------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.9.txz ===== Message from python37-3.7.9: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/tbb-2020.3.txz Installing /packages/All/bash-5.0.18_3.txz Installing /packages/All/perl5-5.32.0.txz SUCCEEDED 00:00:16 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> bowtie2-2.4.1_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> bowtie2-2.4.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bowtie2-2.4.1_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> bowtie2-2.4.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bowtie2-2.4.1_2 for building => SHA256 Checksum OK for BenLangmead-bowtie2-v2.4.1_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> bowtie2-2.4.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bowtie2-2.4.1_2 for building ===> Extracting for bowtie2-2.4.1_2 => SHA256 Checksum OK for BenLangmead-bowtie2-v2.4.1_GH0.tar.gz. Extracted Memory Use: 25.18M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for bowtie2-2.4.1_2 ===> Applying ports patches for bowtie2-2.4.1_2 from /xports/biology/bowtie2/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> bowtie2-2.4.1_2 depends on package: gmake>=4.3 - found ===> bowtie2-2.4.1_2 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> bowtie2-2.4.1_2 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> bowtie2-2.4.1_2 depends on package: gmake>=4.3 - found ===> bowtie2-2.4.1_2 depends on file: /usr/local/bin/python3.7 - found ===> bowtie2-2.4.1_2 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so) ===> Configuring for bowtie2-2.4.1_2 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for bowtie2-2.4.1_2 gmake[1]: Entering directory '/construction/biology/bowtie2/bowtie2-2.4.1' c++ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -isystem /usr/local/include -I third_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -isystem /usr/local/include -I third_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -isystem /usr/local/include -I third_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -isystem /usr/local/include -I third_party \ -o bowtie2-align-l bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ \ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \ -isystem /usr/local/include -I third_party -I . \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ \ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \ -isystem /usr/local/include -I third_party -I . \ -o bowtie2-inspect-l bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_build.cpp:28: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_search.cpp:40: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_inspect.cpp:29: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_inspect.cpp:29: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_build.cpp:28: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_search.cpp:40: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from bt2_idx.h:42, from bt2_build.cpp:28: blockwise_sa.h: In instantiation of 'KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]': bt2_idx.h:1084:33: required from 'void Ebwt::initFromVector(EList&, EList&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString; TIndexOffU = unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' bt2_idx.h:657:3: required from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]' bt2_build.cpp:458:7: required from 'void driver(const string&, EList >&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]' bt2_build.cpp:646:78: required from here blockwise_sa.h:483:17: warning: 'KarkkainenBlockwiseSA >::_done' will be initialized after [-Wreorder] volatile bool *_done; /// is a block processed? ^~~~~ blockwise_sa.h:477:12: warning: 'bool KarkkainenBlockwiseSA >::thread_group_started' [-Wreorder] bool thread_group_started; ^~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:202:2: warning: when initialized here [-Wreorder] KarkkainenBlockwiseSA(const TStr& __text, ^~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In instantiation of 'KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]': bt2_idx.h:1084:33: required from 'void Ebwt::initFromVector(EList&, EList&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = S2bDnaString; TIndexOffU = unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' bt2_idx.h:657:3: required from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]' bt2_build.cpp:458:7: required from 'void driver(const string&, EList >&, const string&, bool, int) [with TStr = S2bDnaString; std::__cxx11::string = std::__cxx11::basic_string]' bt2_build.cpp:657:74: required from here blockwise_sa.h:483:17: warning: 'KarkkainenBlockwiseSA::_done' will be initialized after [-Wreorder] volatile bool *_done; /// is a block processed? ^~~~~ blockwise_sa.h:477:12: warning: 'bool KarkkainenBlockwiseSA::thread_group_started' [-Wreorder] bool thread_group_started; ^~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:202:2: warning: when initialized here [-Wreorder] KarkkainenBlockwiseSA(const TStr& __text, ^~~~~~~~~~~~~~~~~~~~~ In file included from bt2_idx.h:42, from bt2_build.cpp:28: blockwise_sa.h: In instantiation of 'KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]': bt2_idx.h:1084:33: required from 'void Ebwt::initFromVector(EList&, EList&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString; TIndexOffU = long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' bt2_idx.h:657:3: required from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]' bt2_build.cpp:458:7: required from 'void driver(const string&, EList >&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]' bt2_build.cpp:646:78: required from here blockwise_sa.h:483:17: warning: 'KarkkainenBlockwiseSA >::_done' will be initialized after [-Wreorder] volatile bool *_done; /// is a block processed? ^~~~~ blockwise_sa.h:477:12: warning: 'bool KarkkainenBlockwiseSA >::thread_group_started' [-Wreorder] bool thread_group_started; ^~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:202:2: warning: when initialized here [-Wreorder] KarkkainenBlockwiseSA(const TStr& __text, ^~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In instantiation of 'KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]': bt2_idx.h:1084:33: required from 'void Ebwt::initFromVector(EList&, EList&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = S2bDnaString; TIndexOffU = long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' bt2_idx.h:657:3: required from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]' bt2_build.cpp:458:7: required from 'void driver(const string&, EList >&, const string&, bool, int) [with TStr = S2bDnaString; std::__cxx11::string = std::__cxx11::basic_string]' bt2_build.cpp:657:74: required from here blockwise_sa.h:483:17: warning: 'KarkkainenBlockwiseSA::_done' will be initialized after [-Wreorder] volatile bool *_done; /// is a block processed? ^~~~~ blockwise_sa.h:477:12: warning: 'bool KarkkainenBlockwiseSA::thread_group_started' [-Wreorder] bool thread_group_started; ^~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:202:2: warning: when initialized here [-Wreorder] KarkkainenBlockwiseSA(const TStr& __text, ^~~~~~~~~~~~~~~~~~~~~ In file included from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:31, from blockwise_sa.h:35, from bt2_idx.h:42, from bt2_search.cpp:40: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:31: required from here ds.h:2456:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(list_, o.list_, cur_ * sizeof(std::pair)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8.0/bits/stl_algobase.h:64, from /usr/include/c++/8.0/bits/char_traits.h:39, from /usr/include/c++/8.0/ios:40, from /usr/include/c++/8.0/ostream:38, from /usr/include/c++/8.0/iostream:39, from bt2_search.cpp:21: /usr/include/c++/8.0/bits/stl_pair.h:208:12: note: 'struct std::pair' declared here struct pair ^~~~ In file included from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:31, from blockwise_sa.h:35, from bt2_idx.h:42, from bt2_search.cpp:40: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:31: required from here ds.h:2456:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(list_, o.list_, cur_ * sizeof(std::pair)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8.0/bits/stl_algobase.h:64, from /usr/include/c++/8.0/bits/char_traits.h:39, from /usr/include/c++/8.0/ios:40, from /usr/include/c++/8.0/ostream:38, from /usr/include/c++/8.0/iostream:39, from bt2_search.cpp:21: /usr/include/c++/8.0/bits/stl_pair.h:208:12: note: 'struct std::pair' declared here struct pair ^~~~ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from diff_sample.h:24, from diff_sample.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from diff_sample.h:24, from diff_sample.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed.cpp:23: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed.cpp:23: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_seed2.cpp:22: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_seed2.cpp:22: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from random_util.h:25, from aligner_seed2.h:101, from aligner_seed2.cpp:22: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:31: required from here ds.h:2456:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(list_, o.list_, cur_ * sizeof(std::pair)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8.0/utility:70, from aligner_seed2.h:98, from aligner_seed2.cpp:22: /usr/include/c++/8.0/bits/stl_pair.h:208:12: note: 'struct std::pair' declared here struct pair ^~~~ In file included from random_util.h:25, from aligner_seed2.h:101, from aligner_seed2.cpp:22: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:31: required from here ds.h:2456:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(list_, o.list_, cur_ * sizeof(std::pair)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8.0/utility:70, from aligner_seed2.h:98, from aligner_seed2.cpp:22: /usr/include/c++/8.0/bits/stl_pair.h:208:12: note: 'struct std::pair' declared here struct pair ^~~~ In file included from aligner_seed2.cpp:22: aligner_seed2.h: In member function 'size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory&, const EList&, const EList&, PerReadMetrics&)': aligner_seed2.h:1019:10: warning: 'edge.DescentEdge::nex' may be used uninitialized in this function [-Wmaybe-uninitialized] best1 = e; ~~~~~~^~~ aligner_seed2.cpp:585:14: note: 'edge.DescentEdge::nex' was declared here DescentEdge edge; ^~~~ In file included from aligner_seed2.cpp:22: aligner_seed2.h: In member function 'size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory&, const EList&, const EList&, PerReadMetrics&)': aligner_seed2.h:1019:10: warning: 'edge.DescentEdge::nex' may be used uninitialized in this function [-Wmaybe-uninitialized] best1 = e; ~~~~~~^~~ aligner_seed2.cpp:585:14: note: 'edge.DescentEdge::nex' was declared here DescentEdge edge; ^~~~ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from random_util.h:25, from aligner_seed2.h:101, from aligner_driver.h:78, from aligner_driver.cpp:20: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:31: required from here ds.h:2456:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(list_, o.list_, cur_ * sizeof(std::pair)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8.0/utility:70, from aligner_seed2.h:98, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8.0/bits/stl_pair.h:208:12: note: 'struct std::pair' declared here struct pair ^~~~ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/local/include/tbb/tbb.h:21:154: note: #pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual. #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") ^ In file included from random_util.h:25, from aligner_seed2.h:101, from aligner_driver.h:78, from aligner_driver.cpp:20: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:31: required from here ds.h:2456:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(list_, o.list_, cur_ * sizeof(std::pair)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8.0/utility:70, from aligner_seed2.h:98, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8.0/bits/stl_pair.h:208:12: note: 'struct std::pair' declared here struct pair ^~~~ gmake[1]: Leaving directory '/construction/biology/bowtie2/bowtie2-2.4.1' SUCCEEDED 00:02:37 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> bowtie2-2.4.1_2 depends on executable: bash - found ===> bowtie2-2.4.1_2 depends on file: /usr/local/bin/python3.7 - found ===> bowtie2-2.4.1_2 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for bowtie2-2.4.1_2 ===> bowtie2-2.4.1_2 depends on executable: bash - found ===> bowtie2-2.4.1_2 depends on file: /usr/local/bin/python3.7 - found ===> bowtie2-2.4.1_2 depends on package: perl5>=5.32.r0<5.33 - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/bowtie2/bowtie2-2.4.1' mkdir -p /construction/biology/bowtie2/stage/usr/local/bin for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \ cp -f $file /construction/biology/bowtie2/stage/usr/local/bin ; \ done gmake[1]: Leaving directory '/construction/biology/bowtie2/bowtie2-2.4.1' install -s -m 555 /construction/biology/bowtie2/bowtie2-2.4.1/bowtie2*-s /construction/biology/bowtie2/bowtie2-2.4.1/bowtie2*-l /construction/biology/bowtie2/stage/usr/local/bin install -m 555 /construction/biology/bowtie2/bowtie2-2.4.1/scripts/*.sh /construction/biology/bowtie2/bowtie2-2.4.1/scripts/*.pl /construction/biology/bowtie2/stage/usr/local/share/bowtie2/scripts install -m 555 /construction/biology/bowtie2/bowtie2-test /construction/biology/bowtie2/stage/usr/local/bin (cd /construction/biology/bowtie2/bowtie2-2.4.1/doc && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /construction/biology/bowtie2/stage/usr/local/share/doc/bowtie2) (cd /construction/biology/bowtie2/bowtie2-2.4.1/example && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /construction/biology/bowtie2/stage/usr/local/share/examples/bowtie2) ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for bowtie2-2.4.1_2 file sizes/checksums [67]: 0% file sizes/checksums [67]: 100% packing files [67]: 0% packing files [67]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:16 TOTAL TIME 00:03:14