=> "/opt/pkg/bin/bmake" ["-C", "/Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/kallisto", "all", "BATCH=1", "DEPENDS_TARGET=/nonexistent"] WARNING: USE_CMAKE is deprecated; use devel/cmake/build.mk instead. ===> Building for kallisto-0.51.1 /opt/pkg/bin/cmake -S/var/tmp/work/biology/kallisto/work/kallisto-0.51.1 -B/var/tmp/work/biology/kallisto/work/kallisto-0.51.1 --check-build-system CMakeFiles/Makefile.cmake 0 /opt/pkg/bin/cmake -E cmake_progress_start /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/CMakeFiles /var/tmp/work/biology/kallisto/work/kallisto-0.51.1//CMakeFiles/progress.marks /opt/pkg/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1' /opt/pkg/bin/gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/depend gmake[2]: Entering directory '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1' cd /var/tmp/work/biology/kallisto/work/kallisto-0.51.1 && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/work/biology/kallisto/work/kallisto-0.51.1 /var/tmp/work/biology/kallisto/work/kallisto-0.51.1 /var/tmp/work/biology/kallisto/work/kallisto-0.51.1 /var/tmp/work/biology/kallisto/work/kallisto-0.51.1 /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/CMakeFiles/bifrost.dir/DependInfo.cmake "--color=" bifrost gmake[2]: Leaving directory '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1' /opt/pkg/bin/gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build gmake[2]: Entering directory '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1' [ 3%] Creating directories for 'bifrost' /opt/pkg/bin/cmake -Dcfgdir= -P /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/tmp/bifrost-mkdirs.cmake /opt/pkg/bin/cmake -E touch /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-mkdir [ 7%] No download step for 'bifrost' /opt/pkg/bin/cmake -E echo_append /opt/pkg/bin/cmake -E touch /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-download [ 11%] No update step for 'bifrost' /opt/pkg/bin/cmake -E echo_append /opt/pkg/bin/cmake -E touch /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-update [ 15%] No patch step for 'bifrost' /opt/pkg/bin/cmake -E echo_append /opt/pkg/bin/cmake -E touch /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-patch [ 19%] Performing configure step for 'bifrost' cd /var/tmp/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 Warning (deprecated) 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 value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. This warning is for project developers. Use -Wno-author or -Wno-deprecated to suppress it. -- The C compiler identification is AppleClang 17.0.0.17000013 -- The CXX compiler identification is AppleClang 17.0.0.17000013 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /var/tmp/work/biology/kallisto/work/.cwrapper/bin/clang - 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: /var/tmp/work/biology/kallisto/work/.cwrapper/bin/clang++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE Disabling AVX2 instructions on arm64 Build type: Release Maximum k-mer size: 31 Maximum g-mer size: 31 -- Found ZLIB: /opt/pkg/lib/libz.dylib (found version "1.3.1") -- Configuring done (2.5s) -- Generating done (0.1s) -- Build files have been written to: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build cd /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost && /opt/pkg/bin/cmake -E touch /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-configure [ 23%] Performing build step for 'bifrost' cd /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost && cd build && gmake gmake[3]: Entering directory '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build' /opt/pkg/bin/cmake -S/var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost -B/var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build --check-build-system CMakeFiles/Makefile.cmake 0 /opt/pkg/bin/cmake -E cmake_progress_start /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/CMakeFiles /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[4]: Entering directory '/var/tmp/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 '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build' cd /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/src /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color=" bifrost_static gmake[5]: Leaving directory '/var/tmp/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 '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build' [ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o cd /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/src && /var/tmp/work/biology/kallisto/work/.cwrapper/bin/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src -I/opt/pkg/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -O3 -DNDEBUG -arch arm64 -mmacosx-version-min=15.5 -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 /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option] In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:34: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.hpp:157: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 85 | v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:37: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:18: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 507 | v = move(v_tmp); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:37: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1149 | ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) { | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1151 | for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1673 | rsh = move(rqh); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:40: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/MinimizerIndex.hpp:12: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] 536 | printf("bit array of size %lu: \n",_size); | ~~~ ^~~~~ | %llu /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] 540 | printf(" (%lu) ",ii); | ~~~ ^~ | %llu /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] 549 | printf("%lu : %lu, ",ii,_ranks[ii]); | ~~~ ^~ | %llu /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat] 549 | printf("%lu : %lu, ",ii,_ranks[ii]); | ~~~ ^~~~~~~~~~ | %llu In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:43: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Unitig.hpp:7: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 169 | CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {} | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 182 | CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {} | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:43: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 28 | Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {} | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 28 | Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {} | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 87 | Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {} | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 87 | Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {} | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 147 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 147 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 700 | bf = move(filter_out.second.first); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 701 | r = move(filter_out.second.second); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2771 | if (reference_mode) bf2 = move(bf1); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1690 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1690 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2423 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2423 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2534 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2534 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:10: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataManager.hpp:10: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage' 81 | for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load(); | ~ ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataStorage.tcc:345:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 345 | color_names = move(o.color_names); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataStorage.tcc:347:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 347 | overflow = move(o.overflow); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:10: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataManager.hpp:11: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataAccessor.tcc:153:19: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 153 | *uc_ptr = move(uc_); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataAccessor.tcc:197:19: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 197 | *uc_ptr = move(uc_); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataAccessor.tcc:276:52: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 276 | if (!new_cs.isEmpty()) *(p.second.first) = move(new_cs); // Move extracted colors to new (inserted) UnitigColors | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/DataAccessor.tcc:299:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 299 | *(p.second.first) = move(new_cs); // Move extracted colors to new (inserted) UnitigColors | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:369: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:505:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 505 | *uc = move(r_uc); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:826:68: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 826 | if (uc != nullptr) *(p.second.first) = move(*uc); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1758:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1758 | buffers_seq.push_back(move(s)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:318:19: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 318 | v_files = move(files_tmp); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:644:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 644 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 700 | bf = move(filter_out.second.first); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:399:26: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::build' requested here 399 | invalid = !this->build(opt_); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:599:37: note: in instantiation of member function 'ColoredCDBG<>::buildGraph' requested here 599 | success = ccdbg.buildGraph(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 701 | r = move(filter_out.second.second); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 147 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::toDataGraph' requested here 630 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:399:26: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::build' requested here 399 | invalid = !this->build(opt_); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:599:37: note: in instantiation of member function 'ColoredCDBG<>::buildGraph' requested here 599 | success = ccdbg.buildGraph(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 147 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:34: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.hpp:157: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 85 | v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.tcc:80:63: note: while substituting into a lambda expression here 80 | auto copyBlock = [&](const size_t start, const size_t end){ | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:94:16: note: in instantiation of member function 'KmerCovIndex>::toData' requested here 94 | km_unitigs.toData(std::move(o.km_unitigs), nb_threads); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::toDataGraph' requested here 630 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:399:26: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::build' requested here 399 | invalid = !this->build(opt_); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:599:37: note: in instantiation of member function 'ColoredCDBG<>::buildGraph' requested here 599 | success = ccdbg.buildGraph(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:43: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 28 | Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {} | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:106:32: note: in instantiation of member function 'Unitig>::Unitig' requested here 106 | v_unitigs[i] = new Unitig(std::move(o.v_unitigs[i]->getSeq()), std::move(o.v_unitigs[i]->getCov())); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::toDataGraph' requested here 630 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:399:26: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::build' requested here 399 | invalid = !this->build(opt_); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:599:37: note: in instantiation of member function 'ColoredCDBG<>::buildGraph' requested here 599 | success = ccdbg.buildGraph(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:43: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 28 | Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {} | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2771 | if (reference_mode) bf2 = move(bf1); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:696:76: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::filter' requested here 696 | pair> filter_out = filter(opt, nb_unique_kmers, nb_non_unique_kmers); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:399:26: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::build' requested here 399 | invalid = !this->build(opt_); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:599:37: note: in instantiation of member function 'ColoredCDBG<>::buildGraph' requested here 599 | success = ccdbg.buildGraph(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:369: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:726:11: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 726 | *ds = move(new_ds); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:411:9: note: in instantiation of member function 'ColoredCDBG<>::initUnitigColors' requested here 411 | initUnitigColors(opt); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:602:50: note: in instantiation of member function 'ColoredCDBG<>::buildColors' requested here 602 | if (success) success = ccdbg.buildColors(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 700 | bf = move(filter_out.second.first); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:609:36: note: in instantiation of member function 'CompactedDBG<>::build' requested here 609 | success = cdbg.build(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 701 | r = move(filter_out.second.second); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 147 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG<>::toDataGraph' requested here 630 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:609:36: note: in instantiation of member function 'CompactedDBG<>::build' requested here 609 | success = cdbg.build(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 147 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:34: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.hpp:157: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 85 | v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.tcc:80:63: note: while substituting into a lambda expression here 80 | auto copyBlock = [&](const size_t start, const size_t end){ | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:94:16: note: in instantiation of member function 'KmerCovIndex<>::toData' requested here 94 | km_unitigs.toData(std::move(o.km_unitigs), nb_threads); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG<>::toDataGraph' requested here 630 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:609:36: note: in instantiation of member function 'CompactedDBG<>::build' requested here 609 | success = cdbg.build(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:831: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2771 | if (reference_mode) bf2 = move(bf1); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.tcc:696:76: note: in instantiation of member function 'CompactedDBG<>::filter' requested here 696 | pair> filter_out = filter(opt, nb_unique_kmers, nb_non_unique_kmers); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:609:36: note: in instantiation of member function 'CompactedDBG<>::build' requested here 609 | success = cdbg.build(opt); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2423 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:325:34: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::readGraphFromIndexFASTA' requested here 325 | p_readSuccess_checksum = readGraphFromIndexFASTA(input_graph_fn, input_index_fn, k_, g_); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:167:16: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::read' requested here 167 | return read(input_graph_fn, input_index_fn, nb_threads, verbose); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:612:61: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::read' requested here 612 | if (!CompactedDBG, DataStorage>::read(input_graph_fn, nb_threads, verbose)) return false; // Read graph | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:80: note: in instantiation of member function 'ColoredCDBG<>::read' requested here 623 | if (lopt.filename_index_in.length() == 0) success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2423 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2534 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:378:34: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::readGraphFromIndexGFA' requested here 378 | p_readSuccess_checksum = readGraphFromIndexGFA(input_graph_fn, input_index_fn, k_, g_); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:167:16: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::read' requested here 167 | return read(input_graph_fn, input_index_fn, nb_threads, verbose); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:612:61: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::read' requested here 612 | if (!CompactedDBG, DataStorage>::read(input_graph_fn, nb_threads, verbose)) return false; // Read graph | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:80: note: in instantiation of member function 'ColoredCDBG<>::read' requested here 623 | if (lopt.filename_index_in.length() == 0) success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2534 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1690 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1631:12: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::readBinaryGraph' requested here 1631 | return readBinaryGraph(in); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:383:34: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::readBinaryGraph' requested here 383 | p_readSuccess_checksum = readBinaryGraph(input_graph_fn); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:167:16: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::read' requested here 167 | return read(input_graph_fn, input_index_fn, nb_threads, verbose); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:612:61: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::read' requested here 612 | if (!CompactedDBG, DataStorage>::read(input_graph_fn, nb_threads, verbose)) return false; // Read graph | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:80: note: in instantiation of member function 'ColoredCDBG<>::read' requested here 623 | if (lopt.filename_index_in.length() == 0) success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1690 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:369: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:505:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 505 | *uc = move(r_uc); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:481:81: note: while substituting into a lambda expression here 481 | auto join_function = [this](const vector>& unitig_tags) { | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:616:14: note: in instantiation of member function 'ColoredCDBG<>::loadColors' requested here 616 | if (!loadColors(input_graph_fn, input_colors_fn, nb_threads, verbose)) return false; | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:623:80: note: in instantiation of member function 'ColoredCDBG<>::read' requested here 623 | if (lopt.filename_index_in.length() == 0) success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:369: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:225:87: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 225 | const bool ret = CompactedDBG, DataStorage>::mergeData(move(o), nb_threads, verbose); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:644:60: note: in instantiation of member function 'ColoredCDBG<>::merge' requested here 644 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2423 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:325:34: note: in instantiation of member function 'CompactedDBG<>::readGraphFromIndexFASTA' requested here 325 | p_readSuccess_checksum = readGraphFromIndexFASTA(input_graph_fn, input_index_fn, k_, g_); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here 656 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2423 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2534 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:378:34: note: in instantiation of member function 'CompactedDBG<>::readGraphFromIndexGFA' requested here 378 | p_readSuccess_checksum = readGraphFromIndexGFA(input_graph_fn, input_index_fn, k_, g_); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here 656 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2534 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1690 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1631:12: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here 1631 | return readBinaryGraph(in); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:383:34: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here 383 | p_readSuccess_checksum = readBinaryGraph(input_graph_fn); | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here 656 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose); | ^ In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:833: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1690 | unitig = new Unitig(move(cs), move(cc)); | ^ | std:: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2: In file included from /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:369: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1758:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1758 | buffers_seq.push_back(move(s)); | ^ | std:: /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1726:20: note: while substituting into a lambda expression here 1726 | [&]{ | ^ /var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:696:50: note: in instantiation of member function 'ColoredCDBG<>::search' requested here 696 | if (success) success = ccdbg.search(opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.inexact_search, opt.nb_threads, opt.verbose); | ^ 68 warnings and 1 error generated. gmake[5]: *** [src/CMakeFiles/bifrost_static.dir/build.make:82: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1 gmake[5]: Leaving directory '/var/tmp/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 '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build' gmake[3]: *** [Makefile:139: all] Error 2 gmake[3]: Leaving directory '/var/tmp/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 '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1' gmake[1]: *** [CMakeFiles/Makefile2:115: CMakeFiles/bifrost.dir/all] Error 2 gmake[1]: Leaving directory '/var/tmp/work/biology/kallisto/work/kallisto-0.51.1' gmake: *** [Makefile:139: all] Error 2 *** Error code 2 Stop. bmake[1]: stopped making "all" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/kallisto *** Error code 1 Stop. bmake: stopped making "all" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/kallisto