=>> Building biology/canu build started at Wed Apr 3 13:42:26 BST 2024 port directory: /usr/ports/biology/canu package name: canu-2.2_3 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2179 Jul 26 2023 /usr/ports/biology/canu/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: d92c0802ea Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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 MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= 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 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/canu/work/.cache HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/canu/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/canu/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" CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- DESTDIR=/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src CANU_BUILD_ENV=ports PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/canu/work/.cache HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/canu/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/canu/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=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 " CCACHE_DIR="/root/.ccache" 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-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 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="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 FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" 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) 33554432 stack size (kbytes, -s) 524288 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) 8192 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-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> canu-2.2_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of canu-2.2_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by canu-2.2_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by canu-2.2_3 for building => SHA256 Checksum OK for canu-2.2.tar.xz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by canu-2.2_3 for building ===> Extracting for canu-2.2_3 => SHA256 Checksum OK for canu-2.2.tar.xz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for canu-2.2_3 ===> Applying FreeBSD patches for canu-2.2_3 from /usr/ports/biology/canu/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_3 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> canu-2.2_3 depends on package: gmake>=4.4.1 - found ===> Returning to build of canu-2.2_3 ===> canu-2.2_3 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_1.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_1: .......... done ===> canu-2.2_3 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of canu-2.2_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_3 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.84.0.pkg [pkg-builder.dan.net.uk] Installing boost-libs-1.84.0... [pkg-builder.dan.net.uk] `-- Installing icu-74.2,1... [pkg-builder.dan.net.uk] `-- Extracting icu-74.2,1: .......... done [pkg-builder.dan.net.uk] Extracting boost-libs-1.84.0: .......... done ===== Message from boost-libs-1.84.0: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> canu-2.2_3 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of canu-2.2_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for canu-2.2_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for canu-2.2_3 /bin/sh: git: not found Building release v2.2 For 'FreeBSD' '13.2-RELEASE-p10' as '' into '/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/{bin,obj}'. Using '/ccache/libexec/ccache/c++' version '14.0.5'. Using user-supplied CXXFLAGS '-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 '. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/runtime.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/runtime.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/align-parasail-driver.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/align-parasail-driver.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/edlib.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/edlib.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-buffered.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-buffered.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-compressed.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-compressed.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-fasta-fastq.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-fasta-fastq.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-memoryMapped.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-memoryMapped.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/logging.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/logging.C utility/src/utility/logging.C:170:7: warning: 'snprintf' size argument is too large; destination buffer has size 256, but size argument is 1024 [-Wfortify-source] snprintf(rotmes, 1024, "logFile()-- next message will exceed file size limit of " F_U64 "; rotate to new file.\n", ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/strings.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/strings.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/system.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system-stackTrace.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/system-stackTrace.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/sequence.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sequence.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/types.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/types.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-exact.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-exact.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-files.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-files.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-histogram.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-histogram.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-reader.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-reader.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-block.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer-block.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-stream.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer-stream.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer.C utility/src/utility/kmers-writer.C:55:2: warning: how to set prefix size for streaming operations? [-W#warnings] #warning how to set prefix size for streaming operations? ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/bits.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/bits-wordArray.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits-wordArray.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/hexDump.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/hexDump.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/md5.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/md5.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/mt19937ar.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/speedCounter.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sweatShop.C cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/cpuid.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cpuid.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/memory.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/memory.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_trace.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_trace.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qx_dispatch.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qx_dispatch.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qb_de_dispatch.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qb_de_dispatch.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qe_db_dispatch.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qe_db_dispatch.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/cigar.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cigar.c In file included from utility/src/parasail/cigar.c:161: utility/src/parasail/cigar_template.c:171:29: warning: comparison of array 'alphabet_aliases' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (NULL != alphabet_aliases) { ~~~~ ^~~~~~~~~~~~~~~~ In file included from utility/src/parasail/cigar.c:166: utility/src/parasail/cigar_template.c:171:29: warning: comparison of array 'alphabet_aliases' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (NULL != alphabet_aliases) { ~~~~ ^~~~~~~~~~~~~~~~ In file included from utility/src/parasail/cigar.c:171: utility/src/parasail/cigar_template.c:171:29: warning: comparison of array 'alphabet_aliases' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (NULL != alphabet_aliases) { ~~~~ ^~~~~~~~~~~~~~~~ In file included from utility/src/parasail/cigar.c:176: utility/src/parasail/cigar_template.c:171:29: warning: comparison of array 'alphabet_aliases' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (NULL != alphabet_aliases) { ~~~~ ^~~~~~~~~~~~~~~~ In file included from utility/src/parasail/cigar.c:181: utility/src/parasail/cigar_template.c:171:29: warning: comparison of array 'alphabet_aliases' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (NULL != alphabet_aliases) { ~~~~ ^~~~~~~~~~~~~~~~ In file included from utility/src/parasail/cigar.c:186: utility/src/parasail/cigar_template.c:171:29: warning: comparison of array 'alphabet_aliases' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (NULL != alphabet_aliases) { ~~~~ ^~~~~~~~~~~~~~~~ In file included from utility/src/parasail/cigar.c:191: utility/src/parasail/cigar_template.c:171:29: warning: comparison of array 'alphabet_aliases' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (NULL != alphabet_aliases) { ~~~~ ^~~~~~~~~~~~~~~~ In file included from utility/src/parasail/cigar.c:196: utility/src/parasail/cigar_template.c:171:29: warning: comparison of array 'alphabet_aliases' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (NULL != alphabet_aliases) { ~~~~ ^~~~~~~~~~~~~~~~ 8 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqCache.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C stores/ovOverlap.C:59:15: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.ahg5, dat.ovl.ahg3, ^~~~~~~~~~~~ stores/ovOverlap.C:59:29: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.ahg5, dat.ovl.ahg3, ^~~~~~~~~~~~ stores/ovOverlap.C:60:15: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.bhg5, dat.ovl.bhg3, ^~~~~~~~~~~~ stores/ovOverlap.C:60:29: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.bhg5, dat.ovl.bhg3, ^~~~~~~~~~~~ stores/ovOverlap.C:201:2: warning: NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-W#warnings] #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING ^ 5 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C stores/ovStoreWriter.C:33:2: warning: not failing if a valid store [-W#warnings] #warning not failing if a valid store ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C stores/ovStoreHistogram.C:338:35: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, ^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreHistogram.C:338:58: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, ^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreHistogram.C:339:35: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, ^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreHistogram.C:339:58: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, ^~~~~~~~~~~~~~~~~~~~~ 4 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgStore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/objectStore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/objectStore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C utgcns/libNDalign/NDalgorithm-forward.C:219:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:219:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:219:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:220:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:220:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:220:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:244:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:244:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:244:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:245:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:245:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:245:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) 4 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C utgcns/libNDalign/NDalgorithm-reverse.C:220:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:220:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:220:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:221:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:221:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:221:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:244:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:244:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:244:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:245:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:245:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:245:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) 4 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:31: In file included from utgcns/libboost/boost/scoped_ptr.hpp:14: utgcns/libboost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^ utgcns/libboost/boost/graph/adjacency_list.hpp:386:19: note: in instantiation of template class 'boost::scoped_ptr' requested here property_ptr m_property; ^ utgcns/libpbutgcns/AlnGraphBoost.H:84:5: note: in instantiation of template class 'boost::adjacency_list' requested here graphTraits::edge_descriptor bestInEdge; ///< Best scoring in edge ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:1018:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/gfa/gfa.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/gfa/bed.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C ar -rv /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/libcanu.a /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/runtime.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/align-parasail-driver.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/edlib.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-buffered.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-compressed.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-fasta-fastq.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-memoryMapped.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/logging.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/strings.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system-stackTrace.o 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/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/gfa/gfa.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/gfa/bed.o ar: warning: creating /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/libcanu.a a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/runtime.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/align-parasail-driver.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/edlib.o a - 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/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system-stackTrace.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/sequence.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/types.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-exact.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-files.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-histogram.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-reader.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-block.o a - 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/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/cigar.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/computeGlobalScore.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/falconConsensus.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqCache.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqLibrary.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqReadData.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqReadDataWriter.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStore.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreBlob.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreConstructor.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreInfo.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovOverlap.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStore.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreWriter.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreFilter.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreFile.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreHistogram.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgStore.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTig.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/objectStore.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/gfa/gfa.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/gfa/bed.o c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/dumpBlob.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/dumpBlob -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreBuild.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreBuild -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreConfig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreConfig -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreBucketizer.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreBucketizer -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreSorter.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreSorter -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreIndexer.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreIndexer -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreDump.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreDump -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreStats.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreStats -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/sqStoreCreate.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/sqStoreCreate -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/sqStoreDumpFASTQ -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iseqrequester/src/seqrequester stores/sqStoreDumpMetaData.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpMetaData/seqrequester/src/seqrequester/summarize.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iseqrequester/src/seqrequester seqrequester/src/seqrequester/summarize.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/sqStoreDumpMetaData -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpMetaData/seqrequester/src/seqrequester/summarize.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgStoreCompress.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/tgStoreCompress -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgStoreDump.C stores/tgStoreDump.C:643:2: warning: replace this with genericStatistics [-W#warnings] #warning replace this with genericStatistics ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgTigSizeAnalysis.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/tgStoreDump -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreDump/stores/tgStoreDump.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgStoreLoad.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/tgStoreLoad -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgTigDisplay.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/tgTigDisplay -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/loadCorrectedReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/loadCorrectedReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/loadTrimmedReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/loadTrimmedReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadErates/stores/loadErates.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/loadErates.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/loadErates -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadErates/stores/loadErates.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/meryl.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/meryl.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylCommandBuilder.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCommandBuilder.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylCountArray.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCountArray.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylInput.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylInput.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-count.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-count.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countSimple.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countSimple.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countThreads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countThreads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-histogram.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-histogram.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-nextMer.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-nextMer.C meryl/src/meryl/merylOp-nextMer.C:234:8: warning: comparison of array 'name' equal to a null pointer is always false [-Wtautological-pointer-compare] if ((name == NULL) || // If there is no name, we've ^~~~ ~~~~ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/meryl -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/meryl.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylCommandBuilder.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylCountArray.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylInput.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-count.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countSimple.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countThreads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-histogram.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-nextMer.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapCheck/overlapCheck/overlapCheck.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapCheck/overlapCheck.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapCheck -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapCheck/overlapCheck/overlapCheck.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapInCore -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapInCorePartition -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapConvert -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapImport -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C overlapInCore/overlapPair.C:463:2: warning: do we need to check for contained too? [-W#warnings] #warning do we need to check for contained too? ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapPair -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/edalign/overlapInCore/edalign.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/edalign -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/edalign/overlapInCore/edalign.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/prefixEditDistance-matchLimitGenerate -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Imhap/liboverlap mhap/mhapConvert.C mhap/mhapConvert.C:151:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, ^~~~~~~~~~~~~~~ mhap/mhapConvert.C:151:34: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, ^~~~~~~~~~~~~~~ mhap/mhapConvert.C:152:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, ^~~~~~~~~~~~~~~ mhap/mhapConvert.C:152:34: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, ^~~~~~~~~~~~~~~ 4 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/mhapConvert -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iminimap/liboverlap minimap/mmapConvert.C minimap/mmapConvert.C:130:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, ^~~~~~~~~~~~~~~ minimap/mmapConvert.C:130:34: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, ^~~~~~~~~~~~~~~ minimap/mmapConvert.C:131:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, ^~~~~~~~~~~~~~~ minimap/mmapConvert.C:131:34: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, ^~~~~~~~~~~~~~~ 4 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/mmapConvert -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores correction/filterCorrectionOverlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/filterCorrectionOverlaps -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns correction/generateCorrectionLayouts.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/generateCorrectionLayouts -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores correction/filterCorrectionLayouts.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/filterCorrectionLayouts -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/falconsense/correction/falconsense.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns correction/falconsense.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/falconsense/utgcns/stashContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/falconsense -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/falconsense/correction/falconsense.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/falconsense/utgcns/stashContains.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/errorEstimate -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns haplotyping/splitHaplotype.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/splitHaplotype -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-bestEdge.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-largestCovered.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/trimReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-workUnit.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-subReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-trimBad.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustNormal.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustFlipped.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/splitReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/mergeRanges.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/mergeRanges -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapAlign -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/trimRead.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/computeDiff.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/computeDiff.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/findErrors -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/computeDiff.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/fixErrors/overlapErrorAdjustment/fixErrors.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapErrorAdjustment/fixErrors.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/fixErrors/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapErrorAdjustment/correctOverlaps-Correct_Frags.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/fixErrors -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/fixErrors/overlapErrorAdjustment/fixErrors.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/fixErrors/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/findErrors-Dump -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/computeDiff.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/computeDiff.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/correctOverlaps -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/computeDiff.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/bogart.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/bogart.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_AssemblyGraph.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_BestOverlapGraph.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_ChunkGraph.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_DetectSpurs.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Instrumentation.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_FindCircular.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_FindCircular.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Logging.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_MarkRepeatReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_MergeOrphans.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_OptimizePositions.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Outputs.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_OverlapCache.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PopulateUnitig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PromoteToSingleton.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_ReadInfo.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_SetParentAndHang.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitDiscontinuous.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SplitTig_AtReadEnds.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitTig_AtReadEnds.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_TigVector.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_AddRead.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/bogart -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/bogart.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_FindCircular.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Logging.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Outputs.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SplitTig_AtReadEnds.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_TigVector.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/layoutReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/layoutReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Instrumentation.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Instrumentation.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Logging.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Logging.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_OptimizePositions.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_OptimizePositions.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Outputs.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Outputs.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_OverlapCache.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_OverlapCache.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_ReadInfo.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_ReadInfo.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_SetParentAndHang.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_SetParentAndHang.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_TigVector.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_TigVector.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_AddRead.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_AddRead.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/layoutReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/layoutReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Instrumentation.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Logging.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_OptimizePositions.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Outputs.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_OverlapCache.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceContains.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceReadUsingOverlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_ReadInfo.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_SetParentAndHang.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_TigVector.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_AddRead.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/utgcns.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/stashContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C In file included from utgcns/unitigConsensus.C:23: In file included from utgcns/libpbutgcns/AlnGraphBoost.H:57: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:31: In file included from utgcns/libboost/boost/scoped_ptr.hpp:14: utgcns/libboost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^ utgcns/libboost/boost/graph/adjacency_list.hpp:386:19: note: in instantiation of template class 'boost::scoped_ptr' requested here property_ptr m_property; ^ utgcns/libpbutgcns/AlnGraphBoost.H:84:5: note: in instantiation of template class 'boost::adjacency_list' requested here graphTraits::edge_descriptor bestInEdge; ///< Best scoring in edge ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:1018:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/utgcns -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/utgcns.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/stashContains.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/alignGFA -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/alignGFA/gfa/alignGFA.o -lcanu cp -pf pipelines/canu.pl /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/canu cp -pf pipelines/canu-time.pl /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/canu-time cp -pf pipelines/draw-tig.pl /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/draw-tig cp -pf mhap/mhap-2.1.3.jar /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/share/java/classes/mhap-2.1.3.jar cp -pf pipelines/canu/Consensus.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/CorrectReads.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/HaplotypeReads.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Configure.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Defaults.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Execution.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/SequenceStore.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Cloud.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_DNANexus.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_LSF.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Local.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_PBSTorque.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_SGE.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Slurm.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Meryl.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Output.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapBasedTrimming.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapErrorAdjustment.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapInCore.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMhap.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMMap.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapStore.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Report.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Unitig.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ Success! canu installed in /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/canu /bin/mv /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src/build/lib/site_perl /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src/build/lib/perl5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_3 depends on executable: gnuplot - not found ===> Installing existing package /packages/All/gnuplot-5.4.1_6.pkg [pkg-builder.dan.net.uk] Installing gnuplot-5.4.1_6... [pkg-builder.dan.net.uk] `-- Installing at-spi2-core-2.50.1... [pkg-builder.dan.net.uk] | `-- Installing dbus-1.14.10_4,1... [pkg-builder.dan.net.uk] | | `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] | | `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libICE-1.1.0_2,1... [pkg-builder.dan.net.uk] | | `-- Extracting libICE-1.1.0_2,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libSM-1.2.3_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting libSM-1.2.3_1,1: ........ done [pkg-builder.dan.net.uk] | | `-- Installing libX11-1.8.7_1,1... [pkg-builder.dan.net.uk] | | `-- Installing libxcb-1.16.1... [pkg-builder.dan.net.uk] | | | `-- Installing libXau-1.0.9_1... [pkg-builder.dan.net.uk] | | | `-- Extracting libXau-1.0.9_1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing libXdmcp-1.1.5... [pkg-builder.dan.net.uk] | | | `-- Installing xorgproto-2023.2... [pkg-builder.dan.net.uk] | | | `-- Extracting xorgproto-2023.2: .......... done [pkg-builder.dan.net.uk] | | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting libxcb-1.16.1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libX11-1.8.7_1,1: .......... done ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. [pkg-builder.dan.net.uk] | `-- Extracting dbus-1.14.10_4,1: ......... done [pkg-builder.dan.net.uk] | `-- Installing glib-2.80.0,2... [pkg-builder.dan.net.uk] | | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] | | `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing pcre2-10.43... [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting pcre2-10.43: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py39-packaging-23.2... [pkg-builder.dan.net.uk] | | `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | | | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | | | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | | | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting py39-packaging-23.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting glib-2.80.0,2: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXi-1.8_1,1... [pkg-builder.dan.net.uk] | | `-- Installing libXext-1.3.6,1... [pkg-builder.dan.net.uk] | | `-- Extracting libXext-1.3.6,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXfixes-6.0.0_1... [pkg-builder.dan.net.uk] | | `-- Extracting libXfixes-6.0.0_1: ....... done [pkg-builder.dan.net.uk] | `-- Extracting libXi-1.8_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXtst-1.2.3_3... [pkg-builder.dan.net.uk] | `-- Extracting libXtst-1.2.3_3: .......... done [pkg-builder.dan.net.uk] `-- Extracting at-spi2-core-2.50.1: .......... done [pkg-builder.dan.net.uk] `-- Installing cairo-1.17.4_2,3... [pkg-builder.dan.net.uk] | `-- Installing fontconfig-2.15.0_2,1... [pkg-builder.dan.net.uk] | | `-- Installing freetype2-2.13.2... [pkg-builder.dan.net.uk] | | `-- Extracting freetype2-2.13.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting fontconfig-2.15.0_2,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXrender-0.9.10_2... [pkg-builder.dan.net.uk] | `-- Extracting libXrender-0.9.10_2: ....... done [pkg-builder.dan.net.uk] | `-- Installing libglvnd-1.7.0... [pkg-builder.dan.net.uk] | `-- Extracting libglvnd-1.7.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing pixman-0.42.2... [pkg-builder.dan.net.uk] | `-- Extracting pixman-0.42.2: ....... done [pkg-builder.dan.net.uk] | `-- Installing png-1.6.43... [pkg-builder.dan.net.uk] | `-- Extracting png-1.6.43: .......... done [pkg-builder.dan.net.uk] `-- Extracting cairo-1.17.4_2,3: .......... done [pkg-builder.dan.net.uk] `-- Installing gdk-pixbuf2-2.42.10_2... [pkg-builder.dan.net.uk] | `-- Installing jpeg-turbo-3.0.2... [pkg-builder.dan.net.uk] | `-- Extracting jpeg-turbo-3.0.2: .......... done [pkg-builder.dan.net.uk] | `-- Installing libxml2-2.11.7... [pkg-builder.dan.net.uk] | `-- Extracting libxml2-2.11.7: .......... done [pkg-builder.dan.net.uk] | `-- Installing shared-mime-info-2.2_2... [pkg-builder.dan.net.uk] | `-- Extracting shared-mime-info-2.2_2: ......... done [pkg-builder.dan.net.uk] | `-- Installing tiff-4.4.0_3... [pkg-builder.dan.net.uk] | | `-- Installing jbigkit-2.1_2... [pkg-builder.dan.net.uk] | | `-- Extracting jbigkit-2.1_2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libdeflate-1.19... [pkg-builder.dan.net.uk] | | `-- Extracting libdeflate-1.19: .......... done [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting tiff-4.4.0_3: .......... done [pkg-builder.dan.net.uk] `-- Extracting gdk-pixbuf2-2.42.10_2: .......... done [pkg-builder.dan.net.uk] `-- Installing gtk3-3.24.41... [pkg-builder.dan.net.uk] | `-- Installing adwaita-icon-theme-42.0... [pkg-builder.dan.net.uk] | | `-- Installing gtk-update-icon-cache-3.24.31_1... [pkg-builder.dan.net.uk] | | `-- Extracting gtk-update-icon-cache-3.24.31_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing pango-1.50.14... [pkg-builder.dan.net.uk] | | `-- Installing encodings-1.1.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting encodings-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing fribidi-1.0.13_1... [pkg-builder.dan.net.uk] | | `-- Extracting fribidi-1.0.13_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing harfbuzz-8.3.0... [pkg-builder.dan.net.uk] | | | `-- Installing graphite2-1.3.14... [pkg-builder.dan.net.uk] | | | `-- Extracting graphite2-1.3.14: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting harfbuzz-8.3.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXft-2.3.7_1... [pkg-builder.dan.net.uk] | | `-- Extracting libXft-2.3.7_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libthai-0.1.29_1... [pkg-builder.dan.net.uk] | | | `-- Installing libdatrie-0.2.13_2... [pkg-builder.dan.net.uk] | | | `-- Extracting libdatrie-0.2.13_2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libthai-0.1.29_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing xorg-fonts-truetype-7.7_1... [pkg-builder.dan.net.uk] | | | `-- Installing dejavu-2.37_3... [pkg-builder.dan.net.uk] | | | `-- Installing mkfontscale-1.2.3... [pkg-builder.dan.net.uk] | | | | `-- Installing libfontenc-1.1.8... [pkg-builder.dan.net.uk] | | | | `-- Extracting libfontenc-1.1.8: ...... done [pkg-builder.dan.net.uk] | | | `-- Extracting mkfontscale-1.2.3: .... done [pkg-builder.dan.net.uk] | | | `-- Extracting dejavu-2.37_3: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing font-bh-ttf-1.0.3_5... [pkg-builder.dan.net.uk] | | | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing font-misc-ethiopic-1.0.4... [pkg-builder.dan.net.uk] | | | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg-builder.dan.net.uk] | | | `-- Installing font-misc-meltho-1.0.3_5... [pkg-builder.dan.net.uk] | | | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting pango-1.50.14: .......... done [pkg-builder.dan.net.uk] | `-- Extracting adwaita-icon-theme-42.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing colord-1.4.7... [pkg-builder.dan.net.uk] | | `-- Installing hwdata-0.380,1... [pkg-builder.dan.net.uk] | | `-- Extracting hwdata-0.380,1: ...... done [pkg-builder.dan.net.uk] | | `-- Installing lcms2-2.16_1... [pkg-builder.dan.net.uk] | | `-- Extracting lcms2-2.16_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libgudev-237... [pkg-builder.dan.net.uk] | | `-- Installing libudev-devd-0.5.2... [pkg-builder.dan.net.uk] | | `-- Extracting libudev-devd-0.5.2: ..... done [pkg-builder.dan.net.uk] | | `-- Extracting libgudev-237: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libgusb-0.3.10_1... [pkg-builder.dan.net.uk] | | `-- Extracting libgusb-0.3.10_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing polkit-124_2... [pkg-builder.dan.net.uk] | | `-- Installing duktape-lib-2.7.0... [pkg-builder.dan.net.uk] | | `-- Extracting duktape-lib-2.7.0: ...... done ===> Creating groups. Creating group 'polkitd' with gid '565'. ===> Creating users Creating user 'polkitd' with uid '565'. [pkg-builder.dan.net.uk] | | `-- Extracting polkit-124_2: ......... done [pkg-builder.dan.net.uk] | | `-- Installing sqlite3-3.45.1,1... [pkg-builder.dan.net.uk] | | `-- Installing libedit-3.1.20230828_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting libedit-3.1.20230828_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting sqlite3-3.45.1,1: ......... done ===> Creating groups. Creating group 'colord' with gid '970'. ===> Creating users Creating user 'colord' with uid '970'. [pkg-builder.dan.net.uk] | `-- Extracting colord-1.4.7: .......... done [pkg-builder.dan.net.uk] | `-- Installing cups-2.4.7_2... [pkg-builder.dan.net.uk] | | `-- Installing avahi-app-0.8_2... [pkg-builder.dan.net.uk] | | `-- Installing dbus-glib-0.112_1... [pkg-builder.dan.net.uk] | | `-- Extracting dbus-glib-0.112_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gdbm-1.23... [pkg-builder.dan.net.uk] | | `-- Extracting gdbm-1.23: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gnome_subr-1.0... [pkg-builder.dan.net.uk] | | `-- Extracting gnome_subr-1.0: . done [pkg-builder.dan.net.uk] | | `-- Installing libdaemon-0.14_1... [pkg-builder.dan.net.uk] | | `-- Extracting libdaemon-0.14_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libevent-2.1.12... [pkg-builder.dan.net.uk] | | `-- Extracting libevent-2.1.12: .......... done ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. [pkg-builder.dan.net.uk] | | `-- Extracting avahi-app-0.8_2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gnutls-3.7.10_2... [pkg-builder.dan.net.uk] | | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libidn2-2.3.7... [pkg-builder.dan.net.uk] | | | `-- Installing libunistring-1.2... [pkg-builder.dan.net.uk] | | | `-- Extracting libunistring-1.2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libidn2-2.3.7: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libtasn1-4.19.0_1... [pkg-builder.dan.net.uk] | | `-- Extracting libtasn1-4.19.0_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing nettle-3.9.1... [pkg-builder.dan.net.uk] | | `-- Extracting nettle-3.9.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing p11-kit-0.25.3_1... [pkg-builder.dan.net.uk] | | `-- Extracting p11-kit-0.25.3_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing unbound-1.19.3... [pkg-builder.dan.net.uk] | | | `-- Installing libnghttp2-1.60.0... [pkg-builder.dan.net.uk] | | | `-- Extracting libnghttp2-1.60.0: ....... done ===> Creating groups. Using existing group 'unbound'. ===> Creating users Using existing user 'unbound'. [pkg-builder.dan.net.uk] | | `-- Extracting unbound-1.19.3: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting gnutls-3.7.10_2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libpaper-1.1.28_1... [pkg-builder.dan.net.uk] | | `-- Extracting libpaper-1.1.28_1: .......... done ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. [pkg-builder.dan.net.uk] | `-- Extracting cups-2.4.7_2: .......... done [pkg-builder.dan.net.uk] | `-- Installing gsettings-desktop-schemas-42.0... [pkg-builder.dan.net.uk] | `-- Extracting gsettings-desktop-schemas-42.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing hicolor-icon-theme-0.17... [pkg-builder.dan.net.uk] | `-- Extracting hicolor-icon-theme-0.17: . done [pkg-builder.dan.net.uk] | `-- Installing libXcomposite-0.4.6_1,1... [pkg-builder.dan.net.uk] | `-- Extracting libXcomposite-0.4.6_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXcursor-1.2.2... [pkg-builder.dan.net.uk] | `-- Extracting libXcursor-1.2.2: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXdamage-1.1.6... [pkg-builder.dan.net.uk] | `-- Extracting libXdamage-1.1.6: ...... done [pkg-builder.dan.net.uk] | `-- Installing libXinerama-1.1.4_3,1... [pkg-builder.dan.net.uk] | `-- Extracting libXinerama-1.1.4_3,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXrandr-1.5.2_1... [pkg-builder.dan.net.uk] | `-- Extracting libXrandr-1.5.2_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libepoxy-1.5.9... [pkg-builder.dan.net.uk] | `-- Extracting libepoxy-1.5.9: .......... done [pkg-builder.dan.net.uk] | `-- Installing librsvg2-rust-2.56.4_5... [pkg-builder.dan.net.uk] | `-- Extracting librsvg2-rust-2.56.4_5: .......... done [pkg-builder.dan.net.uk] | `-- Installing libxkbcommon-1.6.0_2... [pkg-builder.dan.net.uk] | | `-- Installing wayland-1.22.0... [pkg-builder.dan.net.uk] | | `-- Installing libepoll-shim-0.0.20230411... [pkg-builder.dan.net.uk] | | `-- Extracting libepoll-shim-0.0.20230411: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting wayland-1.22.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing xkeyboard-config-2.41_4... [pkg-builder.dan.net.uk] | | `-- Extracting xkeyboard-config-2.41_4: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libxkbcommon-1.6.0_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting gtk3-3.24.41: .......... done [pkg-builder.dan.net.uk] `-- Installing libgd-2.3.3_10,1... [pkg-builder.dan.net.uk] | `-- Installing libXpm-3.5.17_1... [pkg-builder.dan.net.uk] | | `-- Installing libXt-1.3.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting libXt-1.3.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libXpm-3.5.17_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libimagequant-4.3.0_1... [pkg-builder.dan.net.uk] | `-- Extracting libimagequant-4.3.0_1: ...... done [pkg-builder.dan.net.uk] | `-- Installing webp-1.3.2_1... [pkg-builder.dan.net.uk] | | `-- Installing freeglut-3.2.1... [pkg-builder.dan.net.uk] | | `-- Installing libGLU-9.0.2_2... [pkg-builder.dan.net.uk] | | `-- Extracting libGLU-9.0.2_2: ..... done [pkg-builder.dan.net.uk] | | `-- Installing libXxf86vm-1.1.4_4... [pkg-builder.dan.net.uk] | | `-- Extracting libXxf86vm-1.1.4_4: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting freeglut-3.2.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing giflib-5.2.1_1... [pkg-builder.dan.net.uk] | | `-- Extracting giflib-5.2.1_1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting webp-1.3.2_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting libgd-2.3.3_10,1: .......... done [pkg-builder.dan.net.uk] `-- Installing lua53-5.3.6_1... [pkg-builder.dan.net.uk] `-- Extracting lua53-5.3.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing tex-kpathsea-6.3.5_1... [pkg-builder.dan.net.uk] `-- Extracting tex-kpathsea-6.3.5_1: .......... done [pkg-builder.dan.net.uk] `-- Installing wx30-gtk3-3.0.5.1_4... [pkg-builder.dan.net.uk] | `-- Installing gstreamer1-1.22.10... [pkg-builder.dan.net.uk] | | `-- Installing libunwind-20240221... [pkg-builder.dan.net.uk] | | `-- Extracting libunwind-20240221: .......... done [pkg-builder.dan.net.uk] | `-- Extracting gstreamer1-1.22.10: .......... done [pkg-builder.dan.net.uk] | `-- Installing gstreamer1-plugins-1.22.10... [pkg-builder.dan.net.uk] | | `-- Installing iso-codes-4.15.0... [pkg-builder.dan.net.uk] | | `-- Extracting iso-codes-4.15.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing orc-0.4.34_1... [pkg-builder.dan.net.uk] | | `-- Extracting orc-0.4.34_1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting gstreamer1-plugins-1.22.10: .......... done [pkg-builder.dan.net.uk] | `-- Installing libmspack-0.11alpha... [pkg-builder.dan.net.uk] | `-- Extracting libmspack-0.11alpha: ...... done [pkg-builder.dan.net.uk] | `-- Installing libsoup-2.74.3... [pkg-builder.dan.net.uk] | | `-- Installing glib-networking-2.78.0... [pkg-builder.dan.net.uk] | | `-- Installing libproxy-0.4.18... 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[pkg-builder.dan.net.uk] | | `-- Extracting libwpe-1.12.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libxslt-1.1.37_1... [pkg-builder.dan.net.uk] | | `-- Extracting libxslt-1.1.37_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openjpeg-2.5.2... [pkg-builder.dan.net.uk] | | `-- Extracting openjpeg-2.5.2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing woff2-1.0.2_5... [pkg-builder.dan.net.uk] | | `-- Extracting woff2-1.0.2_5: .......... done [pkg-builder.dan.net.uk] | | `-- Installing wpebackend-fdo-1.12.0... [pkg-builder.dan.net.uk] | | `-- Extracting wpebackend-fdo-1.12.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting webkit2-gtk3-2.34.6_10: .......... done [pkg-builder.dan.net.uk] `-- Extracting wx30-gtk3-3.0.5.1_4: .......... done [pkg-builder.dan.net.uk] Extracting gnuplot-5.4.1_6: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gdk-pixbuf-query-loaders.ucl Generating gdk-pixbuf modules cache ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: gtk-update-icon-cache.ucl Generating GTK icon cache for /usr/local/share/icons/hicolor Generating GTK icon cache for /usr/local/share/icons/Adwaita ==> Running trigger: glib-schemas.ucl Compiling glib schemas ==> Running trigger: shared-mime-info.ucl Building the Shared MIME-Info database cache ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===== Message from freetype2-2.13.2: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from dejavu-2.37_3: -- Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ===== Message from duktape-lib-2.7.0: -- ===> NOTICE: The duktape-lib port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from wayland-1.22.0: -- Wayland requires XDG_RUNTIME_DIR to be defined to a path that will contain "wayland-%d" unix(4) sockets. This is usually handled by consolekit2 (via ck-launch-session) or pam_xdg (via login). ===== Message from libxkbcommon-1.6.0_2: -- If arrow keys don't work under X11 switch to legacy rules e.g., For sh/bash/ksh/zsh run and (optionally) add into ~/.profile: export XKB_DEFAULT_RULES=xorg For csh/tcsh run and (optionally) add into ~/.login: setenv XKB_DEFAULT_RULES xorg ===== Message from freeglut-3.2.1: -- Joystick support is untested and it is unknown if it works. Do not hesitate to contact x11@FreeBSD.org if this causes issues. ===== Message from libsoup-2.74.3: -- libsoup can use NTLM authentication if it is compiled with the SMB option. To use it, you must install a port that provides NTLM, like net/samba412 or net/samba413. ===> canu-2.2_3 depends on executable: gnuplot - found ===> Returning to build of canu-2.2_3 ===> canu-2.2_3 depends on file: /usr/local/openjdk18/bin/java - not found ===> Installing existing package /packages/All/openjdk18-18.0.2+9.1_2.pkg [pkg-builder.dan.net.uk] Installing openjdk18-18.0.2+9.1_2... [pkg-builder.dan.net.uk] `-- Installing alsa-lib-1.2.10_1... [pkg-builder.dan.net.uk] `-- Extracting alsa-lib-1.2.10_1: .......... done [pkg-builder.dan.net.uk] `-- Installing javavmwrapper-2.7.10... [pkg-builder.dan.net.uk] `-- Extracting javavmwrapper-2.7.10: .......... done [pkg-builder.dan.net.uk] Extracting openjdk18-18.0.2+9.1_2: .......... done ===== Message from openjdk18-18.0.2+9.1_2: -- This OpenJDK implementation requires fdescfs(5) mounted on /dev/fd and procfs(5) mounted on /proc. If you have not done it yet, please do the following: mount -t fdescfs fdesc /dev/fd mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: fdesc /dev/fd fdescfs rw 0 0 proc /proc procfs rw 0 0 ===> canu-2.2_3 depends on file: /usr/local/openjdk18/bin/java - found ===> Returning to build of canu-2.2_3 ===> canu-2.2_3 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for canu-2.2_3 ===> Generating temporary packing list (cd /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src/build && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 555 "$@"'\'' . {} + \)' COPYTREE_BIN bin /wrkdirs/usr/ports/biology/canu/work/stage/usr/local) (cd /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src/build && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE "lib share" /wrkdirs/usr/ports/biology/canu/work/stage/usr/local) ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-03T12:42:26+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=d92c0802ea' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for canu-2.2_3 ===> Building canu-2.2_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for canu-2.2_3 build of biology/canu | canu-2.2_3 ended at Wed Apr 3 13:51:47 BST 2024 build time: 00:09:23