=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Skipping vulnerability checks.
WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'.
===> Building for kallisto-0.51.1
/usr/pkg/bin/cmake -S/pbulk/work/biology/kallisto/work/kallisto-0.51.1 -B/pbulk/work/biology/kallisto/work/kallisto-0.51.1 --check-build-system CMakeFiles/Makefile.cmake 0
/usr/pkg/bin/cmake -E cmake_progress_start /pbulk/work/biology/kallisto/work/kallisto-0.51.1/CMakeFiles /pbulk/work/biology/kallisto/work/kallisto-0.51.1//CMakeFiles/progress.marks
/usr/pkg/bin/gmake -f CMakeFiles/Makefile2 all
gmake[1]: Entering directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1'
/usr/pkg/bin/gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/depend
gmake[2]: Entering directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1'
cd /pbulk/work/biology/kallisto/work/kallisto-0.51.1 && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /pbulk/work/biology/kallisto/work/kallisto-0.51.1 /pbulk/work/biology/kallisto/work/kallisto-0.51.1 /pbulk/work/biology/kallisto/work/kallisto-0.51.1 /pbulk/work/biology/kallisto/work/kallisto-0.51.1 /pbulk/work/biology/kallisto/work/kallisto-0.51.1/CMakeFiles/bifrost.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1'
/usr/pkg/bin/gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build
gmake[2]: Entering directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1'
[ 3%] Creating directories for 'bifrost'
/usr/pkg/bin/cmake -Dcfgdir= -P /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/tmp/bifrost-mkdirs.cmake
/usr/pkg/bin/cmake -E touch /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-mkdir
[ 7%] No download step for 'bifrost'
/usr/pkg/bin/cmake -E echo_append
/usr/pkg/bin/cmake -E touch /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-download
[ 11%] No update step for 'bifrost'
/usr/pkg/bin/cmake -E echo_append
/usr/pkg/bin/cmake -E touch /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-update
[ 15%] No patch step for 'bifrost'
/usr/pkg/bin/cmake -E echo_append
/usr/pkg/bin/cmake -E touch /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-patch
[ 19%] Performing configure step for 'bifrost'
cd /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost && mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=32 -DCMAKE_INSTALL_PREFIX= "-DCMAKE_CXX_FLAGS=-Wno-subobject-linkage -Wno-return-type"
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is GNU 10.5.0
-- The CXX compiler identification is GNU 10.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /pbulk/work/biology/kallisto/work/.cwrapper/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /pbulk/work/biology/kallisto/work/.cwrapper/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
Build type: Release
Maximum k-mer size: 31
Maximum g-mer size: 31
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.13")
-- Configuring done (1.2s)
-- Generating done (0.0s)
-- Build files have been written to: /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build
cd /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost && /usr/pkg/bin/cmake -E touch /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-configure
[ 23%] Performing build step for 'bifrost'
cd /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost && cd build && gmake
gmake[3]: Entering directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build'
/usr/pkg/bin/cmake -S/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost -B/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/pkg/bin/cmake -E cmake_progress_start /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/CMakeFiles /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build//CMakeFiles/progress.marks
gmake -f CMakeFiles/Makefile2 all
gmake[4]: Entering directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build'
gmake -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/depend
gmake[5]: Entering directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build'
cd /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build && /usr/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/src /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color="
gmake[5]: Leaving directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build'
gmake -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/build
gmake[5]: Entering directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build'
[ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
cd /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/src && /pbulk/work/biology/kallisto/work/.cwrapper/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src -Wno-subobject-linkage -Wno-return-type -std=c++11 -O3 -DNDEBUG -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp: In function 'size_t rndup(size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:180:12: warning: right shift count >= width of type [-Wshift-count-overflow]
180 | v |= v >> 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp: At global scope:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:186:21: error: redefinition of 'uint32_t rndup(uint32_t)'
186 | BFG_INLINE uint32_t rndup(uint32_t v) {
| ^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:172:19: note: 'size_t rndup(size_t)' previously defined here
172 | BFG_INLINE size_t rndup(size_t v) {
| ^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:30,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/File_Parser.hpp: In static member function 'static int FileParser::getFileFormat(const char*)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/File_Parser.hpp:230:64: warning: right shift count >= width of type [-Wshift-count-overflow]
230 | else if ((reinterpret_cast<size_t*>(buffer)[0] >> 32) == BFG_GRAPHBIN_FORMAT_HEADER) ret_v = 3; // BFG
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/File_Parser.hpp:231:64: warning: right shift count >= width of type [-Wshift-count-overflow]
231 | else if ((reinterpret_cast<size_t*>(buffer)[0] >> 32) == BFG_METABIN_FORMAT_HEADER) ret_v = 4; // BFI
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:37,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp: In member function 'void ReadQualityHasherMinimizer::update(const char*, size_t, const char*, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:453:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
453 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL;
| ^~~~~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp: In member function 'void ReadQualityHasherMinimizer::update(const char*, const char*, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:523:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
523 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL;
| ^~~~~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp: In member function 'void ReadQualityHasherMinimizer::update_p(const char*, size_t, const char*, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:586:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
586 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL;
| ^~~~~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp: In member function 'void ReadQualityHasherMinimizer::update_p(const char*, const char*, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:660:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
660 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL;
| ^~~~~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp: In member function 'void ReadHasherMinimizer::update(const char*, size_t, const char*, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:1199:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
1199 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL;
| ^~~~~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp: In member function 'void ReadHasherMinimizer::update(const char*, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:1264:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
1264 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL;
| ^~~~~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp: In member function 'void ReadHasherMinimizer::update_p(const char*, size_t, const char*, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:1326:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
1326 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL;
| ^~~~~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp: In member function 'void ReadHasherMinimizer::update_p(const char*, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:1396:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
1396 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL;
| ^~~~~~~~~~~~~~~~~~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'bool CompactedDBG<U, G>::build(CDBG_Build_opt&)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:675:56: error: no matching function for call to 'max(long unsigned int, size_t)'
675 | nb_unique_kmers = max(1UL, kms.KmerF0());
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:254:5: note: candidate: 'template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)'
254 | max(const _Tp& __a, const _Tp& __b)
| ^~~
/usr/include/g++/bits/stl_algobase.h:254:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:675:56: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
675 | nb_unique_kmers = max(1UL, kms.KmerF0());
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:300:5: note: candidate: 'template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)'
300 | max(const _Tp& __a, const _Tp& __b, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algobase.h:300:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:675:56: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
675 | nb_unique_kmers = max(1UL, kms.KmerF0());
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3485:5: note: candidate: 'template<class _Tp> _Tp std::max(std::initializer_list<_Tp>)'
3485 | max(initializer_list<_Tp> __l)
| ^~~
/usr/include/g++/bits/stl_algo.h:3485:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:675:56: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
675 | nb_unique_kmers = max(1UL, kms.KmerF0());
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3491:5: note: candidate: 'template<class _Tp, class _Compare> _Tp std::max(std::initializer_list<_Tp>, _Compare)'
3491 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algo.h:3491:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:675:56: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
675 | nb_unique_kmers = max(1UL, kms.KmerF0());
| ^
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:676:66: error: no matching function for call to 'max(long unsigned int, size_t)'
676 | nb_unique_minimizers = max(1UL, kms.MinimizerF0());
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:254:5: note: candidate: 'template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)'
254 | max(const _Tp& __a, const _Tp& __b)
| ^~~
/usr/include/g++/bits/stl_algobase.h:254:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:676:66: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
676 | nb_unique_minimizers = max(1UL, kms.MinimizerF0());
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:300:5: note: candidate: 'template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)'
300 | max(const _Tp& __a, const _Tp& __b, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algobase.h:300:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:676:66: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
676 | nb_unique_minimizers = max(1UL, kms.MinimizerF0());
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3485:5: note: candidate: 'template<class _Tp> _Tp std::max(std::initializer_list<_Tp>)'
3485 | max(initializer_list<_Tp> __l)
| ^~~
/usr/include/g++/bits/stl_algo.h:3485:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:676:66: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
676 | nb_unique_minimizers = max(1UL, kms.MinimizerF0());
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3491:5: note: candidate: 'template<class _Tp, class _Compare> _Tp std::max(std::initializer_list<_Tp>, _Compare)'
3491 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algo.h:3491:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:676:66: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
676 | nb_unique_minimizers = max(1UL, kms.MinimizerF0());
| ^
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:677:121: error: no matching function for call to 'max(long unsigned int, size_t)'
677 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1()));
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:254:5: note: candidate: 'template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)'
254 | max(const _Tp& __a, const _Tp& __b)
| ^~~
/usr/include/g++/bits/stl_algobase.h:254:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:677:121: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
677 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1()));
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:300:5: note: candidate: 'template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)'
300 | max(const _Tp& __a, const _Tp& __b, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algobase.h:300:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:677:121: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
677 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1()));
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3485:5: note: candidate: 'template<class _Tp> _Tp std::max(std::initializer_list<_Tp>)'
3485 | max(initializer_list<_Tp> __l)
| ^~~
/usr/include/g++/bits/stl_algo.h:3485:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:677:121: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
677 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1()));
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3491:5: note: candidate: 'template<class _Tp, class _Compare> _Tp std::max(std::initializer_list<_Tp>, _Compare)'
3491 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algo.h:3491:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:677:121: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
677 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1()));
| ^
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:678:141: error: no matching function for call to 'max(long unsigned int, size_t)'
678 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1()));
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:254:5: note: candidate: 'template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)'
254 | max(const _Tp& __a, const _Tp& __b)
| ^~~
/usr/include/g++/bits/stl_algobase.h:254:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:678:141: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
678 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1()));
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:300:5: note: candidate: 'template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)'
300 | max(const _Tp& __a, const _Tp& __b, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algobase.h:300:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:678:141: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
678 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1()));
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3485:5: note: candidate: 'template<class _Tp> _Tp std::max(std::initializer_list<_Tp>)'
3485 | max(initializer_list<_Tp> __l)
| ^~~
/usr/include/g++/bits/stl_algo.h:3485:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:678:141: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
678 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1()));
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3491:5: note: candidate: 'template<class _Tp, class _Compare> _Tp std::max(std::initializer_list<_Tp>, _Compare)'
3491 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algo.h:3491:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:678:141: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
678 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1()));
| ^
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'const_UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const char*, size_t, const minHashIterator<RepHash>&, bool) const':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:795:43: warning: right shift count >= width of type [-Wshift-count-overflow]
795 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const char*, size_t, const minHashIterator<RepHash>&, bool)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:919:43: warning: right shift count >= width of type [-Wshift-count-overflow]
919 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'const_UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const Kmer&, bool) const':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1043:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1043 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const Kmer&, bool)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1246:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1246 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t, true> > CompactedDBG<U, G>::findPredecessors(const Kmer&, bool) const':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1369:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1369 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t> > CompactedDBG<U, G>::findPredecessors(const Kmer&, bool)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1519:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1519 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t, true> > CompactedDBG<U, G>::findSuccessors(const Kmer&, size_t, bool) const':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1673:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1673 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t> > CompactedDBG<U, G>::findSuccessors(const Kmer&, size_t, bool)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1858:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1858 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'bool CompactedDBG<U, G>::addUnitig(const string&, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4571:38: warning: left shift count >= width of type [-Wshift-count-overflow]
4571 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4573:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow]
4573 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE;
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'void CompactedDBG<U, G>::moveToAbundant()':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4758:92: warning: right shift count >= width of type [-Wshift-count-overflow]
4758 | if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32);
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4758:148: warning: right shift count >= width of type [-Wshift-count-overflow]
4758 | if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32);
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'bool CompactedDBG<U, G>::addUnitig(const string&, size_t, SpinLock&, SpinLock&)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4829:38: warning: left shift count >= width of type [-Wshift-count-overflow]
4829 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4831:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow]
4831 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE;
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'bool CompactedDBG<U, G>::addUnitig(const string&, size_t, size_t, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4965:49: warning: left shift count >= width of type [-Wshift-count-overflow]
4965 | const size_t pos_id_unitig_r = (id_unitig_r << 32) | ((static_cast<size_t>(!is_short_r) - 1) & MASK_CONTIG_TYPE);
| ~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4968:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow]
4968 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE;
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4970:38: warning: left shift count >= width of type [-Wshift-count-overflow]
4970 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'void CompactedDBG<U, G>::swapUnitigs(bool, size_t, size_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5161:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow]
5161 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE;
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5163:37: warning: left shift count >= width of type [-Wshift-count-overflow]
5163 | size_t shift_id_unitig_a = id_a << 32;
| ~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5164:37: warning: left shift count >= width of type [-Wshift-count-overflow]
5164 | size_t shift_id_unitig_b = id_b << 32;
| ~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'typename std::enable_if<(! is_void), void>::type CompactedDBG<U, G>::deleteUnitig_(bool, bool, size_t, bool)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5856:42: warning: left shift count >= width of type [-Wshift-count-overflow]
5856 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5857:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow]
5857 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE;
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'typename std::enable_if<is_void, void>::type CompactedDBG<U, G>::deleteUnitig_(bool, bool, size_t, bool)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6016:42: warning: left shift count >= width of type [-Wshift-count-overflow]
6016 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6017:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow]
6017 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE;
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'void CompactedDBG<U, G>::deleteUnitig_(bool, bool, size_t, const string&)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6161:42: warning: left shift count >= width of type [-Wshift-count-overflow]
6161 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6162:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow]
6162 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE;
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In member function 'UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const Kmer&, const preAllocMinHashIterator<RepHash>&)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6440:42: warning: right shift count >= width of type [-Wshift-count-overflow]
6440 | unitig_id = v(i, flag_v) >> 32;
| ~~~~~~~~~~~~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In member function 'bool CompactedDBG<U, G>::read(const string&, size_t, bool)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:191:79: error: no matching function for call to 'max(long unsigned int, size_t)'
191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:254:5: note: candidate: 'template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)'
254 | max(const _Tp& __a, const _Tp& __b)
| ^~~
/usr/include/g++/bits/stl_algobase.h:254:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:191:79: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:300:5: note: candidate: 'template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)'
300 | max(const _Tp& __a, const _Tp& __b, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algobase.h:300:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:191:79: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3485:5: note: candidate: 'template<class _Tp> _Tp std::max(std::initializer_list<_Tp>)'
3485 | max(initializer_list<_Tp> __l)
| ^~~
/usr/include/g++/bits/stl_algo.h:3485:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:191:79: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3491:5: note: candidate: 'template<class _Tp, class _Compare> _Tp std::max(std::initializer_list<_Tp>, _Compare)'
3491 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algo.h:3491:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:191:79: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:261:79: error: no matching function for call to 'max(long unsigned int, size_t)'
261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:254:5: note: candidate: 'template<class _Tp> const _Tp& std::max(const _Tp&, const _Tp&)'
254 | max(const _Tp& __a, const _Tp& __b)
| ^~~
/usr/include/g++/bits/stl_algobase.h:254:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:261:79: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
In file included from /usr/include/g++/array:40,
from /usr/include/g++/tuple:39,
from /usr/include/g++/functional:54,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:12,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algobase.h:300:5: note: candidate: 'template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)'
300 | max(const _Tp& __a, const _Tp& __b, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algobase.h:300:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:261:79: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'})
261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3485:5: note: candidate: 'template<class _Tp> _Tp std::max(std::initializer_list<_Tp>)'
3485 | max(initializer_list<_Tp> __l)
| ^~~
/usr/include/g++/bits/stl_algo.h:3485:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:261:79: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
In file included from /usr/include/g++/algorithm:62,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Common.hpp:5,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:29,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/usr/include/g++/bits/stl_algo.h:3491:5: note: candidate: 'template<class _Tp, class _Compare> _Tp std::max(std::initializer_list<_Tp>, _Compare)'
3491 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/usr/include/g++/bits/stl_algo.h:3491:5: note: template argument deduction/substitution failed:
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:261:79: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int'
261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05);
| ^
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In member function 'bool CompactedDBG<U, G>::readBinaryMinimizers(std::istream&, uint64_t, std::vector<Minimizer>&, uint32_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1071:52: warning: right shift count >= width of type [-Wshift-count-overflow]
1071 | if (!read_success || ((file_format_version >> 32) != BFG_METABIN_FORMAT_HEADER)) return false;
| ~~~~~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1093:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1093 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1132:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1132 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1141:57: warning: left shift count >= width of type [-Wshift-count-overflow]
1141 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos;
| ~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1161:66: warning: right shift count >= width of type [-Wshift-count-overflow]
1161 | vector<BitContainer> v_bmp_abundant((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1162:69: warning: right shift count >= width of type [-Wshift-count-overflow]
1162 | vector<BitContainer> v_bmp_overcrowded((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1171:58: warning: right shift count >= width of type [-Wshift-count-overflow]
1171 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1172:64: warning: right shift count >= width of type [-Wshift-count-overflow]
1172 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In member function 'bool CompactedDBG<U, G>::readBinaryIndex(std::istream&, uint64_t, std::vector<Minimizer>&, uint32_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1229:52: warning: right shift count >= width of type [-Wshift-count-overflow]
1229 | if (!read_success || ((file_format_version >> 32) != BFG_METABIN_FORMAT_HEADER)) return false;
| ~~~~~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1259:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1259 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1274:61: warning: left shift count >= width of type [-Wshift-count-overflow]
1274 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1307:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1307 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1316:57: warning: left shift count >= width of type [-Wshift-count-overflow]
1316 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos;
| ~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1343:66: warning: right shift count >= width of type [-Wshift-count-overflow]
1343 | vector<BitContainer> v_bmp_abundant((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1344:69: warning: right shift count >= width of type [-Wshift-count-overflow]
1344 | vector<BitContainer> v_bmp_overcrowded((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1353:58: warning: right shift count >= width of type [-Wshift-count-overflow]
1353 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1354:64: warning: right shift count >= width of type [-Wshift-count-overflow]
1354 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In member function 'bool CompactedDBG<U, G>::readBinaryIndex(std::istream&, uint64_t, boophf_t*, uint32_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1425:52: warning: right shift count >= width of type [-Wshift-count-overflow]
1425 | if (!read_success || ((file_format_version >> 32) != BFG_METABIN_FORMAT_HEADER)) return false;
| ~~~~~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1454:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1454 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1472:61: warning: left shift count >= width of type [-Wshift-count-overflow]
1472 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In lambda function:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1481:81: warning: right shift count >= width of type [-Wshift-count-overflow]
1481 | const size_t unitig_id_ = unitig_pos_ids[j] >> 32;
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In member function 'bool CompactedDBG<U, G>::readBinaryIndex(std::istream&, uint64_t, boophf_t*, uint32_t)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1515:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1515 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1524:57: warning: left shift count >= width of type [-Wshift-count-overflow]
1524 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos;
| ~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1551:66: warning: right shift count >= width of type [-Wshift-count-overflow]
1551 | vector<BitContainer> v_bmp_abundant((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1552:69: warning: right shift count >= width of type [-Wshift-count-overflow]
1552 | vector<BitContainer> v_bmp_overcrowded((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1561:58: warning: right shift count >= width of type [-Wshift-count-overflow]
1561 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1562:64: warning: right shift count >= width of type [-Wshift-count-overflow]
1562 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In member function 'std::pair<long long unsigned int, bool> CompactedDBG<U, G>::readBinaryGraph(std::istream&)':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1663:34: warning: right shift count >= width of type [-Wshift-count-overflow]
1663 | if ((file_format_version >> 32) != BFG_GRAPHBIN_FORMAT_HEADER) return {graph_checksum, false};
| ~~~~~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In member function 'bool CompactedDBG<U, G>::writeBinaryGraph(std::ostream&, size_t) const':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1789:92: warning: left shift count >= width of type [-Wshift-count-overflow]
1789 | const size_t fileformat_version = (static_cast<size_t>(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast<size_t>(BFG_GRAPHBIN_FORMAT_VERSION);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1789:92: warning: left shift count >= width of type [-Wshift-count-overflow]
1789 | const size_t fileformat_version = (static_cast<size_t>(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast<size_t>(BFG_GRAPHBIN_FORMAT_VERSION);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In member function 'bool CompactedDBG<U, G>::writeBinaryIndex(std::ostream&, uint64_t, size_t) const':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1847:57: warning: right shift count >= width of type [-Wshift-count-overflow]
1847 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1858:91: warning: left shift count >= width of type [-Wshift-count-overflow]
1858 | const size_t fileformat_version = (static_cast<size_t>(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast<size_t>(BFG_METABIN_FORMAT_VERSION);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1858:91: warning: left shift count >= width of type [-Wshift-count-overflow]
1858 | const size_t fileformat_version = (static_cast<size_t>(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast<size_t>(BFG_METABIN_FORMAT_VERSION);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1887:67: warning: right shift count >= width of type [-Wshift-count-overflow]
1887 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1887:67: warning: right shift count >= width of type [-Wshift-count-overflow]
1887 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In lambda function:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1910:57: warning: right shift count >= width of type [-Wshift-count-overflow]
1910 | const size_t unitig_id = unitig_idx >> 32;
| ~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1917:45: warning: right shift count >= width of type [-Wshift-count-overflow]
1917 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL);
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1928:49: warning: right shift count >= width of type [-Wshift-count-overflow]
1928 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL);
| ~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1932:49: warning: right shift count >= width of type [-Wshift-count-overflow]
1932 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL);
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1947:48: warning: right shift count >= width of type [-Wshift-count-overflow]
1947 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL);
| ~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1951:49: warning: right shift count >= width of type [-Wshift-count-overflow]
1951 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL);
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In member function 'bool CompactedDBG<U, G>::writeBinaryIndex(std::ostream&, uint64_t, size_t) const':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2097:61: warning: right shift count >= width of type [-Wshift-count-overflow]
2097 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1;
| ~~~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2111:40: warning: right shift count >= width of type [-Wshift-count-overflow]
2111 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) {
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2122:61: warning: right shift count >= width of type [-Wshift-count-overflow]
2122 | const size_t unitig_id = unitig_idx >> 32;
| ~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2129:62: warning: right shift count >= width of type [-Wshift-count-overflow]
2129 | const size_t id_bmp = id_special >> 32;
| ~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2178:40: warning: right shift count >= width of type [-Wshift-count-overflow]
2178 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) {
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2189:61: warning: right shift count >= width of type [-Wshift-count-overflow]
2189 | const size_t unitig_id = unitig_idx >> 32;
| ~~~~~~~~~~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataManager.hpp:10,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:10,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataStorage.tcc: In instantiation of 'UnitigColors DataStorage<Unitig_data_t>::joinUnitigColors(const_UnitigColorMap<Unitig_data_t>&, const_UnitigColorMap<Unitig_data_t>&) const [with Unitig_data_t = void; const_UnitigColorMap<Unitig_data_t> = UnitigMap<DataAccessor<void>, DataStorage<void>, true>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataAccessor.tcc:174:64: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataStorage.tcc:1444:36: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
1444 | size_t prev_color_id = 0xffffffffffffffff;
| ^~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataStorage.tcc:1445:35: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
1445 | size_t prev_km_dist = 0xffffffffffffffff;
| ^~~~~~~~~~~~~~~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const Kmer&, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7852:26: required from 'size_t CompactedDBG<U, G>::removeUnitigs(bool, bool, std::vector<Kmer>&) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:733:26: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:601:104: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1246:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1246 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG<U, G>::swapUnitigs(bool, size_t, size_t) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7881:25: required from 'size_t CompactedDBG<U, G>::removeUnitigs(bool, bool, std::vector<Kmer>&) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:733:26: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:601:104: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5163:37: warning: left shift count >= width of type [-Wshift-count-overflow]
5163 | size_t shift_id_unitig_a = id_a << 32;
| ~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5164:37: warning: left shift count >= width of type [-Wshift-count-overflow]
5164 | size_t shift_id_unitig_b = id_b << 32;
| ~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'typename std::enable_if<(! is_void), void>::type CompactedDBG<U, G>::deleteUnitig_(bool, bool, size_t, bool) [with bool is_void = false; Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; typename std::enable_if<(! is_void), void>::type = void; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7974:87: required from 'size_t CompactedDBG<U, G>::removeUnitigs(bool, bool, std::vector<Kmer>&) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:733:26: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:601:104: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5856:42: warning: left shift count >= width of type [-Wshift-count-overflow]
5856 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG<U, G>::addUnitig(const string&, size_t) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7457:30: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG<U, G>::joinUnitigs_(std::vector<Kmer>*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:735:70: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:601:104: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4571:38: warning: left shift count >= width of type [-Wshift-count-overflow]
4571 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4711:62: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow]
4711 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v);
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const Kmer&, bool) [with Unitig_data_t = void; Graph_data_t = void]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7852:26: required from 'size_t CompactedDBG<U, G>::removeUnitigs(bool, bool, std::vector<Kmer>&) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:733:26: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:611:103: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1246:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1246 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG<U, G>::swapUnitigs(bool, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7881:25: required from 'size_t CompactedDBG<U, G>::removeUnitigs(bool, bool, std::vector<Kmer>&) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:733:26: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:611:103: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5163:37: warning: left shift count >= width of type [-Wshift-count-overflow]
5163 | size_t shift_id_unitig_a = id_a << 32;
| ~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5164:37: warning: left shift count >= width of type [-Wshift-count-overflow]
5164 | size_t shift_id_unitig_b = id_b << 32;
| ~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'typename std::enable_if<is_void, void>::type CompactedDBG<U, G>::deleteUnitig_(bool, bool, size_t, bool) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if<is_void, void>::type = void; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7974:87: required from 'size_t CompactedDBG<U, G>::removeUnitigs(bool, bool, std::vector<Kmer>&) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:733:26: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:611:103: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6016:42: warning: left shift count >= width of type [-Wshift-count-overflow]
6016 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG<U, G>::addUnitig(const string&, size_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7648:30: required from 'typename std::enable_if<is_void, unsigned int>::type CompactedDBG<U, G>::joinUnitigs_(std::vector<Kmer>*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if<is_void, unsigned int>::type = unsigned int; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:735:70: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:611:103: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4571:38: warning: left shift count >= width of type [-Wshift-count-overflow]
4571 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4711:62: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow]
4711 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v);
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t, true> > CompactedDBG<U, G>::findPredecessors(const Kmer&, bool) const [with Unitig_data_t = void; Graph_data_t = void]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:469:72: required from 'bool CompactedDBG<U, G>::writeGFA(const string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:82:41: required from 'bool CompactedDBG<U, G>::write(const string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:612:192: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1369:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1369 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t, true> > CompactedDBG<U, G>::findSuccessors(const Kmer&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:470:70: required from 'bool CompactedDBG<U, G>::writeGFA(const string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:82:41: required from 'bool CompactedDBG<U, G>::write(const string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:612:192: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1673:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1673 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In instantiation of 'bool CompactedDBG<U, G>::writeBinaryGraph(std::ostream&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream<char>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1778:28: required from 'bool CompactedDBG<U, G>::writeBinaryGraph(const string&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:84:62: required from 'bool CompactedDBG<U, G>::write(const string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:612:192: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1789:92: warning: left shift count >= width of type [-Wshift-count-overflow]
1789 | const size_t fileformat_version = (static_cast<size_t>(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast<size_t>(BFG_GRAPHBIN_FORMAT_VERSION);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In instantiation of 'bool CompactedDBG<U, G>::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream<char>; uint64_t = long long unsigned int; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1839:28: required from 'bool CompactedDBG<U, G>::writeBinaryIndex(const string&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; uint64_t = long long unsigned int; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:117:41: required from 'bool CompactedDBG<U, G>::write(const string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:612:192: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1847:57: warning: right shift count >= width of type [-Wshift-count-overflow]
1847 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1858:91: warning: left shift count >= width of type [-Wshift-count-overflow]
1858 | const size_t fileformat_version = (static_cast<size_t>(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast<size_t>(BFG_METABIN_FORMAT_VERSION);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1887:67: warning: right shift count >= width of type [-Wshift-count-overflow]
1887 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1888:77: warning: right shift count >= width of type [-Wshift-count-overflow]
1888 | const size_t nb_bmp_km_short = ((km_unitigs.size() * (k_ - g_ + 1)) >> 32) + 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1910:57: warning: right shift count >= width of type [-Wshift-count-overflow]
1910 | const size_t unitig_id = unitig_idx >> 32;
| ~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1917:45: warning: right shift count >= width of type [-Wshift-count-overflow]
1917 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL);
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1928:49: warning: right shift count >= width of type [-Wshift-count-overflow]
1928 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL);
| ~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1932:49: warning: right shift count >= width of type [-Wshift-count-overflow]
1932 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL);
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1947:48: warning: right shift count >= width of type [-Wshift-count-overflow]
1947 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL);
| ~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1951:49: warning: right shift count >= width of type [-Wshift-count-overflow]
1951 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL);
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2097:61: warning: right shift count >= width of type [-Wshift-count-overflow]
2097 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1;
| ~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2111:40: warning: right shift count >= width of type [-Wshift-count-overflow]
2111 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) {
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2122:61: warning: right shift count >= width of type [-Wshift-count-overflow]
2122 | const size_t unitig_id = unitig_idx >> 32;
| ~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2129:62: warning: right shift count >= width of type [-Wshift-count-overflow]
2129 | const size_t id_bmp = id_special >> 32;
| ~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2178:40: warning: right shift count >= width of type [-Wshift-count-overflow]
2178 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) {
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2189:61: warning: right shift count >= width of type [-Wshift-count-overflow]
2189 | const size_t unitig_id = unitig_idx >> 32;
| ~~~~~~~~~~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG<U, G>::annotateSplitUnitig(const string&, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2248:61: required from 'bool CompactedDBG<U, G>::annotateSplitUnitigs(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG<Unitig_data_t>::merge(ColoredCDBG<Unitig_data_t>&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:644:110: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5501:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
5501 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF;
| ^~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5502:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
5502 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF;
| ^~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG<U, G>::annotateSplitUnitig(const string&, LockGraph&, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2289:52: required from 'bool CompactedDBG<U, G>::annotateSplitUnitigs(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG<Unitig_data_t>::merge(ColoredCDBG<Unitig_data_t>&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:644:110: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5652:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
5652 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF;
| ^~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5653:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
5653 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF;
| ^~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG<U, G>::addUnitig(const string&, size_t, SpinLock&, SpinLock&) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2375:62: required from 'void CompactedDBG<U, G>::makeGraphFromFASTA(const string&, size_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:197:13: required from 'bool CompactedDBG<U, G>::read(const string&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:655:137: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4829:38: warning: left shift count >= width of type [-Wshift-count-overflow]
4829 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG<U, G>::moveToAbundant() [with Unitig_data_t = void; Graph_data_t = void]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2385:9: required from 'void CompactedDBG<U, G>::makeGraphFromFASTA(const string&, size_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:197:13: required from 'bool CompactedDBG<U, G>::read(const string&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:655:137: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4758:92: warning: right shift count >= width of type [-Wshift-count-overflow]
4758 | if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32);
| ~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4758:148: warning: right shift count >= width of type [-Wshift-count-overflow]
4758 | if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32);
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4805:78: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow]
4805 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v);
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In instantiation of 'std::pair<long long unsigned int, bool> CompactedDBG<U, G>::readBinaryGraph(std::istream&) [with Unitig_data_t = void; Graph_data_t = void; std::istream = std::basic_istream<char>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1631:27: required from 'std::pair<long long unsigned int, bool> CompactedDBG<U, G>::readBinaryGraph(const string&) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:383:49: required from 'bool CompactedDBG<U, G>::read(const string&, const string&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:656:124: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1663:34: warning: right shift count >= width of type [-Wshift-count-overflow]
1663 | if ((file_format_version >> 32) != BFG_GRAPHBIN_FORMAT_HEADER) return {graph_checksum, false};
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In instantiation of 'bool CompactedDBG<U, G>::readBinaryIndex(std::istream&, uint64_t, std::vector<Minimizer>&, uint32_t) [with Unitig_data_t = void; Graph_data_t = void; std::istream = std::basic_istream<char>; uint64_t = long long unsigned int; uint32_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1020:27: required from 'bool CompactedDBG<U, G>::readBinaryIndex(const string&, uint64_t, bool, uint32_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; uint64_t = long long unsigned int; uint32_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:393:35: required from 'bool CompactedDBG<U, G>::read(const string&, const string&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:656:124: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1229:52: warning: right shift count >= width of type [-Wshift-count-overflow]
1229 | if (!read_success || ((file_format_version >> 32) != BFG_METABIN_FORMAT_HEADER)) return false;
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1259:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1259 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1274:61: warning: left shift count >= width of type [-Wshift-count-overflow]
1274 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos;
| ~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1307:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1307 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1316:57: warning: left shift count >= width of type [-Wshift-count-overflow]
1316 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos;
| ~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1343:66: warning: right shift count >= width of type [-Wshift-count-overflow]
1343 | vector<BitContainer> v_bmp_abundant((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1344:69: warning: right shift count >= width of type [-Wshift-count-overflow]
1344 | vector<BitContainer> v_bmp_overcrowded((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1353:58: warning: right shift count >= width of type [-Wshift-count-overflow]
1353 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1354:64: warning: right shift count >= width of type [-Wshift-count-overflow]
1354 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG<U, G>::annotateSplitUnitig(const string&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2248:61: required from 'bool CompactedDBG<U, G>::annotateSplitUnitigs(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2134:13: required from 'bool CompactedDBG<U, G>::merge(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:676:93: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5501:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
5501 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF;
| ^~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5502:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
5502 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF;
| ^~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG<U, G>::annotateSplitUnitig(const string&, LockGraph&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2289:52: required from 'bool CompactedDBG<U, G>::annotateSplitUnitigs(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2134:13: required from 'bool CompactedDBG<U, G>::merge(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:676:93: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5652:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
5652 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF;
| ^~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5653:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
5653 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF;
| ^~~~~~~~~~~~~~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const Kmer&, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; const_UnitigMap<Unitig_data_t, Graph_data_t> = UnitigMap<DataAccessor<void>, DataStorage<void>, true>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7277:50: required from 'void CompactedDBG<U, G>::createJoinHT(std::vector<Kmer>*, KmerHashTable<char>&, size_t) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7327:17: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG<U, G>::joinUnitigs_(std::vector<Kmer>*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:735:70: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:601:104: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1043:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1043 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t, true> > CompactedDBG<U, G>::findPredecessors(const Kmer&, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:469:72: required from 'bool CompactedDBG<U, G>::writeGFA(const string&, size_t, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:82:41: required from 'bool CompactedDBG<U, G>::write(const string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG<Unitig_data_t>::write(const string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:603:146: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1369:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1369 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t, true> > CompactedDBG<U, G>::findSuccessors(const Kmer&, size_t, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:470:70: required from 'bool CompactedDBG<U, G>::writeGFA(const string&, size_t, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:82:41: required from 'bool CompactedDBG<U, G>::write(const string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG<Unitig_data_t>::write(const string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:603:146: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1673:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1673 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In instantiation of 'bool CompactedDBG<U, G>::writeBinaryGraph(std::ostream&, size_t) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::ostream = std::basic_ostream<char>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1778:28: required from 'bool CompactedDBG<U, G>::writeBinaryGraph(const string&, size_t) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:84:62: required from 'bool CompactedDBG<U, G>::write(const string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG<Unitig_data_t>::write(const string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:603:146: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1789:92: warning: left shift count >= width of type [-Wshift-count-overflow]
1789 | const size_t fileformat_version = (static_cast<size_t>(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast<size_t>(BFG_GRAPHBIN_FORMAT_VERSION);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In instantiation of 'bool CompactedDBG<U, G>::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::ostream = std::basic_ostream<char>; uint64_t = long long unsigned int; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1839:28: required from 'bool CompactedDBG<U, G>::writeBinaryIndex(const string&, uint64_t, size_t) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; uint64_t = long long unsigned int; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:117:41: required from 'bool CompactedDBG<U, G>::write(const string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG<Unitig_data_t>::write(const string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:603:146: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1847:57: warning: right shift count >= width of type [-Wshift-count-overflow]
1847 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1858:91: warning: left shift count >= width of type [-Wshift-count-overflow]
1858 | const size_t fileformat_version = (static_cast<size_t>(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast<size_t>(BFG_METABIN_FORMAT_VERSION);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1887:67: warning: right shift count >= width of type [-Wshift-count-overflow]
1887 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1888:77: warning: right shift count >= width of type [-Wshift-count-overflow]
1888 | const size_t nb_bmp_km_short = ((km_unitigs.size() * (k_ - g_ + 1)) >> 32) + 1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1910:57: warning: right shift count >= width of type [-Wshift-count-overflow]
1910 | const size_t unitig_id = unitig_idx >> 32;
| ~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1917:45: warning: right shift count >= width of type [-Wshift-count-overflow]
1917 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL);
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1928:49: warning: right shift count >= width of type [-Wshift-count-overflow]
1928 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL);
| ~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1932:49: warning: right shift count >= width of type [-Wshift-count-overflow]
1932 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL);
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1947:48: warning: right shift count >= width of type [-Wshift-count-overflow]
1947 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL);
| ~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1951:49: warning: right shift count >= width of type [-Wshift-count-overflow]
1951 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL);
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2097:61: warning: right shift count >= width of type [-Wshift-count-overflow]
2097 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1;
| ~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2111:40: warning: right shift count >= width of type [-Wshift-count-overflow]
2111 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) {
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2122:61: warning: right shift count >= width of type [-Wshift-count-overflow]
2122 | const size_t unitig_id = unitig_idx >> 32;
| ~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2129:62: warning: right shift count >= width of type [-Wshift-count-overflow]
2129 | const size_t id_bmp = id_special >> 32;
| ~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2178:40: warning: right shift count >= width of type [-Wshift-count-overflow]
2178 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) {
| ~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2189:61: warning: right shift count >= width of type [-Wshift-count-overflow]
2189 | const size_t unitig_id = unitig_idx >> 32;
| ~~~~~~~~~~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const Kmer&, bool) const [with Unitig_data_t = void; Graph_data_t = void; const_UnitigMap<Unitig_data_t, Graph_data_t> = UnitigMap<void, void, true>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7277:50: required from 'void CompactedDBG<U, G>::createJoinHT(std::vector<Kmer>*, KmerHashTable<char>&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:7529:17: required from 'typename std::enable_if<is_void, unsigned int>::type CompactedDBG<U, G>::joinUnitigs_(std::vector<Kmer>*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if<is_void, unsigned int>::type = unsigned int; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:735:70: required from 'bool CompactedDBG<U, G>::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:611:103: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1043:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1043 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:40,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_<is_const>::iterator_() [with bool is_const = true]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2037:60: required from 'bool CompactedDBG<U, G>::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream<char>; uint64_t = long long unsigned int; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1839:28: required from 'bool CompactedDBG<U, G>::writeBinaryIndex(const string&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; uint64_t = long long unsigned int; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:117:41: required from 'bool CompactedDBG<U, G>::write(const string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:612:192: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/MinimizerIndex.hpp:29:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
29 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL) {}
| ^~~~~~~~~~~~~~~~~~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG<U, G>::addUnitig(const string&, size_t, SpinLock&, SpinLock&) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2375:62: required from 'void CompactedDBG<U, G>::makeGraphFromFASTA(const string&, size_t) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:197:13: required from 'bool CompactedDBG<U, G>::read(const string&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:612:65: required from 'bool ColoredCDBG<Unitig_data_t>::read(const string&, const string&, size_t, bool) [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:163: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4829:38: warning: left shift count >= width of type [-Wshift-count-overflow]
4829 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG<U, G>::moveToAbundant() [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2385:9: required from 'void CompactedDBG<U, G>::makeGraphFromFASTA(const string&, size_t) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:197:13: required from 'bool CompactedDBG<U, G>::read(const string&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:612:65: required from 'bool ColoredCDBG<Unitig_data_t>::read(const string&, const string&, size_t, bool) [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:163: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4758:92: warning: right shift count >= width of type [-Wshift-count-overflow]
4758 | if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32);
| ~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4758:148: warning: right shift count >= width of type [-Wshift-count-overflow]
4758 | if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32);
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4805:78: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow]
4805 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v);
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In instantiation of 'std::pair<long long unsigned int, bool> CompactedDBG<U, G>::readBinaryGraph(std::istream&) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::istream = std::basic_istream<char>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1631:27: required from 'std::pair<long long unsigned int, bool> CompactedDBG<U, G>::readBinaryGraph(const string&) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:383:49: required from 'bool CompactedDBG<U, G>::read(const string&, const string&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:706:65: required from 'bool ColoredCDBG<Unitig_data_t>::read(const string&, const string&, const string&, size_t, bool) [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:624:150: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1663:34: warning: right shift count >= width of type [-Wshift-count-overflow]
1663 | if ((file_format_version >> 32) != BFG_GRAPHBIN_FORMAT_HEADER) return {graph_checksum, false};
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc: In instantiation of 'bool CompactedDBG<U, G>::readBinaryIndex(std::istream&, uint64_t, std::vector<Minimizer>&, uint32_t) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::istream = std::basic_istream<char>; uint64_t = long long unsigned int; uint32_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1020:27: required from 'bool CompactedDBG<U, G>::readBinaryIndex(const string&, uint64_t, bool, uint32_t) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; uint64_t = long long unsigned int; uint32_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:393:35: required from 'bool CompactedDBG<U, G>::read(const string&, const string&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:706:65: required from 'bool ColoredCDBG<Unitig_data_t>::read(const string&, const string&, const string&, size_t, bool) [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:624:150: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1229:52: warning: right shift count >= width of type [-Wshift-count-overflow]
1229 | if (!read_success || ((file_format_version >> 32) != BFG_METABIN_FORMAT_HEADER)) return false;
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1259:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1259 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1274:61: warning: left shift count >= width of type [-Wshift-count-overflow]
1274 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos;
| ~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1307:41: warning: left shift count >= width of type [-Wshift-count-overflow]
1307 | const size_t id_bmp = i << 32;
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1316:57: warning: left shift count >= width of type [-Wshift-count-overflow]
1316 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos;
| ~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1343:66: warning: right shift count >= width of type [-Wshift-count-overflow]
1343 | vector<BitContainer> v_bmp_abundant((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1344:69: warning: right shift count >= width of type [-Wshift-count-overflow]
1344 | vector<BitContainer> v_bmp_overcrowded((nb_special_minz >> 32) + 1);
| ~~~~~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1353:58: warning: right shift count >= width of type [-Wshift-count-overflow]
1353 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1354:64: warning: right shift count >= width of type [-Wshift-count-overflow]
1354 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL);
| ~~^~~~~
In file included from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831,
from /pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1:
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t> > CompactedDBG<U, G>::findPredecessors(const Kmer&, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5538:59: required from 'bool CompactedDBG<U, G>::annotateSplitUnitig(const string&, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2248:61: required from 'bool CompactedDBG<U, G>::annotateSplitUnitigs(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG<Unitig_data_t>::merge(ColoredCDBG<Unitig_data_t>&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:644:110: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1519:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1519 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t> > CompactedDBG<U, G>::findSuccessors(const Kmer&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5539:57: required from 'bool CompactedDBG<U, G>::annotateSplitUnitig(const string&, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2248:61: required from 'bool CompactedDBG<U, G>::annotateSplitUnitigs(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG<Unitig_data_t>::merge(ColoredCDBG<Unitig_data_t>&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:644:110: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1858:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1858 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG<U, G>::deleteUnitig_(bool, bool, size_t, const string&) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int; std::string = std::__cxx11::basic_string<char>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4774:38: required from 'void CompactedDBG<U, G>::moveToAbundant() [with Unitig_data_t = void; Graph_data_t = void]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2385:9: required from 'void CompactedDBG<U, G>::makeGraphFromFASTA(const string&, size_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:197:13: required from 'bool CompactedDBG<U, G>::read(const string&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:655:137: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6161:42: warning: left shift count >= width of type [-Wshift-count-overflow]
6161 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t> > CompactedDBG<U, G>::findPredecessors(const Kmer&, bool) [with Unitig_data_t = void; Graph_data_t = void]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5538:59: required from 'bool CompactedDBG<U, G>::annotateSplitUnitig(const string&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2248:61: required from 'bool CompactedDBG<U, G>::annotateSplitUnitigs(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2134:13: required from 'bool CompactedDBG<U, G>::merge(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:676:93: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1519:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1519 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'std::vector<UnitigMap<Unitig_data_t, Graph_data_t> > CompactedDBG<U, G>::findSuccessors(const Kmer&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5539:57: required from 'bool CompactedDBG<U, G>::annotateSplitUnitig(const string&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2248:61: required from 'bool CompactedDBG<U, G>::annotateSplitUnitigs(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2134:13: required from 'bool CompactedDBG<U, G>::merge(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:676:93: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:1858:43: warning: right shift count >= width of type [-Wshift-count-overflow]
1858 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG<U, G>::addUnitig(const string&, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6369:30: required from 'typename std::enable_if<is_void, bool>::type CompactedDBG<U, G>::extractUnitig_(size_t&, size_t&, size_t&, size_t&, const std::vector<std::pair<int, int> >&) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if<is_void, bool>::type = bool; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6616:46: required from 'std::pair<unsigned int, unsigned int> CompactedDBG<U, G>::splitAllUnitigs() [with Unitig_data_t = void; Graph_data_t = void]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2137:44: required from 'bool CompactedDBG<U, G>::merge(const CompactedDBG<U, G>&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:676:93: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4965:49: warning: left shift count >= width of type [-Wshift-count-overflow]
4965 | const size_t pos_id_unitig_r = (id_unitig_r << 32) | ((static_cast<size_t>(!is_short_r) - 1) & MASK_CONTIG_TYPE);
| ~~~~~~~~~~~~~^~~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4970:38: warning: left shift count >= width of type [-Wshift-count-overflow]
4970 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:5137:62: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow]
5137 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v);
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const char*, size_t, const minHashIterator<RepHash>&, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; const_UnitigMap<Unitig_data_t, Graph_data_t> = UnitigMap<DataAccessor<void>, DataStorage<void>, true>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4537:36: required from 'const_UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::findUnitig(const char*, size_t, size_t, const minHashIterator<RepHash>&) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; const_UnitigMap<Unitig_data_t, Graph_data_t> = UnitigMap<DataAccessor<void>, DataStorage<void>, true>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Search.tcc:668:72: required from 'std::vector<std::pair<unsigned int, UnitigMap<Unitig_data_t, Graph_data_t, true> > > CompactedDBG<U, G>::searchSequence(const string&, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1570:90: required from 'bool ColoredCDBG<Unitig_data_t>::search(const std::vector<std::__cxx11::basic_string<char> >&, const string&, double, bool, size_t, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:696:167: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:795:43: warning: right shift count >= width of type [-Wshift-count-overflow]
795 | unitig_id = unitig_id_pos >> 32;
| ~~~~~~~~~~~~~~^~~~~
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::find(const char*, size_t, const minHashIterator<RepHash>&, bool) const [with Unitig_data_t = void; Graph_data_t = void; const_UnitigMap<Unitig_data_t, Graph_data_t> = UnitigMap<void, void, true>; size_t = unsigned int]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4537:36: required from 'const_UnitigMap<Unitig_data_t, Graph_data_t> CompactedDBG<U, G>::findUnitig(const char*, size_t, size_t, const minHashIterator<RepHash>&) const [with Unitig_data_t = void; Graph_data_t = void; const_UnitigMap<Unitig_data_t, Graph_data_t> = UnitigMap<void, void, true>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Search.tcc:937:72: required from 'std::vector<std::pair<unsigned int, UnitigMap<Unitig_data_t, Graph_data_t, true> > > CompactedDBG<U, G>::searchSequence(const string&, bool, bool, bool, bool, double, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Search.tcc:1132:85: required from 'bool CompactedDBG<U, G>::search(const std::vector<std::__cxx11::basic_string<char> >&, const string&, double, bool, size_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:705:166: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:795:43: warning: right shift count >= width of type [-Wshift-count-overflow]
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG<U, G>::deleteUnitig_(bool, bool, size_t, const string&) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; size_t = unsigned int; std::string = std::__cxx11::basic_string<char>]':
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:4774:38: required from 'void CompactedDBG<U, G>::moveToAbundant() [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2385:9: required from 'void CompactedDBG<U, G>::makeGraphFromFASTA(const string&, size_t) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:197:13: required from 'bool CompactedDBG<U, G>::read(const string&, size_t, bool) [with Unitig_data_t = DataAccessor<void>; Graph_data_t = DataStorage<void>; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:612:65: required from 'bool ColoredCDBG<Unitig_data_t>::read(const string&, const string&, size_t, bool) [with Unitig_data_t = void; std::string = std::__cxx11::basic_string<char>; size_t = unsigned int]'
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:163: required from here
/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:6161:42: warning: left shift count >= width of type [-Wshift-count-overflow]
6161 | size_t pos_id_unitig = id_unitig << 32;
| ~~~~~~~~~~^~~~~
gmake[5]: *** [src/CMakeFiles/bifrost_static.dir/build.make:82: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
gmake[5]: Leaving directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build'
gmake[4]: *** [CMakeFiles/Makefile2:115: src/CMakeFiles/bifrost_static.dir/all] Error 2
gmake[4]: Leaving directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build'
gmake[3]: *** [Makefile:139: all] Error 2
gmake[3]: Leaving directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build'
gmake[2]: *** [CMakeFiles/bifrost.dir/build.make:89: ext/bifrost/src/bifrost-stamp/bifrost-build] Error 2
gmake[2]: Leaving directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1'
gmake[1]: *** [CMakeFiles/Makefile2:115: CMakeFiles/bifrost.dir/all] Error 2
gmake[1]: Leaving directory '/pbulk/work/biology/kallisto/work/kallisto-0.51.1'
gmake: *** [Makefile:139: all] Error 2
*** Error code 2
Stop.
make[1]: stopped in /usr/pkgsrc/biology/kallisto
*** Error code 1
Stop.
make: stopped in /usr/pkgsrc/biology/kallisto