=>> Building biology/canu build started at Mon Dec 29 03:56:32 EST 2025 port directory: /usr/ports/biology/canu package name: canu-2.2_8 building for: FreeBSD 143amd64-deluxe-desktop-job-02 14.3-RELEASE-p2 FreeBSD 14.3-RELEASE-p2 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2157 Dec 16 05:29 /usr/ports/biology/canu/Makefile Ports top last git commit: 3dd9e2202282 Ports top unclean checkout: yes Port dir last git commit: 67fb95fb3bd5 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1403000 Jail OSVERSION: 1403000 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p2 UNAME_r=14.3-RELEASE-p2 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=3.4.4 MASTERMNT=/mnt/data/.m/143amd64-deluxe-desktop/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/mnt/data/.m/143amd64-deluxe-desktop/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=143amd64-deluxe-desktop SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/mnt/data/.m/143amd64-deluxe-desktop/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 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=/usr/local/bin/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=/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" --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=/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=" " 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 " CXXSTD=c++14 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=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 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/5.42 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" 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 #### #### # Work around some weirdness when fetching golang modules GO_TAGS+=netcgo .if ${.CURDIR:M*/www/chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/www/ungoogled-chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/lang/rust*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/lang/gcc*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/www/iridium*} MAKE_JOBS_NUMBER=16 .endif .if ${.CURDIR:M*/devel/electron*} MAKE_JOBS_NUMBER=20 .endif .if ${.CURDIR:M*/databases/mongodb*} MAKE_JOBS_NUMBER=12 .endif .if ${.CURDIR:M*/devel/llvm*} MAKE_JOBS_NUMBER=16 .endif # Speed things up a bit MAKE_JOBS_NUMBER?=8 #### #### #MAKE_JOBS_NUMBER?=4 # Alows us to build ports non-interactivly DISABLE_LICENSES=yes LICENSES_ACCEPTED+= DCC # Enable SNDIO on anything that supports it #OPTIONS_SET+=PULSEAUDIO OPTIONS_SET+=SNDIO # Yes we have MS Windows x11-fonts_webfonts_SET+=EXTRAFONTS CLEARTYPE # Desktop Specific Options sysutils_gksu_UNSET+=NAUTILUS x11-wm_compiz-fusion_UNSET+=EMERALD accessibility_redshift_SET+=GUI VIDMODE # These ports default to other audio servers, audio_espeak_UNSET+=PORTAUDIO www_qt5-webengine_UNSET+=ALSA www_qt6-webengine_UNSET+=ALSA audio_rhvoice_UNSET+=AO comms_morse_UNSET+=OSS audio_harp_UNSET+=OSS # Somehow these options are being set and result in ports being rebuilt needlessly becuase they are actually turned off audio_alsa-plugins_SET+=FFMPEG JACK PULSEAUDIO SAMPLERATE SPEEX #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---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 pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_8 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [143amd64-deluxe-desktop-job-02] Installing pkg-2.5.1... [143amd64-deluxe-desktop-job-02] Extracting pkg-2.5.1: .......... done ===> canu-2.2_8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of canu-2.2_8 =========================================================================== =================================================== ===== 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_8 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by canu-2.2_8 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=nobody UID=65534 GID=65534 ===> Fetching all distfiles required by canu-2.2_8 for building ===> Extracting for canu-2.2_8 => 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=nobody UID=65534 GID=65534 ===> Patching for canu-2.2_8 ===> Applying FreeBSD patches for canu-2.2_8 from /usr/ports/biology/canu/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_8 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [143amd64-deluxe-desktop-job-02] Installing gmake-4.4.1... [143amd64-deluxe-desktop-job-02] `-- Installing gettext-runtime-0.26... [143amd64-deluxe-desktop-job-02] | `-- Installing indexinfo-0.3.1_1... [143amd64-deluxe-desktop-job-02] | `-- Extracting indexinfo-0.3.1_1: . done [143amd64-deluxe-desktop-job-02] `-- Extracting gettext-runtime-0.26: .......... done [143amd64-deluxe-desktop-job-02] Extracting gmake-4.4.1: .......... done ===> canu-2.2_8 depends on package: gmake>=4.4.1 - found ===> Returning to build of canu-2.2_8 ===> canu-2.2_8 depends on file: /usr/local/openjdk8/bin/java - not found ===> Installing existing package /packages/All/openjdk8-8.472.08.1.pkg [143amd64-deluxe-desktop-job-02] Installing openjdk8-8.472.08.1... [143amd64-deluxe-desktop-job-02] `-- Installing alsa-lib-1.2.14... [143amd64-deluxe-desktop-job-02] `-- Extracting alsa-lib-1.2.14: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing dejavu-2.37_3... [143amd64-deluxe-desktop-job-02] | `-- Installing fontconfig-2.17.1,1... [143amd64-deluxe-desktop-job-02] | | `-- Installing expat-2.7.3... [143amd64-deluxe-desktop-job-02] | | `-- Extracting expat-2.7.3: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing freetype2-2.14.1... [143amd64-deluxe-desktop-job-02] | | `-- Installing brotli-1.2.0,1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting brotli-1.2.0,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing png-1.6.53... [143amd64-deluxe-desktop-job-02] | | `-- Extracting png-1.6.53: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting freetype2-2.14.1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting fontconfig-2.17.1,1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing mkfontscale-1.2.3... [143amd64-deluxe-desktop-job-02] | | `-- Installing libfontenc-1.1.8... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libfontenc-1.1.8: ...... done [143amd64-deluxe-desktop-job-02] | `-- Extracting mkfontscale-1.2.3: .... done [143amd64-deluxe-desktop-job-02] `-- Extracting dejavu-2.37_3: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing giflib-5.2.2... [143amd64-deluxe-desktop-job-02] `-- Extracting giflib-5.2.2: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing java-zoneinfo-2021.e... [143amd64-deluxe-desktop-job-02] `-- Extracting java-zoneinfo-2021.e: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing javavmwrapper-2.7.10... [143amd64-deluxe-desktop-job-02] `-- Extracting javavmwrapper-2.7.10: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing libX11-1.8.12,1... [143amd64-deluxe-desktop-job-02] | `-- Installing libxcb-1.17.0... [143amd64-deluxe-desktop-job-02] | | `-- Installing libXau-1.0.12... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libXau-1.0.12: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libXdmcp-1.1.5... [143amd64-deluxe-desktop-job-02] | | `-- Installing xorgproto-2024.1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting xorgproto-2024.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libXdmcp-1.1.5: ...... done [143amd64-deluxe-desktop-job-02] | `-- Extracting libxcb-1.17.0: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting libX11-1.8.12,1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing libXext-1.3.6,1... [143amd64-deluxe-desktop-job-02] `-- Extracting libXext-1.3.6,1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing libXi-1.8.2,1... [143amd64-deluxe-desktop-job-02] | `-- Installing libXfixes-6.0.1... [143amd64-deluxe-desktop-job-02] | `-- Extracting libXfixes-6.0.1: ....... done [143amd64-deluxe-desktop-job-02] `-- Extracting libXi-1.8.2,1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing libXrender-0.9.12... [143amd64-deluxe-desktop-job-02] `-- Extracting libXrender-0.9.12: ....... done [143amd64-deluxe-desktop-job-02] `-- Installing libXt-1.3.0,1... [143amd64-deluxe-desktop-job-02] | `-- Installing libICE-1.1.2,1... [143amd64-deluxe-desktop-job-02] | `-- Extracting libICE-1.1.2,1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libSM-1.2.6,1... [143amd64-deluxe-desktop-job-02] | `-- Extracting libSM-1.2.6,1: ........ done [143amd64-deluxe-desktop-job-02] `-- Extracting libXt-1.3.0,1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing libXtst-1.2.5... [143amd64-deluxe-desktop-job-02] `-- Extracting libXtst-1.2.5: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing libinotify-20240724_3... [143amd64-deluxe-desktop-job-02] `-- Extracting libinotify-20240724_3: .......... done [143amd64-deluxe-desktop-job-02] Extracting openjdk8-8.472.08.1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ===== Message from freetype2-2.14.1: -- 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 libinotify-20240724_3: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from openjdk8-8.472.08.1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> canu-2.2_8 depends on file: /usr/local/openjdk8/bin/java - found ===> Returning to build of canu-2.2_8 ===> canu-2.2_8 depends on package: perl5>=5.42.r<5.43 - not found ===> Installing existing package /packages/All/perl5-5.42.0_1.pkg [143amd64-deluxe-desktop-job-02] Installing perl5-5.42.0_1... [143amd64-deluxe-desktop-job-02] Extracting perl5-5.42.0_1: .......... done ===> canu-2.2_8 depends on package: perl5>=5.42.r<5.43 - found ===> Returning to build of canu-2.2_8 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_8 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.89.0_1.pkg [143amd64-deluxe-desktop-job-02] Installing boost-libs-1.89.0_1... [143amd64-deluxe-desktop-job-02] `-- Installing icu-76.1,1... [143amd64-deluxe-desktop-job-02] `-- Extracting icu-76.1,1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing zstd-1.5.7_1... [143amd64-deluxe-desktop-job-02] `-- Extracting zstd-1.5.7_1: .......... done [143amd64-deluxe-desktop-job-02] Extracting boost-libs-1.89.0_1: .......... done ===== Message from boost-libs-1.89.0_1: -- 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_8 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of canu-2.2_8 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for canu-2.2_8 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for canu-2.2_8 /bin/sh: git: not found Building release v2.2 For 'FreeBSD' '14.3-RELEASE-p2' as '' into '/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/{bin,obj}'. Using '/usr/bin/c++' version '19.1.7'. 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/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/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.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/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/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/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-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/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/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 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 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] 170 | snprintf(rotmes, 1024, "logFile()-- next message will exceed file sic++ -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 ze limit of " F_U64 "; rotate to new file.\n", | ^ 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 1 warning generated. 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 utility/src/utility/kmers-exact.C:264:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 264 | uint64 minp[nf]; | ^~ utility/src/utility/kmers-exact.C:264:17: note: read of non-const variable 'nf' is not allowed in a constant expression utility/src/utility/kmers-exact.C:260:12: note: declared here 260 | uint32 nf = _input->numFiles(); | ^ utility/src/utility/kmers-exact.C:265:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 265 | uint64 maxp[nf]; | ^~ utility/src/utility/kmers-exact.C:265:17: note: read of non-const variable 'nf' is not allowed in a constant expression utility/src/utility/kmers-exact.C:260:12: note: declared here 260 | uint32 nf = _input->numFiles(); | ^ 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 2 warnings 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 utility/src/utility/kmers-writer-block.C:221:36: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 221 | merylFileBlockReader inBlocks[_iteration + 1]; | ^~~~~~~~~~~~~~ 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 utility/src/utility/kmers-writer-block.C:221:36: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function utility/src/utility/kmers-writer-block.C:222:36: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 222 | FILE *inFiles [_iteration + 1]; | ^~~~~~~~~~~~~~ utility/src/utility/kmers-writer-block.C:222:36: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function utility/src/utility/kmers-writer-block.C:248:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 248 | uint32 p[_iteration+1]; // Position in s[] and v[] | ^~~~~~~~~~~~ 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 utility/src/utility/kmers-writer-block.C:248:15: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function utility/src/utility/kmers-writer-block.C:249:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 249 | uint64 l[_iteration+1]; // Number of entries in s[] and v[] | ^~~~~~~~~~~~ utility/src/utility/kmers-writer-block.C:249:15: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function utility/src/utility/kmers-writer-block.C:250:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 250 | kmdata *s[_iteration+1]; // Pointer to the suffixes for piece x | ^~~~~~~~~~~~ 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 utility/src/utility/kmers-writer-block.C:250:15: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function utility/src/utility/kmers-writer-block.C:251:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 251 | kmvalu *v[_iteration+1]; // Pointer to the values for piece x | ^~~~~~~~~~~~ utility/src/utility/kmers-writer-block.C:251:15: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function 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 utility/src/utility/kmers-writer.C:55:2: warning: how to set prefix size for streaming operations? [-W#warnings] 55 | #warning how to set prefix size for streaming operations? | ^ 6 warnings generated. 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 1 warning generated. 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 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 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] 171 | 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] 171 | 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] 171 | 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] 171 | 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] 171 | 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] 171 | 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] 171 | 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] 171 | if (NULL != alphabet_aliases) { | ~~~~ ^~~~~~~~~~~~~~~~ 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 8 warnings generated. 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 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 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/ovOverlap.C:59:15: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ~~~~~~~~~ 56 | a_iid, b_iid, 57 | flipped() ? 'I' : 'N', 58 | span(), 59 | dat.ovl.ahg5, dat.ovl.ahg3, | ^~~~~~~~~~~~ stores/ovOverlap.C:59:29: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ~~~~~~~~~ 56 | a_iid, b_iid, 57 | flipped() ? 'I' : 'N', 58 | span(), 59 | dat.ovl.ahg5, dat.ovl.ahg3, | ^~~~~~~~~~~~ stores/ovOverlap.C:60:15: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ~~~~~~~~~ 56 | a_iid, b_iid, 57 | flipped() ? 'I' : 'N', 58 | span(), 59 | dat.ovl.ahg5, dat.ovl.ahg3, 60 | dat.ovl.bhg5, dat.ovl.bhg3, | ^~~~~~~~~~~~ stores/ovOverlap.C:60:29: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ~~~~~~~~~ 56 | 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 a_iid, b_iid, 57 | flipped() ? 'I' : 'N', 58 | span(), 59 | dat.ovl.ahg5, dat.ovl.ahg3, 60 | dat.ovl.bhg5, dat.ovl.bhg3, | ^~~~~~~~~~~~ stores/ovOverlap.C:201:2: warning: NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-W#warnings] 201 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING | ^ 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 5 warnings generated. 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 stores/ovStoreWriter.C:33:2: warning: not failing if a valid store [-W#warnings] 33 | #warning not failing if a valid storec++ -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 | ^ stores/ovStoreWriter.C:327: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 28: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 327 | ovStoreInfo infopiece[_numSlices + 1]; | ^~~~~~~~~~~~~~ stores/ovStoreWriter.C:327:28: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function stores/ovStoreHistogram.C:338:35: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 337 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ~~~~~~~~~ 338 | 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] 337 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ~~~~~~~~~ 338 | 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] 337 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\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 n", | ~~~~~~~~~ 338 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, 2 339 | warning s generated . overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, | ^~~~~~~~~~~~~~~~~~~~~ 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 stores/ovStoreHistogram.C:339:58: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 337 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ~~~~~~~~~ 338 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, 339 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, | ^~~~~~~~~~~~~~~~~~~~~ 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 4 warnings generated. 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 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 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 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 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/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/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 utgcns/libNDalign/NDalgorithm-forward.C:219:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] 219 | 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 219 | 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 219 | 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] 220 | 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 220 | 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 220 | 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] 244 | 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 244 | 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 244 | 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] 245 | 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 245 | 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 245 | Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; | ^ | ( ) utgcns/libNDalign/NDalgorithm-reverse.C:220:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] 220 | 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 220 | Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 :4 warnings0 generated;. | ^ | ( ) utgcns/libNDalign/NDalgorithm-reverse.C:220:84: note: place parentheses around the '?:' expression to evaluate it first 220 | Dst = Edit_Ac++ -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 rray_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] 221 | 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 221 | 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 221 | Err = Edit_Array_Lazy[ei-1][d-1].errs +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 (gapCost == PEDFREEGAP) ? 0 : 0; | ^ | ( ) utgcns/libNDalign/NDalgorithm-reverse.C:244:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] 244 | 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 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 244 | 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 244 | Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; | ^ | ( ) In file included from utgcns/libNDalign/NDalgorithm-reverse.Cutgcns/libpbutgcns/AlnGraphBoost.C::245:5884:: In file included from warning: utgcns/libboost/boost/graph/graph_traits.hpp:operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses]27: In file included from 245utgcns/libboost/boost/pending/property.hpp | : 13 : In file included from utgcns/libboost/boost/type_traits.hpp: 31: In file included from utgcns/libboost/boost/type_traits/has_nothrow_assign.hpp: 12 : utgcns/libboost/boost/type_traits/has_trivial_assign.hpp :32: 40: Ewarning: rbuiltin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins]r 32 | = B OOS T _ESdTATIiC_CtO_NSATrANrTa(yb_oLoalz,y [veailu-e 1]=[ BOdO+S1T]_H.AeSr_rTsR I VIA+L (_gASSIGN(T)); | ^ autgcns/libboost/boost/type_traits/intrinsics.hppp:157:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN' C o157 | s#t = = dPeEfDiFnReE EBGOAOPS)T _?H A0S _:T R1I;V I A| L ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^_ Autgcns/libNDalign/NDalgorithm-reverse.CS:S245I:G84N:( Tnote: )place parentheses around the '+' expression to silence this warning ( _245_ | Err h a = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; | ^ | ( ) sutgcns/libNDalign/NDalgorithm-reverse.C:245:84: note: place parentheses around the '?:' expression to evaluate it first _ 245 | Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEtDFREEGAP) ? 0 : 1; | ^ | ( ) rivial_assign(T) && !is_volatile::value) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:58: In file included from 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 utgcns/libboost/boost/graph/graph_traits.hpp:27: In file included from utgcns/libboost/boost/pending/property.hpp:13: In file included from utgcns/libboost/boost/type_traits.hpp:31: utgcns/libboost/boost/type_traits/has_nothrow_assign.hpp:26:40: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] 26 | BOOST_STATIC_CONSTANT(bool, value = BOOST_HAS_NOTHROW_ASSIGN(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:169:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' 169 | # define BOOST_HAS_NOTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:58: In file included from utgcns/libboost/boost/graph/graph_traits.hpp:27: In file included from utgcns/libboost/boost/pending/property.hpp:13: In file included from utgcns/libboost/boost/type_traits.hpp:32: In file included from utgcns/libboost/boost/type_traits/has_nothrow_constructor.hpp:12: utgcns/libboost/boost/type_traits/has_trivial_constructor.hpp:31:10: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] 31 | BOOST4_ warningHsA generatedS. _TRIVIAL_CONSTRUCTOR(T) | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:151:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' 151c++ -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 | # define BOOST_HAS_TRc++ -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 IVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:58: In file included from utgcns/libboost/boost/graph/graph_traits.hpp:27: In file included from utgcns/libboost/boost/pending/property.hpp:13: In file included from utgcns/libboost/boost/type_traits.hpp:32: utgcns/libboost/boost/type_traits/has_nothrow_constructor.hpp:24:40: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] 24 | BOOST_STATIC_CONSTANT(bool, value = BOOST_HAS_NOTHROW_CONSTRUCTOR(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:163:47: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' 163 | # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) __has_nothrow_constructor(T) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:58: In file included from utgcns/libboost/boost/graph/graph_traits.hpp:27: In file included from utgcns/libboost/boost/pending/property.hpp:13: In file included from utgcns/libboost/boost/type_traits.hpp:33: In file included from 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 utgcns/libboost/boost/type_traits/has_nothrow_copy.hpp:12: utgcns/libboost/boost/type_traits/has_trivial_copy.hpp:31:40: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 31 | BOOST_STATIC_CONSTANT(bool, value = BOOST_HAS_TRIVIAL_COPY(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:154:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' 154 | # define BOOST_HAS_TRIVIAL_COPY(T) (__has_trivial_copy(T) && !is_reference::value && !is_volatile::value) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:58: In file included from utgcns/libboost/boost/graph/graph_traits.hpp:27: In file included from utgcns/libboost/boost/pending/property.hpp:13: In file included from utgcns/libboost/boost/type_traits.hpp:33: utgcns/libboost/boost/type_traits/has_nothrow_copy.hpp:24:40: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] 24 | BOOST_STATIC_CONSTANT(bool, value = BOOST_HAS_NOTHROW_COPY(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:166:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' 166 | # define BOOST_HAS_NOTHROW_COPY(T) (__has_nothrow_copy(T) && !is_volatile::value && !is_reference::value) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:58: In file included from utgcns/libboost/boost/graph/graph_traits.hpp:27: In file included from utgcns/libboost/boost/pending/property.hpp:13: In file included from utgcns/libboost/boost/type_traits.hpp:34: In file included from utgcns/libboost/boost/type_traits/has_nothrow_destructor.hpp:12: utgcns/libboost/boost/type_traits/has_trivial_destructor.hpp:28:40: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 28 | BOOST_STATIC_CONSTANT(bool, value = BOOST_HAS_TRIVIAL_DESTRUCTOR(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:160:46: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' 160 | # define BOOST_HAS_TRIVIAL_DESTRUCTOR(T) __has_trivial_destructor(T) | ^ 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 In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:438:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 438 | BOOST_HASH_SPECIALIZE(bool) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_functic++ -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 on { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:439:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 439 | BOOST_HASH_SPECIALIZE(char) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:440:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 440 | BOOST_HASH_SPECIALIZE(signed char) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:441:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 441 | BOOST_HASH_SPECIALIZE(unsigned char) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:443:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 443 | BOOST_HASH_SPECIALIZE(wchar_t) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:445:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 445 | BOOST_HASH_SPECIALIZE(short) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEc++ -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 PRECATED_IN_Cc++ -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 XX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:446:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 446 | BOOST_HASH_SPECIALIZE(unsigned shortc++ -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 ) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:447:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 447 | BOOST_HASH_SPECIALIZE(int) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_Tc++ -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 EMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ 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 /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:448:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 448 | BOOST_HASH_SPECIALIZE(unsigned int) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_functc++ -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 ion \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ 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 /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:449:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 449 | BOOST_HASH_SPECIALIZE(long) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:450:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 450 | BOOST_HASH_SPECIALIZE(unsigned long) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:452:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 452 | BOOST_HASH_SPECIALIZE(float) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:453:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 453 | BOOST_HASH_SPECIALIZE(double) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRstores/tgStoreDump.CECATE:D643 __:a2t:t rwarning: ireplace this with genericStatistics [-W#warnings] b u643t | e#_war_n(ing (r_e_depplraeccea tetdh_i_)s) w | i ^ thIn file included from utgcns/libpbutgcns/AlnGraphBoost.Cg:e59n: eIn file included from rutgcns/libboost/boost/graph/adjacency_list.hppi:cS21: tIn file included from autgcns/libboost/boost/unordered_set.hppt:i17: sIn file included from tutgcns/libboost/boost/unordered/unordered_set.hppi:c21s: In file included from utgcns/libboost/boost/functional/hash.hpp| : ^6 : utgcns/libboost/boost/functional/hash/hash.hpp:454:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 454 | BOOST_HASH_SPECIALIZE(long double) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:456:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 456 | BOOST_HASH_SPECIALIZE_REF(std::string) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:430:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE_REF' 430 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.Cc++ -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 :59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:458:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 458 | BOOST_HASH_SPECIALIZE_REF(std::wstring) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:430:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE_REF' 430 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:462:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 462 | BOOST_HASH_SPECIALIZE(boost::long_long_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_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 DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: 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 In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:463:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 463 | BOOST_HASH_SPECIALIZE(booc++ -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 st::ulong_long_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:467:5: warning: 'unary_function<__int128, unsigned long>' is deprecated [-Wdeprecated-declarations] 467 | BOOST_HASH_SPECIALIZE(boost::int128_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<__int128, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:468:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 468 | BOOST_HASH_SPECIALIZE(boost::uint128_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLA1 warning generated. TE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736: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 41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:472:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 472 | BOOST_HASH_SPECIALIZE(std::type_index) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 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 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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 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] 68 | 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 386 | property_ptr m_property; | ^ utgcns/libpbutgcns/AlnGraphBoost.H:84:5: note: in instantiation of template class 'boost::adjacency_list' requested herec++ -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 84 | 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 29 | class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49c++ -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 : note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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/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 meryl/src/meryl/merylOp-nextMer.C:234:8: warning: comparison of array 'name' equal to a null pointer is always false [-Wtautological-pointer-compare] 234 | if ((name == NULL) || // If there is no name, we've | ^~~~ ~~~~ 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 1 warning generated. 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/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/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 29 warnings generated. 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/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 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/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/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 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 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/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 overlapInCore/overlapPair.C:463:2: warning: do we need to check for contained too? [-W#warnings] 463 | #warning do we need to check for contained too? | ^ 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/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 1 warning generated. 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 mhap/mhapConvert.C:151:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 147 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ~~~~ 148 | ovStr, 149 | ov.a_iid, alen, 150 | ov.b_iid, blen, 151 | 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] 147 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ~~~~ 148 | ovStr, 149 | ov.a_iid, alen, 150 | ov.b_iid, blen, 151 | 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] 147 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len 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 %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ~~~~ 148 | ovStr, 149 | minimap/mmapConvert.C : 130 : 17 : warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] o v127. | a _ i i d , a lfepnr, i n150t | f ( s t d e r r , " I N V ALovI.Db _OiiVdE,RL AbPle n", F151_ | U 3 2 " ( len % 6d) " Fov.dat_.U32o v"l .ahg5(, ov.dat.ovl.laehng 3, % 152 | 6 d ) ohva.ndgat.ovsl. bh"g 5F_OV " ", Fo_OvV. da"t .-ovl.bhg3, | ^~~~~~~~~~~~~~~ mhap/mhapConvert.C":152 :34:F _warning: Oformat specifies type 'unsigned long' but the argument has type 'int' [-Wformat]V "147 | " F_OV "%s \n " , | ~~~~ fpr 128 | i n ov.a_iid, alen, t f129( | s t ov.b_iid, blen, d e130 | r r ,ov.dat.ovl.ah g5, ov.dat.ovl.ahg3, | ^~~~~~~~~~~~~~~ "minimap/mmapConvert.C%:130:34: warning: sformat specifies type 'unsigned long' but the argument has type 'int' [-Wformat] \ 127 | n fprintf(stIderr, "INVALID OVERLAP " NF_U32 " (len %V6d) " F_U32 " (lAen %6d) hLangs " F_OV " " IF_OV " D- " F_OV " " F_OV "%s\n", | ~~~~ O VERLAP re128a | d o" F_U32 " (len %d) and read " F_U32 " (lenv %d) hangs " F_OV "/" F_OV " and ". aF__iOiV "/" F_OV d"%s\,n "a,l en, | 129 ~~~~ | 148 | o v.b _oviStr, i d149, b | len, 130 | o v . a _ i i d , aolve.nd,a t .150o | v l . a h g 5 , o v . d a t . oovvl..ba_higi3d,, b| l ^~~~~~~~~~~~~~~e nminimap/mmapConvert.C,: 131 :15117 | : warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 127 | fopvr.idnattf.(osvtld.earhrg,5 ," IoNvV.AdLaItD. oOvVlE.RaLhAgP3 ," F152_ | U 3 2 " ( l e n % 6 d ) "o vF._dUa3t2. o"v l(.lbehng 5%,6 do)v .hdaantg.so v"l .Fb_hOgV3 ," "| ^~~~~~~~~~~~~~~F _OV " - " F_OV " " F_OV "%s\n", | ~~~~ 128 | 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 ov.a_iid, alen, 129 | ov.b_iid, blen, 130 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, 131 | 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] 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", | ~~~~ 128 | ov.a_iid, alen, 129 | ov.b_iid, blen, 130 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, 131 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ^~~~~~~~~~~~~~~ 4 warnings generated. 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 4 warnings generated. 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/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/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/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/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/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/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/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/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/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/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 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 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/ 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 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/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/cpuid.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/memory.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_trace.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qx_dispatch.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qb_de_dispatch.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qe_db_dispatch.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/cigar.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/computeGlobalScore.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/falconConsensus.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqCache.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqLibrary.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqReadData.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqReadDataWriter.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStore.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreBlob.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreConstructor.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreInfo.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovOverlap.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStore.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreWriter.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreFilter.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreFile.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreHistogram.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgStore.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTig.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/objectStore.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /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 - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-buffered.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-compressed.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-fasta-fastq.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-memoryMapped.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/logging.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/strings.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system.o a - /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 - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-stream.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/bits.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/bits-wordArray.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/hexDump.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/md5.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/cpuid.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/memory.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_trace.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qx_dispatch.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qb_de_dispatch.o a - /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qe_db_dispatch.o a - /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/bin/dumpBlob -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/bin/ovStoreBuild -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/bin/ovStoreConfig -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/bin/ovStoreBucketizer -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/bin/ovStoreSorter -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/bin/ovStoreIndexer -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/bin/ovStoreDump -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/bin/ovStoreStats -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/bin/sqStoreCreate -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/bin/sqStoreDumpFASTQ -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/bin/sqStoreDumpMetaData -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/bin/tgStoreCompress -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/bin/tgStoreDump -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/bin/tgStoreLoad -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/bin/tgTigDisplay -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/bin/loadCorrectedReads -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/bin/loadTrimmedReads -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/bin/loadErates -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/bin/meryl -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/bin/overlapCheck -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 In file included from utgcns/unitigConsensus.C:c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapInCore -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 23: In file included from utgcns/libpbutgcns/AlnGraphBoost.H:57: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:18: In file included from utgcns/libboost/boost/unordered/detail/equivalent.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/table.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/buckets.hpp:15: c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapInCorePartition -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 In file included from utgcns/libboost/boost/unordered/detail/util.hpp:20: In file included from utgcns/libboost/boost/move/move.hpp:23: c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapConvert -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 In file included from utgcns/libboost/boost/move/traits.hpp:18: utgcns/libboost/boost/type_traits/has_trivial_destructor.hpp:c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapImport -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 28:40: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 28 | BOOST_STATIC_CONSTANT(bool,c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapPair -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 value = BOOST_HASc++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/edalign -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 _TRIVIAL_DESTRUCTOR(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:160:46: note: expanded from macro 'BOOST_HAS_TRIVIAL_DESTRUCTOR' c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/prefixEditDistance-matchLimitGenerate -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 160 | # define BOOST_HAS_TRIVIAL_DESTRUCTOR(c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/mhapConvert -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 T) __has_trivial_destructor(T) c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/mmapConvert -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 | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/filterCorrectionOverlaps -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 17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:18: In file included from utgcns/libboost/boost/unordered/detail/equivalent.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/table.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/buckets.hpp:c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/generateCorrectionLayouts -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 15: In file included from utgcns/libboost/boost/unordered/detail/util.hpp:20: In file included from utgcns/libboost/boost/move/move.hpp:23: In file included from utgcns/libboost/boost/move/traits.hpp:19: In file included from utgcns/libboost/boost/type_traits/is_nothrow_move_constructible.hpp:16: In file included from utgcns/libboost/boost/type_traits/has_nothrow_copy.hpp:12: utgcns/libboost/boost/type_traits/has_trivial_copy.hpp:31:40: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/filterCorrectionLayouts -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 31 | BOOST_STATIC_CONSTANT(bool, value = BOOST_HAc++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/falconsense -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 S_TRIVIAL_COPY(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/errorEstimate -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 154:41: note: expanded from macro 'BOOST_HAS_TRIVIAL_COPY' 154 | # define BOOST_c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/splitHaplotype -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 HAS_TRIVIAL_COPY(T) (__has_trivc++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/trimReads -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 ial_copy(T) && !is_reference::value && c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/splitReads -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 !is_volatile::value) c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/mergeRanges -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 | ^ 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:21c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapAlign -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 : In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:18: In file included from utgcns/libboost/boost/unordered/detail/equivalent.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/table.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/buckets.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/util.hpp:20: In file included from utgcns/libboost/boost/move/move.hpp:23: In file included from utgcns/libboost/boost/move/traits.hpp:19: c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/findErrors -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 In file included from utgcns/libboost/boost/type_traits/is_nothrow_move_constructible.hpp:16: utgcns/libboost/boost/type_traits/has_nothrow_copy.hpp:24:40: warning: builtin __has_nothrow_copy is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] 24 | c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/fixErrors -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 BOOST_STATIC_CONSTANT(bool, vac++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/findErrors-Dump -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 lue = BOOST_HAS_NOTHRc++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/correctOverlaps -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 OW_COPY(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:166:41: note: expanded from macro 'BOOST_HAS_NOTHROW_COPY' 166 | # define c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/bogart -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 BOOST_HAS_NOTHROW_COPY(T) (c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/layoutReads -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/p_orts/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 _has_nothrow_copy(T) && !is_volatile::value && !is_reference::value) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:18: In file included from utgcns/libboost/boost/unordered/detail/equivalent.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/table.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/buckets.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/util.hpp:20: In file included from utgcns/libboost/boost/move/move.hpp:23: In file included from utgcns/libboost/boost/move/traits.hpp:20: In file included from utgcns/libboost/boost/type_traits/is_nothrow_move_assignable.hpp:16: In file included from utgcns/libboost/boost/type_traits/has_nothrow_assign.hpp:12: utgcns/libboost/boost/type_traits/has_trivial_assign.hpp:32:40: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 32 | BOOST_STATIC_CONSTANT(bool, value = BOOST_HAS_TRIVIAL_ASSIGN(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:157:43: note: expanded from macro 'BOOST_HAS_TRIVIAL_ASSIGN' 157 | # define BOOST_HAS_TRIVIAL_ASSIGN(T) (__has_trivial_assign(T) && !is_volatile::value) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:18: In file included from utgcns/libboost/boost/unordered/detail/equivalent.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/table.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/buckets.hpp:15: In file included from utgcns/libboost/boost/unordered/detail/util.hpp:20: In file included from utgcns/libboost/boost/move/move.hpp:23: In file included from utgcns/libboost/boost/move/traits.hpp:20: In file included from utgcns/libboost/boost/type_traits/is_nothrow_move_assignable.hpp:16: utgcns/libboost/boost/type_traits/has_nothrow_assign.hpp:26:40: warning: builtin __has_nothrow_assign is deprecated; use __is_nothrow_assignable instead [-Wdeprecated-builtins] 26 | BOOST_STATIC_CONSTANT(bool, value = BOOST_HAS_NOTHROW_ASSIGN(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:169:43: note: expanded from macro 'BOOST_HAS_NOTHROW_ASSIGN' 169 | # define BOOST_HAS_Nc++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/alignGFA -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 OTHROW_ASSIGN(T) (__has_nothrow_assign(T) && !is_volatile::value) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:438:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 438 | BOOST_HASH_SPECIALIZE(bool) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:439:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 439 | BOOST_HASH_SPECIALIZE(char) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:440:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 440 | BOOST_HASH_SPECIALIZE(signed char) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:441:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 441 | BOOST_HASH_SPECIALIZE(unsigned char) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:443:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 443 | BOOST_HASH_SPECIALIZE(wchar_t) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:445:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 445 | BOOST_HASH_SPECIALIZE(short) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:446:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 446 | BOOST_HASH_SPECIALIZE(unsigned short) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:447:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 447 | BOOST_HASH_SPECIALIZE(int) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:448:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 448 | BOOST_HASH_SPECIALIZE(unsigned int) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:449:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 449 | BOOST_HASH_SPECIALIZE(long) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:450:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 450 | BOOST_HASH_SPECIALIZE(unsigned long) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:452:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 452 | BOOST_HASH_SPECIALIZE(float) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:453:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 453 | BOOST_HASH_SPECIALIZE(double) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:454:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 454 | BOOST_HASH_SPECIALIZE(long double) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:456:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 456 | BOOST_HASH_SPECIALIZE_REF(std::string) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:430:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE_REF' 430 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:458:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 458 | BOOST_HASH_SPECIALIZE_REF(std::wstring) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:430:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE_REF' 430 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:462:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 462 | BOOST_HASH_SPECIALIZE(boost::long_long_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:463:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 463 | BOOST_HASH_SPECIALIZE(boost::ulong_long_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:467:5: warning: 'unary_function<__int128, unsigned long>' is deprecated [-Wdeprecated-declarations] 467 | BOOST_HASH_SPECIALIZE(boost::int128_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<__int128, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:468:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 468 | BOOST_HASH_SPECIALIZE(boost::uint128_type) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:21: In file included from utgcns/libboost/boost/unordered_set.hpp:17: In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21: In file included from utgcns/libboost/boost/functional/hash.hpp:6: utgcns/libboost/boost/functional/hash/hash.hpp:472:5: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 472 | BOOST_HASH_SPECIALIZE(std::type_index) | ^ utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE' 420 | : public std::unary_function \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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:33: In file included from utgcns/libboost/boost/graph/graph_traits.hpp:27: In file included from utgcns/libboost/boost/pending/property.hpp:13: In file included from utgcns/libboost/boost/type_traits.hpp:32: In file included from utgcns/libboost/boost/type_traits/has_nothrow_constructor.hpp:12: utgcns/libboost/boost/type_traits/has_trivial_constructor.hpp:31:10: warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] 31 | BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:151:47: note: expanded from macro 'BOOST_HAS_TRIVIAL_CONSTRUCTOR' 151 | # define BOOST_HAS_TRIVIAL_CONSTRUCTOR(T) __has_trivial_constructor(T) | ^ 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:33: In file included from utgcns/libboost/boost/graph/graph_traits.hpp:27: In file included from utgcns/libboost/boost/pending/property.hpp:13: In file included from utgcns/libboost/boost/type_traits.hpp:32: utgcns/libboost/boost/type_traits/has_nothrow_constructor.hpp:24:40: warning: builtin __has_nothrow_constructor is deprecated; use __is_nothrow_constructible instead [-Wdeprecated-builtins] 24 | BOOST_STATIC_CONSTANT(bool, value = BOOST_HAS_NOTHROW_CONSTRUCTOR(T)); | ^ utgcns/libboost/boost/type_traits/intrinsics.hpp:163:47: note: expanded from macro 'BOOST_HAS_NOTHROW_CONSTRUCTOR' 163 | # define BOOST_HAS_NOTHROW_CONSTRUCTOR(T) __has_nothrow_constructor(T) | ^ 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] 68 | 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 386 | property_ptr m_property; | ^ utgcns/libpbutgcns/AlnGraphBoost.H:84:5: note: in instantiation of template class 'boost::adjacency_list' requested here 84 | 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 29 | class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 29 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/utgcns -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 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_8 depends on executable: gnuplot - not found ===> Installing existing package /packages/All/gnuplot-5.4.10_3.pkg [143amd64-deluxe-desktop-job-02] Installing gnuplot-5.4.10_3... [143amd64-deluxe-desktop-job-02] `-- Installing at-spi2-core-2.56.6... [143amd64-deluxe-desktop-job-02] | `-- Installing dbus-1.16.2_4,1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libxml2-2.14.6... [143amd64-deluxe-desktop-job-02] | | `-- Installing readline-8.3.1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting readline-8.3.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libxml2-2.14.6: .......... done ===> Creating groups Creating group 'messagebus' with gid '556' ===> Creating users Creating user 'messagebus' with uid '556' [143amd64-deluxe-desktop-job-02] | `-- Extracting dbus-1.16.2_4,1: ......... done [143amd64-deluxe-desktop-job-02] | `-- Installing glib-2.84.4,2... [143amd64-deluxe-desktop-job-02] | | `-- Installing libffi-3.5.1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libffi-3.5.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libiconv-1.18_1... 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[143amd64-deluxe-desktop-job-02] | `-- Extracting gsettings-desktop-schemas-47.1_2: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting at-spi2-core-2.56.6: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing cairo-1.18.2,3... [143amd64-deluxe-desktop-job-02] | `-- Installing lzo2-2.10_1... [143amd64-deluxe-desktop-job-02] | `-- Extracting lzo2-2.10_1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing pixman-0.46.2... [143amd64-deluxe-desktop-job-02] | `-- Extracting pixman-0.46.2: ...... done [143amd64-deluxe-desktop-job-02] `-- Extracting cairo-1.18.2,3: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing gdk-pixbuf2-2.44.1... [143amd64-deluxe-desktop-job-02] | `-- Installing jpeg-turbo-3.1.3... [143amd64-deluxe-desktop-job-02] | `-- Extracting jpeg-turbo-3.1.3: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing shared-mime-info-2.4_2... [143amd64-deluxe-desktop-job-02] | `-- Extracting shared-mime-info-2.4_2: ......... done [143amd64-deluxe-desktop-job-02] | `-- Installing tiff-4.7.1... [143amd64-deluxe-desktop-job-02] | | `-- Installing jbigkit-2.1_3... [143amd64-deluxe-desktop-job-02] | | `-- Extracting jbigkit-2.1_3: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing lerc-4.0.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting lerc-4.0.0: ..... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libdeflate-1.25... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libdeflate-1.25: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting tiff-4.7.1: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting gdk-pixbuf2-2.44.1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing gtk3-3.24.51... [143amd64-deluxe-desktop-job-02] | `-- Installing adwaita-icon-theme-47.0... [143amd64-deluxe-desktop-job-02] | | `-- Installing adwaita-icon-theme-legacy-46.2... [143amd64-deluxe-desktop-job-02] | | `-- Installing gtk-update-icon-cache-3.24.42... [143amd64-deluxe-desktop-job-02] | | `-- Extracting gtk-update-icon-cache-3.24.42: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting adwaita-icon-theme-legacy-46.2: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting adwaita-icon-theme-47.0: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing colord-1.4.8... [143amd64-deluxe-desktop-job-02] | | `-- Installing hwdata-0.402,1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting hwdata-0.402,1: ...... done [143amd64-deluxe-desktop-job-02] | | `-- Installing lcms2-2.17... [143amd64-deluxe-desktop-job-02] | | `-- Extracting lcms2-2.17: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libgudev-237... [143amd64-deluxe-desktop-job-02] | | `-- Installing libudev-devd-0.6.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libudev-devd-0.6.0: ..... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libgudev-237: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libgusb-0.4.9_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing json-glib-1.10.8... [143amd64-deluxe-desktop-job-02] | | | `-- Installing gobject-introspection-1.84.0,1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting gobject-introspection-1.84.0,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting json-glib-1.10.8: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libgusb-0.4.9_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing polkit-125_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing duktape-lib-2.7.0_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting duktape-lib-2.7.0_1: ...... done ===> Creating groups Creating group 'polkitd' with gid '565' ===> Creating users Creating user 'polkitd' with uid '565' [143amd64-deluxe-desktop-job-02] | | `-- Extracting polkit-125_1: ......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing sqlite3-3.50.4_2,1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libedit-3.1.20251016_1,1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libedit-3.1.20251016_1,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting sqlite3-3.50.4_2,1: .......... done ===> Creating groups Creating group 'colord' with gid '970' ===> Creating users Creating user 'colord' with uid '970' [143amd64-deluxe-desktop-job-02] | `-- Extracting colord-1.4.8: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing cups-2.4.16... [143amd64-deluxe-desktop-job-02] | | `-- Installing avahi-app-0.8_6... [143amd64-deluxe-desktop-job-02] | | `-- Installing dbus-glib-0.114... [143amd64-deluxe-desktop-job-02] | | `-- Extracting dbus-glib-0.114: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing gdbm-1.26... [143amd64-deluxe-desktop-job-02] | | `-- Extracting gdbm-1.26: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing gnome_subr-1.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting gnome_subr-1.0: . done [143amd64-deluxe-desktop-job-02] | | `-- Installing libdaemon-0.14_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libdaemon-0.14_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libevent-2.1.12... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libevent-2.1.12: .......... done ===> Creating groups Creating group 'avahi' with gid '558' ===> Creating users Creating user 'avahi' with uid '558' [143amd64-deluxe-desktop-job-02] | | `-- Extracting avahi-app-0.8_6: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing gnutls-3.8.11... [143amd64-deluxe-desktop-job-02] | | `-- Installing gmp-6.3.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting gmp-6.3.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libidn2-2.3.8... [143amd64-deluxe-desktop-job-02] | | | `-- Installing libunistring-1.4.1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libunistring-1.4.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libidn2-2.3.8: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libtasn1-4.20.0_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libtasn1-4.20.0_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing nettle-3.10.2... [143amd64-deluxe-desktop-job-02] | | `-- Extracting nettle-3.10.2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing p11-kit-0.25.10... [143amd64-deluxe-desktop-job-02] | | `-- Extracting p11-kit-0.25.10: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting gnutls-3.8.11: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libpaper-1.1.28_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libpaper-1.1.28_1: .......... done ===> Creating groups Creating group 'cups' with gid '193' ===> Creating users Creating user 'cups' with uid '193' [143amd64-deluxe-desktop-job-02] | `-- Extracting cups-2.4.16: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing fribidi-1.0.16... [143amd64-deluxe-desktop-job-02] | `-- Extracting fribidi-1.0.16: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing harfbuzz-12.2.0... [143amd64-deluxe-desktop-job-02] | | `-- Installing graphite2-1.3.14... [143amd64-deluxe-desktop-job-02] | | `-- Extracting graphite2-1.3.14: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting harfbuzz-12.2.0: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing hicolor-icon-theme-0.18... [143amd64-deluxe-desktop-job-02] | `-- Extracting hicolor-icon-theme-0.18: . done [143amd64-deluxe-desktop-job-02] | `-- Installing libXcomposite-0.4.6_1,1... [143amd64-deluxe-desktop-job-02] | `-- Extracting libXcomposite-0.4.6_1,1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXcursor-1.2.3... [143amd64-deluxe-desktop-job-02] | `-- Extracting libXcursor-1.2.3: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXdamage-1.1.6... [143amd64-deluxe-desktop-job-02] | `-- Extracting libXdamage-1.1.6: ...... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXinerama-1.1.5,1... [143amd64-deluxe-desktop-job-02] | `-- Extracting libXinerama-1.1.5,1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXrandr-1.5.4... [143amd64-deluxe-desktop-job-02] | `-- Extracting libXrandr-1.5.4: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libepoxy-1.5.10... [143amd64-deluxe-desktop-job-02] | | `-- Installing libglvnd-1.7.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libglvnd-1.7.0: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting libepoxy-1.5.10: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing librsvg2-rust-2.61.3... [143amd64-deluxe-desktop-job-02] | | `-- Installing dav1d-1.5.2... [143amd64-deluxe-desktop-job-02] | | `-- Extracting dav1d-1.5.2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing pango-1.56.4... [143amd64-deluxe-desktop-job-02] | | `-- Installing libXft-2.3.8... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libXft-2.3.8: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libthai-0.1.29_2... [143amd64-deluxe-desktop-job-02] | | | `-- Installing libdatrie-0.2.14_1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libdatrie-0.2.14_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libthai-0.1.29_2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting pango-1.56.4: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting librsvg2-rust-2.61.3: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libxkbcommon-1.13.0_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing wayland-1.24.0_2... [143amd64-deluxe-desktop-job-02] | | `-- Installing libepoll-shim-0.0.20240608... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libepoll-shim-0.0.20240608: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting wayland-1.24.0_2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing xkeyboard-config-2.41_4... [143amd64-deluxe-desktop-job-02] | | `-- Extracting xkeyboard-config-2.41_4: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting libxkbcommon-1.13.0_1: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting gtk3-3.24.51: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing libgd-2.3.3_13,1... [143amd64-deluxe-desktop-job-02] | `-- Installing webp-1.6.0... [143amd64-deluxe-desktop-job-02] | `-- Extracting webp-1.6.0: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting libgd-2.3.3_13,1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing lua53-5.3.6_1... [143amd64-deluxe-desktop-job-02] `-- Extracting lua53-5.3.6_1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing tex-kpathsea-6.4.1... [143amd64-deluxe-desktop-job-02] `-- Extracting tex-kpathsea-6.4.1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing wx30-gtk3-3.0.5.1_7... [143amd64-deluxe-desktop-job-02] | `-- Installing gstreamer1-1.26.9_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libunwind-20250904... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libunwind-20250904: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting gstreamer1-1.26.9_1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing gstreamer1-plugins-1.26.9... [143amd64-deluxe-desktop-job-02] | | `-- Installing iso-codes-4.19.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting iso-codes-4.19.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libdrm-2.4.131,1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libpciaccess-0.18.1_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libpciaccess-0.18.1_1: ..... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libdrm-2.4.131,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing orc-0.4.41_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting orc-0.4.41_1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting gstreamer1-plugins-1.26.9: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libGLU-9.0.3... [143amd64-deluxe-desktop-job-02] | `-- Extracting libGLU-9.0.3: ..... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXxf86vm-1.1.6... [143amd64-deluxe-desktop-job-02] | `-- Extracting libXxf86vm-1.1.6: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libmspack-0.11alpha... [143amd64-deluxe-desktop-job-02] | `-- Extracting libmspack-0.11alpha: ...... done [143amd64-deluxe-desktop-job-02] | `-- Installing libsoup-2.74.3_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing glib-networking-2.80.1_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libproxy-0.5.10_1... [143amd64-deluxe-desktop-job-02] | | | `-- Installing curl-8.17.0... [143amd64-deluxe-desktop-job-02] | | | `-- Installing libnghttp2-1.68.0... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libnghttp2-1.68.0: ....... done [143amd64-deluxe-desktop-job-02] | | | `-- Installing libpsl-0.21.5_2... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libpsl-0.21.5_2: ........ done [143amd64-deluxe-desktop-job-02] | | | `-- Installing libssh2-1.11.1,3... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libssh2-1.11.1,3: .......... done [143amd64-deluxe-desktop-job-02] | | | `-- Extracting curl-8.17.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libproxy-0.5.10_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting glib-networking-2.80.1_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libgcrypt-1.11.2... [143amd64-deluxe-desktop-job-02] | | `-- Installing libgpg-error-1.58... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libgpg-error-1.58: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libgcrypt-1.11.2: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting libsoup-2.74.3_1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing webkit2-gtk_40-2.46.6_4... [143amd64-deluxe-desktop-job-02] | | `-- Installing enchant2-2.8.10... [143amd64-deluxe-desktop-job-02] | | `-- Installing hunspell-1.7.2_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting hunspell-1.7.2_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting enchant2-2.8.10: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing geoclue-2.8.0... [143amd64-deluxe-desktop-job-02] | | `-- Installing libnotify-0.8.7... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libnotify-0.8.7: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libsoup3-3.6.5_2... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libsoup3-3.6.5_2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting geoclue-2.8.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing graphene-1.10.8_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-pygobject-3.50.2... [143amd64-deluxe-desktop-job-02] | | | `-- Installing py311-cairo-1.28.0,1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting py311-cairo-1.28.0,1: .......... done [143amd64-deluxe-desktop-job-02] | | | `-- Installing pygobject-common-3.50.2... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting pygobject-common-3.50.2: .. done [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-pygobject-3.50.2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting graphene-1.10.8_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing gstreamer1-plugins-bad-1.26.9... [143amd64-deluxe-desktop-job-02] | | `-- Extracting gstreamer1-plugins-bad-1.26.9: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing gstreamer1-plugins-gl-1.26.9... [143amd64-deluxe-desktop-job-02] | | `-- Extracting gstreamer1-plugins-gl-1.26.9: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing harfbuzz-icu-12.2.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting harfbuzz-icu-12.2.0: ..... done [143amd64-deluxe-desktop-job-02] | | `-- Installing hyphen-2.8.8... [143amd64-deluxe-desktop-job-02] | | `-- Extracting hyphen-2.8.8: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libavif-1.3.0_2... [143amd64-deluxe-desktop-job-02] | | `-- Installing aom-3.13.1... [143amd64-deluxe-desktop-job-02] | | | `-- Installing vmaf-3.0.0... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting vmaf-3.0.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting aom-3.13.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libyuv-0.0.1903... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libyuv-0.0.1903: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libavif-1.3.0_2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libjxl-0.11.1_2... [143amd64-deluxe-desktop-job-02] | | `-- Installing highway-1.3.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting highway-1.3.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing openexr-3.4.4... [143amd64-deluxe-desktop-job-02] | | | `-- Installing Imath-3.2.2_1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting Imath-3.2.2_1: .......... done [143amd64-deluxe-desktop-job-02] | | | `-- Installing openjph-0.25.3... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting openjph-0.25.3: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting openexr-3.4.4: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libjxl-0.11.1_2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libsecret-0.21.7_2... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libsecret-0.21.7_2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libsysinfo-0.0.3_3... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libsysinfo-0.0.3_3: ...... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libxslt-1.1.43_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libxslt-1.1.43_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing mesa-libs-24.1.7_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libxshmfence-1.3.3... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libxshmfence-1.3.3: ...... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting mesa-libs-24.1.7_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing woff2-1.0.2_5... [143amd64-deluxe-desktop-job-02] | | `-- Extracting woff2-1.0.2_5: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting webkit2-gtk_40-2.46.6_4: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting wx30-gtk3-3.0.5.1_7: .......... done [143amd64-deluxe-desktop-job-02] Extracting gnuplot-5.4.10_3: .......... done ==> 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 Generating GTK icon cache for /usr/local/share/icons/AdwaitaLegacy ==> Running trigger: glib-schemas.ucl Compiling glib schemas Warning: Schema ?org.gnome.system.locale? has path ?/system/locale/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy? has path ?/system/proxy/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy.http? has path ?/system/proxy/http/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy.https? has path ?/system/proxy/https/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy.ftp? has path ?/system/proxy/ftp/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. Warning: Schema ?org.gnome.system.proxy.socks? has path ?/system/proxy/socks/?. Paths starting with ?/apps/?, ?/desktop/? or ?/system/? are deprecated. ==> Running trigger: shared-mime-info.ucl Building the Shared MIME-Info database cache ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===== Message from wayland-1.24.0_2: -- 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-1.13.0_1: -- 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 libsoup-2.74.3_1: -- 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. ===== Message from libjxl-0.11.1_2: -- Additional packages recommended for new users: - imlib2-jxl (e.g., feh, scrot) - kf5-kimageformats (e.g., nomacs, flameshot, skanlite) - gimp-jxl-plugin ===> canu-2.2_8 depends on executable: gnuplot - found ===> Returning to build of canu-2.2_8 ===> canu-2.2_8 depends on file: /usr/local/openjdk8/bin/java - found ===> canu-2.2_8 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for canu-2.2_8 ===> 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=2025-12-29T08:56:32+0000' 'PKG_NOTE_ports_top_git_hash=3dd9e2202282' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=67fb95fb3bd5' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.4' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for canu-2.2_8 ===> Building canu-2.2_8 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for canu-2.2_8 build of biology/canu | canu-2.2_8 ended at Mon Dec 29 03:58:04 EST 2025 build time: 00:01:33