From nobody Sat Jul 15 08:13:32 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4R31M02v9gz4n5tc for ; Sat, 15 Jul 2023 08:13:32 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4R31M01824z446m for ; Sat, 15 Jul 2023 08:13:32 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689408812; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=lCwP5cic7aNL/nOHggeuZXrBKzrYbJrVZCCctTmJkzQ=; b=DQLpf9X4gOkuxP/b2xl7U3FyNDOpdzQ49uXKGtVL2bwdmKpd2HgKmyB1dRswwZr00dOkW1 ldEJM8/f1jpkh6VBx5pD8v2GadYJDNN+96+VTkk0I/C8z62JFBNV/ijBX6OV0kzCHlJuHH IHGNemt360DtoVKYEdZvE3mUd6BJ7yUJ5c8CCnUFDpo/zzCvcBXjj8GOV3+AVDVWk4+16z eijDY2pD04ugVcehhPuxLV1qVym3Wy7esL24Cn6NKl7jaCC0nAJwxAImTJUWhsrcbdIhSn KweUrcmwULuHITiqq/L8hNgRBIMVwetn4q0SRInz0TkQwapkvbascbT3iPnsow== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1689408812; a=rsa-sha256; cv=none; b=TslRsC8m+uEmAcmiuswqAG7FIbVDuGsfTyYhUBr61vCTvK3cfA8nsBcUXldBlTL94aGPYb 78lbF/SRvd/JjHdeha5/eGEcHXx4AbiDgYIVXEmH3MYuI9drIiGQsvSdWydnXJgAxyeBY/ 8LAkllVeubRqVRT22FIqKO6ErPj7A45vkvcFNxDnTZ3XbyQYVnRxneOL6HY5CEorOp3jcL 12weGwW/YpSTIrKGZkMiCmAXyLYID5zPfp74ENv1t4MN4JZwAEbW2x8oSk8rZT20gObqLn gCc0nQDiiCyf6GuiDPFZqNzdxZbm1xn1hBJn6qvWT9NLKk8aSlZoBs+F16ZwRQ== Received: from beefy5.nyi.freebsd.org (beefy5.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:14]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4R31M00D6gzsRT for ; Sat, 15 Jul 2023 08:13:32 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 36 by beefy5.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy5.nyi.freebsd.org); Sat, 15 Jul 2023 08:13:32 +0000 To: jwb@FreeBSD.org Subject: [package - 124i386-default][biology/kallisto] Failed for kallisto-0.50.0,1 in build Cc: pkg-fallout@FreeBSD.org Date: Sat, 15 Jul 2023 08:13:32 +0000 Message-Id: <64b2552c.36.7a3cdb83@beefy5.nyi.freebsd.org> From: X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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/kallisto-0.50.0,1.log Build URL: https://pkg-status.freebsd.org/beefy5/build.html?mastername=124i386-default&build=8fb94260154e Log: =>> Building biology/kallisto build started at Sat Jul 15 08:12:57 UTC 2023 port directory: /usr/ports/biology/kallisto package name: kallisto-0.50.0,1 building for: FreeBSD 124i386-default-job-13 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: 13 ---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--- ===> The following configuration options are available for kallisto-0.50.0,1: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/kallisto/work/.cache HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/kallisto/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/kallisto/work/.cache HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/kallisto/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lhts -lz -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX=" /usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_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-- PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=12.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/kallisto" EXAMPLESDIR="share/examples/kallisto" DATADIR="share/kallisto" WWWDIR="www/kallisto" ETCDIR="etc/kallisto" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/kallisto DOCSDIR=/usr/local/share/doc/kallisto EXAMPLESDIR=/usr/local/share/examples/kallisto WWWDIR=/usr/local/www/kallisto ETCDIR=/usr/local/etc/kallisto --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-- =================================================== ===> License BSD2CLAUSE accepted by the user =========================================================================== =================================================== ===> kallisto-0.50.0,1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [124i386-default-job-13] Installing pkg-1.20.4... [124i386-default-job-13] Extracting pkg-1.20.4: .......... done ===> kallisto-0.50.0,1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of kallisto-0.50.0,1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user => pachterlab-kallisto-v0.50.0_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.50.0?dummy=/pachterlab-kallisto-v0.50.0_GH0.tar.gz fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.50.0?dummy=/pachterlab-kallisto-v0.50.0_GH0.tar.gz: size unknown fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.50.0?dummy=/pachterlab-kallisto-v0.50.0_GH0.tar.gz: size of remote file is not known pachterlab-kallisto-v0.50.0_GH0.tar.gz 5799 kB 5652 kBps 01s ===> Fetching all distfiles required by kallisto-0.50.0,1 for building =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.50.0,1 for building => SHA256 Checksum OK for pachterlab-kallisto-v0.50.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.50.0,1 for building ===> Extracting for kallisto-0.50.0,1 => SHA256 Checksum OK for pachterlab-kallisto-v0.50.0_GH0.tar.gz. /bin/rm -f -rf /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/htslib =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for kallisto-0.50.0,1 ===> Applying FreeBSD patches for kallisto-0.50.0,1 from /usr/ports/biology/kallisto/files =========================================================================== =================================================== ===> kallisto-0.50.0,1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.26.1_1.pkg In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:2375:53: 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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:197:13: note: in instantiation of member function 'CompactedDBG<>::makeGraphFromFASTA' requested here makeGraphFromFASTA(input_graph_fn, nb_threads); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4758:92: warning: shift count >= width of type [-Wshift-count-overflow] if (static_cast(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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:2385:9: note: in instantiation of member function 'CompactedDBG<>::moveToAbundant' requested here moveToAbundant(); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:197:13: note: in instantiation of member function 'CompactedDBG<>::makeGraphFromFASTA' requested here makeGraphFromFASTA(input_graph_fn, nb_threads); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4758:148: warning: shift count >= width of type [-Wshift-count-overflow] if (static_cast(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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:2385:9: note: in instantiation of member function 'CompactedDBG<>::moveToAbundant' requested here moveToAbundant(); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:197:13: note: in instantiation of member function 'CompactedDBG<>::makeGraphFromFASTA' requested here makeGraphFromFASTA(input_graph_fn, nb_threads); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:831: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1663:34: 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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1631:12: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here return readBinaryGraph(in); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:383:34: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here p_readSuccess_checksum = readBinaryGraph(input_graph_fn); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:831: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1229:52: 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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1020:12: note: in instantiation of member function 'CompactedDBG<>::readBinaryIndex' requested here return readBinaryIndex(in, checksum, minz, threads); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:393:20: note: in instantiation of member function 'CompactedDBG<>::readBinaryIndex' requested here invalid = !readBinaryIndex(input_index_fn, p_readSuccess_checksum.first); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:831: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1259:41: warning: shift count >= width of type [-Wshift-count-overflow] const size_t id_bmp = i << 32; ^ ~~ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1274:61: warning: shift count >= width of type [-Wshift-count-overflow] const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; ^ ~~ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1307:41: warning: shift count >= width of type [-Wshift-count-overflow] const size_t id_bmp = i << 32; ^ ~~ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1316:57: 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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1343:66: warning: shift count >= width of type [-Wshift-count-overflow] vector v_bmp_abundant((nb_special_minz >> 32) + 1); ^ ~~ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1344:69: warning: shift count >= width of type [-Wshift-count-overflow] vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); ^ ~~ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1353:58: warning: shift count >= width of type [-Wshift-count-overflow] const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); ^ ~~ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1354:64: 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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:795:43: warning: shift count >= width of type [-Wshift-count-overflow] unitig_id = unitig_id_pos >> 32; ^ ~~ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4537:32: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::find' requested here const_UnitigMap um = find(s, pos, it_min); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Search.tcc:668:62: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::findUnitig' requested here const const_UnitigMap um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/ColoredCDBG.tcc:1570:76: note: in instantiation of member function 'CompactedDBG, DataStorage<>>::searchSequence' requested here const vector>> v_um_e = this->searchSequence(query, true, false, false, false, false); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1: In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:795:43: warning: shift count >= width of type [-Wshift-count-overflow] unitig_id = unitig_id_pos >> 32; ^ ~~ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4537:32: note: in instantiation of member function 'CompactedDBG<>::find' requested here const_UnitigMap um = find(s, pos, it_min); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Search.tcc:937:62: note: in instantiation of member function 'CompactedDBG<>::findUnitig' requested here const const_UnitigMap um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi); ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Search.tcc:1132:71: note: in instantiation of member function 'CompactedDBG<>::searchSequence' requested here const vector>> v = dbg.searchSequence( s, true, inexact_search, inexact_search, ^ /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/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); ^ 214 warnings and 9 errors generated. gmake[6]: *** [src/CMakeFiles/bifrost_static.dir/build.make:76: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1 gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build' gmake[5]: *** [CMakeFiles/Makefile2:102: src/CMakeFiles/bifrost_static.dir/all] Error 2 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build' gmake[4]: *** [Makefile:136: all] Error 2 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build' gmake[3]: *** [CMakeFiles/bifrost.dir/build.make:89: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-build] Error 2 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake[2]: *** [CMakeFiles/Makefile2:105: CMakeFiles/bifrost.dir/all] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' gmake[1]: *** [Makefile:139: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build' *** Error code 1 Stop. make: stopped in /usr/ports/biology/kallisto