Date: Tue, 26 Jun 2018 03:33:11 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-arm64-default][biology/canu] Failed for canu-1.7 in build Message-ID: <201806260333.w5Q3XBSX054450@thunderx1.nyi.freebsd.org>
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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 Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/canu/Makefile 468321 2018-04-26 04:16:15Z jwb $ Log URL: http://thunderx1.nyi.freebsd.org/data/head-arm64-default/p472730_s335353/logs/canu-1.7.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=head-arm64-default&build=p472730_s335353 Log: =>> Building biology/canu build started at Tue Jun 26 03:27:55 UTC 2018 port directory: /usr/ports/biology/canu package name: canu-1.7 building for: FreeBSD head-arm64-default-job-05 12.0-CURRENT FreeBSD 12.0-CURRENT 1200069 arm64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/canu/Makefile 468321 2018-04-26 04:16:15Z jwb $ Poudriere version: 3.2.7-1-g7087c444 Host OSVERSION: 1200060 Jail OSVERSION: 1200069 Job Id: 05 !!! Jail is newer than host. (Jail: 1200069, Host: 1200060) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200069 UNAME_v=FreeBSD 12.0-CURRENT 1200069 UNAME_r=12.0-CURRENT 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=3.2.7-1-g7087c444 MASTERMNT=/usr/local/poudriere/data/.m/head-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-arm64-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 ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/canu/work HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/canu/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- DESTDIR=/wrkdirs/usr/ports/biology/canu/work/canu-1.7/src PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/canu/work HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/canu/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc6" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing" CPP="cpp6" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/l ib/gcc6 -L/usr/local/lib/gcc6" LIBS="" CXX="g++6" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6" 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-- PORTDOCS="" PORTEXAMPLES="" JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.26.2 PERL_VER=5.26 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.26 DOCSDIR="share/doc/canu" EXAMPLESDIR="share/examples/canu" DATADIR="share/canu" WWWDIR="www/canu" ETCDIR="etc/canu" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="1.8+" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/canu DOCSDIR=/usr/local/share/doc/canu EXAMPLESDIR=/usr/local/share/examples/canu WWWDIR=/usr/local/www/canu ETCDIR=/usr/local/etc/canu --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 #### /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 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: aarch64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: aarch64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-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_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: aarch64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.0-CURRENT OSREL=12.0 OSVERSION=1200069 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 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) 1048576 stack size (kbytes, -s) 1048576 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 GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> canu-1.7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz [head-arm64-default-job-05] Installing pkg-1.10.5_1... [head-arm64-default-job-05] Extracting pkg-1.10.5_1: .......... done ===> canu-1.7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of canu-1.7 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.7 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.7 for building => SHA256 Checksum OK for marbl-canu-v1.7_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.7 for building ===> Extracting for canu-1.7 => SHA256 Checksum OK for marbl-canu-v1.7_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for canu-1.7 ===> Applying FreeBSD patches for canu-1.7 /usr/bin/sed -i.bak -e 's|-O4||g' -e 's|-funroll-loops||g' -e 's|-fexpensive-optimizations||g' -e 's|amd64|aarch64|g' /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/Makefile /usr/bin/sed -i.bak -e 's|\\$bin/mhap-|/usr/local/share/java/classes/mhap-|g' /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/pipelines/canu/OverlapMhap.pm /usr/bin/sed -i.bak -e 's|RealBin/lib|RealBin/../lib/perl5/site_perl/canu|g' /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/pipelines/canu.pl =========================================================================== =======================<phase: build-depends >============================ ===> canu-1.7 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz [head-arm64-default-job-05] Installing gmake-4.2.1_2... [head-arm64-default-job-05] `-- Installing gettext-runtime-0.19.8.1_1... [head-arm64-default-job-05] | `-- Installing indexinfo-0.3.1... [head-arm64-default-job-05] | `-- Extracting indexinfo-0.3.1: .... done [head-arm64-default-job-05] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done <snip> ^ meryl/libkmer/positionDB.H:160:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "shift2 = "F_U32"\n", _shift2); ^ meryl/libkmer/positionDB.H:161:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "M = "F_X64"\n", m); ^ meryl/libkmer/positionDB.H:162:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "H = "F_X64"\n", h); ^ meryl/libkmer/positionDB.H:163:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "C = "F_X64"\n", c); ^ meryl/libkmer/positionDB.H:164:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "R = "F_X64"\n", r); ^ meryl/libkmer/positionDB-mismatch.C:348:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "positionDB::getUpToNMismatches()-- Can't allocate space for initial positions, requested "F_U64" uint64's.\n", posnMax); ^ g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/positionDB-sort.o -c -MD -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-1.7/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon meryl/libkmer/positionDB-sort.C In file included from meryl/libkmer/positionDB-sort.C:34:0: meryl/libkmer/positionDB.H:159:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "shift1 = "F_U32"\n", _shift1); ^ meryl/libkmer/positionDB.H:160:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "shift2 = "F_U32"\n", _shift2); ^ meryl/libkmer/positionDB.H:161:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "M = "F_X64"\n", m); ^ meryl/libkmer/positionDB.H:162:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "H = "F_X64"\n", h); ^ meryl/libkmer/positionDB.H:163:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "C = "F_X64"\n", c); ^ meryl/libkmer/positionDB.H:164:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "R = "F_X64"\n", r); ^ meryl/libkmer/positionDB-sort.C:69:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: Bucket "F_U64" starts at "F_U64" ends at "F_U64"?\n", b, st, ed); ^ meryl/libkmer/positionDB-sort.C:69:42: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: Bucket "F_U64" starts at "F_U64" ends at "F_U64"?\n", b, st, ed); ^ meryl/libkmer/positionDB-sort.C:69:60: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: Bucket "F_U64" starts at "F_U64" ends at "F_U64"?\n", b, st, ed); ^ meryl/libkmer/positionDB-sort.C:110:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: unset posn bucket="F_U64" t="F_S64" le="F_U32"\n", b, t, le); ^ meryl/libkmer/positionDB-sort.C:110:55: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: unset posn bucket="F_U64" t="F_S64" le="F_U32"\n", b, t, le); ^ meryl/libkmer/positionDB-sort.C:110:65: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: unset posn bucket="F_U64" t="F_S64" le="F_U32"\n", b, t, le); ^ meryl/libkmer/positionDB-sort.C:118:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "%4"F_U32P"] chck="F_X64" posn="F_U64"\n", t, _sortedChck[t], _sortedPosn[t]); ^ meryl/libkmer/positionDB-sort.C:118:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "%4"F_U32P"] chck="F_X64" posn="F_U64"\n", t, _sortedChck[t], _sortedPosn[t]); ^ meryl/libkmer/positionDB-sort.C:118:47: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "%4"F_U32P"] chck="F_X64" posn="F_U64"\n", t, _sortedChck[t], _sortedPosn[t]); ^ meryl/libkmer/positionDB-sort.C:142:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: bucket="F_U64" t="F_U32" le="F_U32": "F_X64" > "F_X64"\n", ^ meryl/libkmer/positionDB-sort.C:142:44: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: bucket="F_U64" t="F_U32" le="F_U32": "F_X64" > "F_X64"\n", ^ meryl/libkmer/positionDB-sort.C:142:54: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: bucket="F_U64" t="F_U32" le="F_U32": "F_X64" > "F_X64"\n", ^ meryl/libkmer/positionDB-sort.C:142:65: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: bucket="F_U64" t="F_U32" le="F_U32": "F_X64" > "F_X64"\n", ^ meryl/libkmer/positionDB-sort.C:142:74: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stdout, "ERROR: bucket="F_U64" t="F_U32" le="F_U32": "F_X64" > "F_X64"\n", ^ g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/positionDB.o -c -MD -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-1.7/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon meryl/libkmer/positionDB.C In file included from meryl/libkmer/positionDB.C:38:0: meryl/libkmer/positionDB.H:159:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "shift1 = "F_U32"\n", _shift1); ^ meryl/libkmer/positionDB.H:160:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "shift2 = "F_U32"\n", _shift2); ^ meryl/libkmer/positionDB.H:161:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "M = "F_X64"\n", m); ^ meryl/libkmer/positionDB.H:162:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "H = "F_X64"\n", h); ^ meryl/libkmer/positionDB.H:163:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "C = "F_X64"\n", c); ^ meryl/libkmer/positionDB.H:164:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] fprintf(stderr, "R = "F_X64"\n", r); ^ /usr/local/bin/ar rv /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/lib/libcanu.a /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_global.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/AS_UTL_decodeRange.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/AS_UTL_fasta.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/AS_UTL_fileIO.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/AS_UTL_reverseComplement.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/AS_UTL_stackTrace.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/AS_UTL_alloc.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj /lib/libcanu.a/AS_UTL/bitEncodings.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/bitPackedFile.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/bitPackedArray.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/dnaAlphabets.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/hexDump.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/md5.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/memoryMappedFile.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/mt19937ar.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/readBuffer.o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/ FreeBSD-arm64/obj/lib/libcanu.a/AS_UTL/speed! 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/wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/stores/libsnappy/snappy.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libmeryl.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libsequence.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-applyAlignment.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-baseCall.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abColumn.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/gfa/gfa.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/gfa/bed.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/existDB-create-from-fasta.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/existDB-create-from-meryl.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/existDB-create-from-sequence.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/existDB-state.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/existDB.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/positionDB-access.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/positionDB-dump.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/positionDB-file.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/positionDB-mismatch.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/positionDB-sort.o a - /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/lib/libcanu.a/meryl/libkmer/positionDB.o g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-1.7/src -IAS_UTL stores/dumpBlob.C g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/bin/dumpBlob -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -L/wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/lib /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/lib/libcanu.a(AS_global.o): In function `AS_configure(int, char**)': AS_global.C:(.text+0x28): undefined reference to `omp_set_num_threads' collect2: error: ld returned 1 exit status gmake[1]: *** [Makefile:650: /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-arm64/bin/dumpBlob] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/canu/work/canu-1.7/src' *** Error code 1 Stop. make: stopped in /usr/ports/biology/canu
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