From nobody Sat Jul 22 20:11:30 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 4R7cyB4W2Mz4p3Pn for ; Sat, 22 Jul 2023 20:11:30 +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 4R7cyB2VJqz4Hph for ; Sat, 22 Jul 2023 20:11:30 +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=1690056690; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=pMY+8z+B0XEUXGdbo0tNL8bWj3+iUUvEV7dLymB5gOU=; b=r4HnWMPstDW0RhRZ5EvJrfOWeCUp/QhMWNWqmzNwgznizsMRY4zd5byJoBVgSCxXhB0AeP 37kK5MCVEbmhJa2WNbSY06n6WqmJ39D4Z0B3C6VDlXnaKSiXtRXxNoxB/2Veqp18EYA0cB lQvcEeysEjpv68Ll8Et3yjZJ2sQfmOePD3zoKjnPLkQqWPPMjolPGkp4H4XTOuoesvXMMb R3pK998dhC8hv34B/5Z8OemN1gkG9TTPtMtEjYucRyF2SC/3C1Tw+8JDs8xVwPTSZFxleV MWE1qEyF6CNuwlOEhv3UQpCZDmbdS0g5Egw19NVZb4ub+FpIdX3kw5PXxGmiBQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1690056690; a=rsa-sha256; cv=none; b=H7yVLy087jCPZSCh5sig6craJerkkZ4zhMOyu4rIsoIl36XG1i/UGefTSflYlvdaMx31wh Kqw1qk2lznA6is7RffXdHMq4mrFHaBDgb+NemSVliLiUOxICOE2jlnfWVlvBLPB+NwTTL6 38XOedYnSxbXb+4QcP+iLl1rSQuhVlXeRwo3SMJNwg7phVfv1kbR6wAaLeRT7Zla4FX9sK HlFtrz+GUQqW0lWnPIjMdVIHMVIz+7nxCyVIV/qXjrsw6vu7p89c2+De80QS3Rm3VhdzEX g01GO5CATXY2rqtHbid+PdF21hMlaKIxLTGdXk4EyZmvVQlfWwfcvdZ3G3bNLw== Received: from beefy15.nyi.freebsd.org (beefy15.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:1e]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4R7cyB1WZfz17Q9 for ; Sat, 22 Jul 2023 20:11:30 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 1502 by beefy15.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy15.nyi.freebsd.org); Sat, 22 Jul 2023 20:11:30 +0000 To: jwb@FreeBSD.org Subject: [package - 131i386-default][biology/salmon] Failed for salmon-1.10.2 in build Cc: pkg-fallout@FreeBSD.org Date: Sat, 22 Jul 2023 20:11:30 +0000 Message-Id: <64bc37f2.1502.3b08ffdf@beefy15.nyi.freebsd.org> From: 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/beefy15/data/131i386-default/150bed43bfd4/logs/salmon-1.10.2.log Build URL: https://pkg-status.freebsd.org/beefy15/build.html?mastername=131i386-default&build=150bed43bfd4 Log: =>> Building biology/salmon build started at Sat Jul 22 20:10:16 UTC 2023 port directory: /usr/ports/biology/salmon package name: salmon-1.10.2 building for: FreeBSD 131i386-default-job-03 13.1-RELEASE-p8 FreeBSD 13.1-RELEASE-p8 i386 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1301000 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1301000 UNAME_v=FreeBSD 13.1-RELEASE-p8 UNAME_r=13.1-RELEASE-p8 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 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/131i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/131i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=131i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/131i386-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-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/salmon/work/.cache HOME=/wrkdirs/usr/ports/biology/salmon/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/salmon/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/salmon/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/salmon/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/salmon/work/.cache HOME=/wrkdirs/usr/ports/biology/salmon/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/salmon/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/salmon/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig DONTSTRIP=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lpthread -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/ usr/local" BSD_INSTALL_PROGRAM="install -m 555" BSD_INSTALL_LIB="install -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="debug" OSREL=13.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/salmon" EXAMPLESDIR="share/examples/salmon" DATADIR="share/salmon" WWWDIR="www/salmon" ETCDIR="etc/salmon" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/salmon DOCSDIR=/usr/local/share/doc/salmon EXAMPLESDIR=/usr/local/share/examples/salmon WWWDIR=/usr/local/www/salmon ETCDIR=/usr/local/etc/salmon --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-freebsd13.1 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-freebsd13.1 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-freebsd13.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=13.1-RELEASE-p8 OSREL=13.1 OSVERSION=1301000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---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 GPLv3 accepted by the user =========================================================================== =================================================== ===> salmon-1.10.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [131i386-default-job-03] Installing pkg-1.20.4... [131i386-default-job-03] Extracting pkg-1.20.4: .......... done ===> salmon-1.10.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of salmon-1.10.2 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user => COMBINE-lab-salmon-v1.10.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/COMBINE-lab-salmon-v1.10.2_GH0.tar.gz fetch: https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/COMBINE-lab-salmon-v1.10.2_GH0.tar.gz: size unknown fetch: https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/COMBINE-lab-salmon-v1.10.2_GH0.tar.gz: size of remote file is not known COMBINE-lab-salmon-v1.10.2_GH0.tar.gz 7024 kB 10 MBps 01s => COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/COMBINE-lab/pufferfish/tar.gz/salmon-v1.10.2?dummy=/COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz fetch: https://codeload.github.com/COMBINE-lab/pufferfish/tar.gz/salmon-v1.10.2?dummy=/COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz: size unknown fetch: https://codeload.github.com/COMBINE-lab/pufferfish/tar.gz/salmon-v1.10.2?dummy=/COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz: size of remote file is not known COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz 3289 kB 5612 kBps 00s => jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-15?dummy=/jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz fetch: https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-15?dummy=/jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz: size unknown fetch: https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-15?dummy=/jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz: size of remote file is not known jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz 3302 kB 4708 kBps 01s => samtools-htscodecs-5aecc6e_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/samtools/htscodecs/tar.gz/5aecc6e?dummy=/samtools-htscodecs-5aecc6e_GH0.tar.gz fetch: https://codeload.github.com/samtools/htscodecs/tar.gz/5aecc6e?dummy=/samtools-htscodecs-5aecc6e_GH0.tar.gz: size unknown fetch: https://codeload.github.com/samtools/htscodecs/tar.gz/5aecc6e?dummy=/samtools-htscodecs-5aecc6e_GH0.tar.gz: size of remote file is not known samtools-htscodecs-5aecc6e_GH0.tar.gz 3116 kB 15 MBps 01s ===> Fetching all distfiles required by salmon-1.10.2 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by salmon-1.10.2 for building => SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz. => SHA256 Checksum OK for samtools-htscodecs-5aecc6e_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:1156:37: error: non-constant-expression cannot be narrowed from type 'uint64_t' (aka 'unsigned long long') to 'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing] return PackedContigInfo{i, (*data_)[i], len}; ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:1156:37: note: insert an explicit cast to silence this issue return PackedContigInfo{i, (*data_)[i], len}; ^ static_cast( ) /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:1156:40: error: non-constant-expression cannot be narrowed from type 'std::__vector_base>::value_type' (aka 'unsigned long long') to 'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing] return PackedContigInfo{i, (*data_)[i], len}; ^~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:1156:40: note: insert an explicit cast to silence this issue return PackedContigInfo{i, (*data_)[i], len}; ^~~~~~~~~~~ static_cast( ) In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:691:38: warning: format specifies type 'unsigned long' but the argument has type 'std::vector::size_type' (aka 'unsigned int') [-Wformat] printf("rank array : size %lu \n",_ranks.size()); ~~~ ^~~~~~~~~~~~~ %u /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:822:35: error: expected ')' return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:822:21: note: to match this '(' return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:822:23: error: use of undeclared identifier '__uint128_t' return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:819:46: warning: unused parameter 'word' [-Wunused-parameter] static inline uint64_t fastrange64(uint64_t word, uint64_t p) { ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:819:61: warning: unused parameter 'p' [-Wunused-parameter] static inline uint64_t fastrange64(uint64_t word, uint64_t p) { ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:27: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] mer_base_static(unsigned int k, const char* s) : super(k_) { ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] lhs_setter& operator=(const lhs_setter& rhs) { ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:250:14: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here auto c = seqVec[i]; ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:917:12: warning: variable 'totalKmersIshouldSee' set but not used [-Wunused-but-set-variable] size_t totalKmersIshouldSee{0} ; ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' first required here for (destructive_iterator it = ht.destructive_begin(); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_move_from' requested here _move_from(mover, ht, min_buckets_wanted); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::sparse_hashtable' requested here sparse_hashtable tmp(MoveDontCopy, *this, resize_to); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_resize_delta' requested here if (_resize_delta(1)) ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>>, unsigned long long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::find_or_insert>>::DefaultValue, unsigned long long &>' requested here return rep.template find_or_insert(std::forward(key)).second; ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>>::operator[]' requested here path[ref_cnt].resize(contigCntPerPath); ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] lhs_setter& operator=(const lhs_setter& rhs) { ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:195:63: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long long, 8, unsigned long long, std::allocator, 64, false>::operator[]' requested here for (uint64_t i = 0; i < contigCntr; i++) edgeVec_[i] = 0; ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] lhs_setter& operator=(const lhs_setter& rhs) { ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:310:24: note: in instantiation of member function 'compact::vector_imp::vector, 64, false>, unsigned long long, 0, unsigned long long, std::allocator, 64, false>::operator[]' requested here (*cpos_offsets)[0] = 0; ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here for (destructive_iterator it = ht.destructive_begin(); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here _move_from(mover, ht, min_buckets_wanted); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested here sparse_hashtable tmp(MoveDontCopy, *this, resize_to); ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_resize_delta' requested here if (_resize_delta(1)) ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::find_or_insert, unsigned int, VecHasher>::DefaultValue, std::vector &>' requested here return rep.template find_or_insert(std::forward(key)).second; ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:37: note: in instantiation of function template specialization 'spp::sparse_hash_map, unsigned int, VecHasher>::operator[] &>' requested here eqID = eqMap[tlist]; ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] lhs_setter& operator=(const lhs_setter& rhs) { ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:120:20: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long long, 1, unsigned long long, std::allocator, 64, false>::operator[]' requested here return ((*rank_)[endPos] == 1); ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:1032:8: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ^~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:660:46: note: in instantiation of member function 'boomphf::mphf>::totalBitSize' requested here jointLog->info("mphf size = {} MB", (bphf->totalBitSize() / 8) / std::pow(2, 20)); ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:1034:8: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat] _final_hash.size()*42*8, 100*(float)(_final_hash.size()*42*8)/totalsize, ^~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:1035:8: warning: format specifies type 'unsigned long' but the argument has type 'std::unordered_map>::size_type' (aka 'unsigned int') [-Wformat] _final_hash.size() ); ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] lhs_setter& operator=(const lhs_setter& rhs) { ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:737:17: note: in instantiation of member function 'compact::vector_imp::vector, 64, true>, unsigned long long, 0, unsigned long long, std::allocator, 64, true>::operator[]' requested here posVec[idx] = kb1.pos(); ^ 23 warnings and 4 errors generated. gmake[3]: *** [external/pufferfish/src/CMakeFiles/puffer.dir/build.make:79: external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake[2]: *** [CMakeFiles/Makefile2:458: external/pufferfish/src/CMakeFiles/puffer.dir/all] Error 2 gmake[2]: *** Waiting for unfinished jobs.... [ 28%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp gmake[3]: *** [external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make:93: external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o] Abort trap (core dumped) gmake[3]: *** Waiting for unfinished jobs.... gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake[2]: *** [CMakeFiles/Makefile2:326: external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/all] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake[1]: *** [Makefile:169: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/salmon