‘.KmerSpectrum::_d_SNP’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘bool {anonymous}::parseDate8601(const char*, time_t&)’: 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void MakeMgr::WriteDependencyGraph(filename_t, Bool, const vec >*, const vec*, const std::map, FeudalString >*, const std::map >*, String) const’: system/MiscUtil.cc:1193:5: warning: this ‘if’ 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 ‘if’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ only has 32 bits [-Wshift-overflow=] { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } ~~~~~~~~~~^~~~~ paths/long/VariantReadSupport.cc: In function ‘void FindReadHomesBest(const vecbasevector&, const vecqualvector&, const HyperBasevector&, vec, std::allocator > > >*, vec, vec >*, int, bool)’: 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ only has 32 bits [-Wshift-overflow=] { data1i_[0] = ( data1i_[0] & ((512 - 1) << 24) ) ^ lookback; } ~~~~~~~~~~^~~~~ paths/AlignHyperKmerPath.cc: In function ‘void ReorderToFollowReference(HyperKmerPath&, vec&, const vec >&)’: paths/AlignHyperKmerPath.cc:229:26: warning: this ‘if’ 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 ‘if’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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 ‘void tagged_rpint::SetLookback(int)’: ./paths/KmerPathInterval.h:364:50: warning: result of ‘(511 << 24)’ requires 34 bits to represent, but ‘int’ 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'