[package - 124i386-default][biology/bifrost] Failed for bifrost-1.2.1 in build
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Date: Mon, 17 Jul 2023 01:09:19 UTC
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy5/data/124i386-default/8fb94260154e/logs/bifrost-1.2.1.log Build URL: https://pkg-status.freebsd.org/beefy5/build.html?mastername=124i386-default&build=8fb94260154e Log: =>> Building biology/bifrost build started at Mon Jul 17 01:09:01 UTC 2023 port directory: /usr/ports/biology/bifrost package name: bifrost-1.2.1 building for: FreeBSD 124i386-default-job-08 12.4-RELEASE-p3 FreeBSD 12.4-RELEASE-p3 i386 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1204000 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1204000 UNAME_v=FreeBSD 12.4-RELEASE-p3 UNAME_r=12.4-RELEASE-p3 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/124i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/124i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=124i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/124i386-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bifrost/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bifrost/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bifrost/work/.cache HOME=/wrkdirs/usr/ports/biology/bifrost/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bifrost/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bifrost/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bifrost/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bifrost/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bifrost/work/.cache HOME=/wrkdirs/usr/ports/biology/bifrost/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bifrost/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bifrost/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/bifrost/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTA LL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=12.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bifrost" EXAMPLESDIR="share/examples/bifrost" DATADIR="share/bifrost" WWWDIR="www/bifrost" ETCDIR="etc/bifrost" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bifrost DOCSDIR=/usr/local/share/doc/bifrost EXAMPLESDIR=/usr/local/share/examples/bifrost WWWDIR=/usr/local/www/bifrost ETCDIR=/usr/local/etc/bifrost --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd12.4 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd12.4 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd12.4 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=12.4-RELEASE-p3 OSREL=12.4 OSVERSION=1204000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License BSD2CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> bifrost-1.2.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [124i386-default-job-08] Installing pkg-1.20.4... [124i386-default-job-08] Extracting pkg-1.20.4: .......... done ===> bifrost-1.2.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bifrost-1.2.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD2CLAUSE accepted by the user => pmelsted-bifrost-v1.2.1_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/pmelsted/bifrost/tar.gz/v1.2.1?dummy=/pmelsted-bifrost-v1.2.1_GH0.tar.gz fetch: https://codeload.github.com/pmelsted/bifrost/tar.gz/v1.2.1?dummy=/pmelsted-bifrost-v1.2.1_GH0.tar.gz: size unknown fetch: https://codeload.github.com/pmelsted/bifrost/tar.gz/v1.2.1?dummy=/pmelsted-bifrost-v1.2.1_GH0.tar.gz: size of remote file is not known pmelsted-bifrost-v1.2.1_GH0.tar.gz 884 kB 6165 kBps 00s ===> Fetching all distfiles required by bifrost-1.2.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by bifrost-1.2.1 for building => SHA256 Checksum OK for pmelsted-bifrost-v1.2.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by bifrost-1.2.1 for building ===> Extracting for bifrost-1.2.1 => SHA256 Checksum OK for pmelsted-bifrost-v1.2.1_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bifrost-1.2.1 ===> Applying FreeBSD patches for bifrost-1.2.1 from /usr/ports/biology/bifrost/files =========================================================================== =======================<phase: build-depends >============================ ===> bifrost-1.2.1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.26.1_1.pkg [124i386-default-job-08] Installing cmake-core-3.26.1_1... [124i386-default-job-08] `-- Installing expat-2.5.0... [124i386-default-job-08] `-- Extracting expat-2.5.0: .......... done [124i386-default-job-08] `-- Installing jsoncpp-1.9.5... <snip> ~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:2289:33: note: in instantiation of member function 'CompactedDBG<DataAccessor<void>, DataStorage<>>::annotateSplitUnitig' requested here annotateSplitUnitig(it_unitig->referenceUnitigToString(), lck_g/*, t*/, false); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/ColoredCDBG.tcc:203:62: note: in instantiation of member function 'CompactedDBG<DataAccessor<void>, DataStorage<>>::annotateSplitUnitigs' requested here ret = CompactedDBG<DataAccessor<U>, DataStorage<U>>::annotateSplitUnitigs(o, nb_threads, verbose); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:644:60: note: in instantiation of member function 'ColoredCDBG<>::merge' requested here if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); ^ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:818: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:5653:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion] size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; ~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:4829:38: warning: shift count >= width of type [-Wshift-count-overflow] size_t pos_id_unitig = id_unitig << 32; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1921:53: note: in instantiation of member function 'CompactedDBG<>::addUnitig' requested here for (const auto& s : v_seq) addUnitig(s, (s.length() == k_) ? v_kmers_sz++ : v_unitigs_sz++, lck_unitig, lck_kmer); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:197:10: note: in instantiation of member function 'CompactedDBG<>::makeGraphFromFASTA' requested here makeGraphFromFASTA(input_graph_fn, nb_threads); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:655:79: note: in instantiation of member function 'CompactedDBG<>::read' requested here if (lopt.filename_index_in.length() == 0) success = cdbg1.read(lopt.filename_graph_in, lopt.nb_threads, lopt.verbose); ^ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:818: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:4831:40: warning: implicit conversion from 'unsigned long long' to 'const size_t' (aka 'const unsigned int') changes value from 18446744071562067968 to 2147483648 [-Wconstant-conversion] const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; ~~~~ ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:4758:92: warning: shift count >= width of type [-Wshift-count-overflow] if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1931:9: note: in instantiation of member function 'CompactedDBG<>::moveToAbundant' requested here moveToAbundant(); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:197:10: note: in instantiation of member function 'CompactedDBG<>::makeGraphFromFASTA' requested here makeGraphFromFASTA(input_graph_fn, nb_threads); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:655:79: note: in instantiation of member function 'CompactedDBG<>::read' requested here if (lopt.filename_index_in.length() == 0) success = cdbg1.read(lopt.filename_graph_in, lopt.nb_threads, lopt.verbose); ^ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:818: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:4758:148: warning: shift count >= width of type [-Wshift-count-overflow] if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:4805:78: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744069414584321 to 1 [-Wconstant-conversion] else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v); ~~~~~~~~~ ~~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:6161:42: warning: shift count >= width of type [-Wshift-count-overflow] size_t pos_id_unitig = id_unitig << 32; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:4774:25: note: in instantiation of member function 'CompactedDBG<>::deleteUnitig_' requested here deleteUnitig_(true, false, id_swap, unitig_str); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1931:9: note: in instantiation of member function 'CompactedDBG<>::moveToAbundant' requested here moveToAbundant(); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:197:10: note: in instantiation of member function 'CompactedDBG<>::makeGraphFromFASTA' requested here makeGraphFromFASTA(input_graph_fn, nb_threads); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:655:79: note: in instantiation of member function 'CompactedDBG<>::read' requested here if (lopt.filename_index_in.length() == 0) success = cdbg1.read(lopt.filename_graph_in, lopt.nb_threads, lopt.verbose); ^ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:818: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:6162:44: warning: implicit conversion from 'unsigned long long' to 'const size_t' (aka 'const unsigned int') changes value from 18446744071562067968 to 2147483648 [-Wconstant-conversion] const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; ~~~~ ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:820: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1209:34: warning: shift count >= width of type [-Wshift-count-overflow] if ((file_format_version >> 32) != BFG_GRAPHBIN_FORMAT_HEADER) return {graph_checksum, false}; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1177:12: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here return readBinaryGraph(in); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:383:31: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here p_readSuccess_checksum = readBinaryGraph(input_graph_fn); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose); ^ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:820: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:994:52: warning: shift count >= width of type [-Wshift-count-overflow] if (!read_success || ((file_format_version >> 32) != BFG_METABIN_FORMAT_HEADER)) return false; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:946:12: note: in instantiation of member function 'CompactedDBG<>::readBinaryIndex' requested here return readBinaryIndex(in, checksum); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:393:17: note: in instantiation of member function 'CompactedDBG<>::readBinaryIndex' requested here invalid = !readBinaryIndex(input_index_fn, p_readSuccess_checksum.first); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose); ^ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:820: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1016:41: warning: shift count >= width of type [-Wshift-count-overflow] const size_t id_bmp = i << 32; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1031:61: warning: shift count >= width of type [-Wshift-count-overflow] const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1064:41: warning: shift count >= width of type [-Wshift-count-overflow] const size_t id_bmp = i << 32; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1073:57: warning: shift count >= width of type [-Wshift-count-overflow] const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1100:66: warning: shift count >= width of type [-Wshift-count-overflow] vector<BitContainer> v_bmp_abundant((nb_special_minz >> 32) + 1); ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1101:69: warning: shift count >= width of type [-Wshift-count-overflow] vector<BitContainer> v_bmp_overcrowded((nb_special_minz >> 32) + 1); ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1110:58: warning: shift count >= width of type [-Wshift-count-overflow] const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/IO.tcc:1111:64: warning: shift count >= width of type [-Wshift-count-overflow] const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); ^ ~~ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:818: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:5501:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion] size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; ~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:2248:42: note: in instantiation of member function 'CompactedDBG<>::annotateSplitUnitig' requested here for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:2134:13: note: in instantiation of member function 'CompactedDBG<>::annotateSplitUnitigs' requested here if (annotateSplitUnitigs(o, nb_threads, verbose)){ ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:676:50: note: in instantiation of member function 'CompactedDBG<>::merge' requested here success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); ^ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:818: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:5502:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion] size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; ~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:5652:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion] size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; ~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:2289:33: note: in instantiation of member function 'CompactedDBG<>::annotateSplitUnitig' requested here annotateSplitUnitig(it_unitig->referenceUnitigToString(), lck_g/*, t*/, false); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:2134:13: note: in instantiation of member function 'CompactedDBG<>::annotateSplitUnitigs' requested here if (annotateSplitUnitigs(o, nb_threads, verbose)){ ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:676:50: note: in instantiation of member function 'CompactedDBG<>::merge' requested here success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); ^ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:818: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:5653:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion] size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; ~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:795:43: warning: shift count >= width of type [-Wshift-count-overflow] unitig_id = unitig_id_pos >> 32; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:4537:32: note: in instantiation of member function 'CompactedDBG<DataAccessor<void>, DataStorage<>>::find' requested here const_UnitigMap<U, G> um = find(s, pos, it_min); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Search.tcc:668:62: note: in instantiation of member function 'CompactedDBG<DataAccessor<void>, DataStorage<>>::findUnitig' requested here const const_UnitigMap<U, G> um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/ColoredCDBG.tcc:1576:76: note: in instantiation of member function 'CompactedDBG<DataAccessor<void>, DataStorage<>>::searchSequence' requested here const vector<pair<size_t, const_UnitigColorMap<U>>> v_um_e = this->searchSequence(query, true, false, false, false, false); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:696:50: note: in instantiation of member function 'ColoredCDBG<>::search' requested here if (success) success = ccdbg.search(opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.inexact_search, opt.nb_threads, opt.verbose); ^ In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:818: /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:795:43: warning: shift count >= width of type [-Wshift-count-overflow] unitig_id = unitig_id_pos >> 32; ^ ~~ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.tcc:4537:32: note: in instantiation of member function 'CompactedDBG<>::find' requested here const_UnitigMap<U, G> um = find(s, pos, it_min); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Search.tcc:937:62: note: in instantiation of member function 'CompactedDBG<>::findUnitig' requested here const const_UnitigMap<U, G> um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi); ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Search.tcc:1132:71: note: in instantiation of member function 'CompactedDBG<>::searchSequence' requested here const vector<pair<size_t, const_UnitigMap<U, G>>> v = dbg.searchSequence( s, true, inexact_search, inexact_search, ^ /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:705:49: note: in instantiation of member function 'CompactedDBG<>::search' requested here if (success) success = cdbg.search(opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.inexact_search, opt.nb_threads, opt.verbose); ^ 192 warnings and 9 errors generated. ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/bifrost