=>> Building biology/canu build started at Wed May 7 15:14:56 BST 2025 port directory: /usr/ports/biology/canu package name: canu-2.2_6 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2157 Feb 16 09:27 /usr/ports/biology/canu/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: fa53920e72 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 " 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=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 DOCSDIR="share/doc/canu" EXAMPLESDIR="share/examples/canu" DATADIR="share/canu" WWWDIR="www/canu" ETCDIR="etc/canu" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/canu DOCSDIR=/usr/local/share/doc/canu EXAMPLESDIR=/usr/local/share/examples/canu WWWDIR=/usr/local/www/canu ETCDIR=/usr/local/etc/canu --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> canu-2.2_6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of canu-2.2_6 =========================================================================== =================================================== ===== 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_6 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by canu-2.2_6 for building => SHA256 Checksum OK for canu-2.2.tar.xz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by canu-2.2_6 for building ===> Extracting for canu-2.2_6 => SHA256 Checksum OK for canu-2.2.tar.xz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for canu-2.2_6 ===> Applying FreeBSD patches for canu-2.2_6 from /usr/ports/biology/canu/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_6 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> canu-2.2_6 depends on package: gmake>=4.4.1 - found ===> Returning to build of canu-2.2_6 ===> canu-2.2_6 depends on file: /usr/local/openjdk21/bin/java - not found ===> Installing existing package /packages/All/openjdk21-21.0.7+6.1.pkg [pkg-builder.dan.net.uk] Installing openjdk21-21.0.7+6.1... [pkg-builder.dan.net.uk] `-- Installing alsa-lib-1.2.13... [pkg-builder.dan.net.uk] `-- Extracting alsa-lib-1.2.13: .......... done [pkg-builder.dan.net.uk] `-- Installing fontconfig-2.15.0_3,1... [pkg-builder.dan.net.uk] | `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] | `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing freetype2-2.13.3... [pkg-builder.dan.net.uk] | `-- Extracting freetype2-2.13.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting fontconfig-2.15.0_3,1: .......... done [pkg-builder.dan.net.uk] `-- Installing giflib-5.2.2... [pkg-builder.dan.net.uk] `-- Extracting giflib-5.2.2: .......... done [pkg-builder.dan.net.uk] `-- Installing harfbuzz-10.3.0... [pkg-builder.dan.net.uk] | `-- Installing glib-2.84.1_2,2... [pkg-builder.dan.net.uk] | | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] | | `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libinotify-20240724_1... [pkg-builder.dan.net.uk] | | `-- Extracting libinotify-20240724_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing pcre2-10.45_1... [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting pcre2-10.45_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py311-packaging-24.2... [pkg-builder.dan.net.uk] | | `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | | | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | | | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | | | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting py311-packaging-24.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting glib-2.84.1_2,2: .......... done [pkg-builder.dan.net.uk] | `-- Installing graphite2-1.3.14... [pkg-builder.dan.net.uk] | `-- Extracting graphite2-1.3.14: .......... done [pkg-builder.dan.net.uk] `-- Extracting harfbuzz-10.3.0: .......... done [pkg-builder.dan.net.uk] `-- Installing javavmwrapper-2.7.10... [pkg-builder.dan.net.uk] `-- Extracting javavmwrapper-2.7.10: .......... done [pkg-builder.dan.net.uk] `-- Installing jpeg-turbo-3.1.0... [pkg-builder.dan.net.uk] `-- Extracting jpeg-turbo-3.1.0: .......... done [pkg-builder.dan.net.uk] `-- Installing lcms2-2.17... [pkg-builder.dan.net.uk] | `-- Installing tiff-4.7.0... [pkg-builder.dan.net.uk] | | `-- Installing jbigkit-2.1_3... [pkg-builder.dan.net.uk] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing lerc-4.0.0... [pkg-builder.dan.net.uk] | | `-- Extracting lerc-4.0.0: ..... done [pkg-builder.dan.net.uk] | | `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] | | `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] | `-- Extracting tiff-4.7.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting lcms2-2.17: .......... done [pkg-builder.dan.net.uk] `-- Installing libX11-1.8.12,1... [pkg-builder.dan.net.uk] | `-- Installing libxcb-1.17.0... [pkg-builder.dan.net.uk] | | `-- Installing libXau-1.0.11... [pkg-builder.dan.net.uk] | | `-- Extracting libXau-1.0.11: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXdmcp-1.1.5... [pkg-builder.dan.net.uk] | | `-- Installing xorgproto-2024.1... [pkg-builder.dan.net.uk] | | `-- Extracting xorgproto-2024.1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg-builder.dan.net.uk] | `-- Extracting libxcb-1.17.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting libX11-1.8.12,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXext-1.3.6,1... [pkg-builder.dan.net.uk] `-- Extracting libXext-1.3.6,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXi-1.8.1,1... [pkg-builder.dan.net.uk] | `-- Installing libXfixes-6.0.1... [pkg-builder.dan.net.uk] | `-- Extracting libXfixes-6.0.1: ....... done [pkg-builder.dan.net.uk] `-- Extracting libXi-1.8.1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXrandr-1.5.4... [pkg-builder.dan.net.uk] | `-- Installing libXrender-0.9.12... [pkg-builder.dan.net.uk] | `-- Extracting libXrender-0.9.12: ....... done [pkg-builder.dan.net.uk] `-- Extracting libXrandr-1.5.4: .......... done [pkg-builder.dan.net.uk] `-- Installing libXt-1.3.0,1... [pkg-builder.dan.net.uk] | `-- Installing libICE-1.1.1,1... [pkg-builder.dan.net.uk] | `-- Extracting libICE-1.1.1,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libSM-1.2.6,1... [pkg-builder.dan.net.uk] | `-- Extracting libSM-1.2.6,1: ........ done [pkg-builder.dan.net.uk] `-- Extracting libXt-1.3.0,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXtst-1.2.4... [pkg-builder.dan.net.uk] `-- Extracting libXtst-1.2.4: .......... done [pkg-builder.dan.net.uk] `-- Installing png-1.6.47... [pkg-builder.dan.net.uk] `-- Extracting png-1.6.47: .......... done [pkg-builder.dan.net.uk] `-- Installing xorg-fonts-truetype-7.7_1... [pkg-builder.dan.net.uk] | `-- Installing dejavu-2.37_3... [pkg-builder.dan.net.uk] | | `-- Installing mkfontscale-1.2.3... [pkg-builder.dan.net.uk] | | `-- Installing libfontenc-1.1.8... [pkg-builder.dan.net.uk] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg-builder.dan.net.uk] | `-- Extracting dejavu-2.37_3: .......... done [pkg-builder.dan.net.uk] | `-- Installing encodings-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting encodings-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing font-bh-ttf-1.0.3_5... [pkg-builder.dan.net.uk] | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg-builder.dan.net.uk] | `-- Installing font-misc-ethiopic-1.0.4... [pkg-builder.dan.net.uk] | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg-builder.dan.net.uk] | `-- Installing font-misc-meltho-1.0.3_5... [pkg-builder.dan.net.uk] | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg-builder.dan.net.uk] Extracting openjdk21-21.0.7+6.1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from freetype2-2.13.3: -- 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 libinotify-20240724_1: -- 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 python311-3.11.12: -- 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 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 openjdk21-21.0.7+6.1: -- This OpenJDK implementation may require fdescfs(5) mounted on /dev/fd and procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t fdescfs fdesc /dev/fd mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: fdesc /dev/fd fdescfs rw 0 0 proc /proc procfs rw 0 0 ===> canu-2.2_6 depends on file: /usr/local/openjdk21/bin/java - found ===> Returning to build of canu-2.2_6 ===> canu-2.2_6 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_3.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_3: .......... done ===> canu-2.2_6 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of canu-2.2_6 ===> canu-2.2_6 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> canu-2.2_6 depends on file: /usr/local/bin/ccache - found ===> Returning to build of canu-2.2_6 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_6 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.87.0_1.pkg [pkg-builder.dan.net.uk] Installing boost-libs-1.87.0_1... [pkg-builder.dan.net.uk] `-- Installing icu-76.1,1... [pkg-builder.dan.net.uk] `-- Extracting icu-76.1,1: .......... done [pkg-builder.dan.net.uk] Extracting boost-libs-1.87.0_1: .......... done ===== Message from boost-libs-1.87.0_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_6 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of canu-2.2_6 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for canu-2.2_6 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for canu-2.2_6 /bin/sh: git: not found Building release v2.2 For 'FreeBSD' '14.2-RELEASE' as '' into '/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/{bin,obj}'. Using '/usr/local/libexec/ccache/c++' version '18.1.6'. Using user-supplied CXXFLAGS '-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 '. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/runtime.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/runtime.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/align-parasail-driver.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/align-parasail-driver.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/edlib.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/edlib.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-buffered.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-buffered.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-compressed.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-compressed.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-fasta-fastq.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-fasta-fastq.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-memoryMapped.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-memoryMapped.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/logging.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/logging.C utility/src/utility/logging.C:170:7: warning: 'snprintf' size argument is too large; destination buffer has size 256, but size argument is 1024 [-Wfortify-source] 170 | snprintf(rotmes, 1024, "logFile()-- next message will exceed file size limit of " F_U64 "; rotate to new file.\n", | ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/strings.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/strings.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/system.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system-stackTrace.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/system-stackTrace.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/sequence.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sequence.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/types.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/types.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-exact.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-exact.C 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(); | ^ 2 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-files.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-files.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-histogram.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-histogram.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-reader.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-reader.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-block.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer-block.C 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]; | ^~~~~~~~~~~~~~ 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[] | ^~~~~~~~~~~~ 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 | ^~~~~~~~~~~~ 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 6 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-stream.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer-stream.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer.C utility/src/utility/kmers-writer.C:55:2: warning: how to set prefix size for streaming operations? [-W#warnings] 55 | #warning how to set prefix size for streaming operations? | ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/bits.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/bits-wordArray.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits-wordArray.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/hexDump.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/hexDump.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/md5.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/md5.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/mt19937ar.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/speedCounter.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sweatShop.C cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/cpuid.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cpuid.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/memory.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/memory.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_trace.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_trace.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qx_dispatch.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qx_dispatch.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qb_de_dispatch.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qb_de_dispatch.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/sg_qe_db_dispatch.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qe_db_dispatch.c cc -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/parasail/cigar.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cigar.c In file included from utility/src/parasail/cigar.c:161: utility/src/parasail/cigar_template.c:171:29: warning: comparison of array 'alphabet_aliases' not equal to a null pointer is always true [-Wtautological-pointer-compare] 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) { | ~~~~ ^~~~~~~~~~~~~~~~ 8 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqCache.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C stores/ovOverlap.C:59:15: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 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 | 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 | ^ 5 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C stores/ovStoreWriter.C:33:2: warning: not failing if a valid store [-W#warnings] 33 | #warning not failing if a valid store | ^ stores/ovStoreWriter.C:327:28: 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 2 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C stores/ovStoreHistogram.C:338:35: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 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\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, | ^~~~~~~~~~~~~~~~~~~~~ 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, | ^~~~~~~~~~~~~~~~~~~~~ 4 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgStore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/stores/objectStore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/objectStore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C utgcns/libNDalign/NDalgorithm-forward.C:219:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] 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; | ^ | ( ) 4 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C utgcns/libNDalign/NDalgorithm-reverse.C:220:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] 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 : 0; | ^ | ( ) utgcns/libNDalign/NDalgorithm-reverse.C:220:84: note: place parentheses around the '?:' expression to evaluate it first 220 | Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; | ^ | ( ) utgcns/libNDalign/NDalgorithm-reverse.C:221:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] 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 + (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 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; | ^ | ( ) utgcns/libNDalign/NDalgorithm-reverse.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-reverse.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-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 == PEDFREEGAP) ? 0 : 1; | ^ | ( ) 4 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C In file included from utgcns/libpbutgcns/AlnGraphBoost.C: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: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: 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/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: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 | 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/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 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) | ^ 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_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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_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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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: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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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: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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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: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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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' 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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: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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 29 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/gfa/gfa.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/gfa/bed.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C ar -rv /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/libcanu.a /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/runtime.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/align-parasail-driver.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/edlib.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-buffered.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-compressed.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-fasta-fastq.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/files-memoryMapped.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/logging.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/strings.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/system-stackTrace.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/sequence.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/types.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-exact.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-files.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-histogram.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-reader.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-block.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-stream.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/kmers.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/bits.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/bits-wordArray.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/hexDump.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/md5.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o /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/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/dumpBlob.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/dumpBlob -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreBuild.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreBuild -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreConfig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreConfig -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreBucketizer.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreBucketizer -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreSorter.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreSorter -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreIndexer.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreIndexer -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreDump.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreDump -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/ovStoreStats.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/ovStoreStats -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/sqStoreCreate.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/sqStoreCreate -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/sqStoreDumpFASTQ -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iseqrequester/src/seqrequester stores/sqStoreDumpMetaData.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpMetaData/seqrequester/src/seqrequester/summarize.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iseqrequester/src/seqrequester seqrequester/src/seqrequester/summarize.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/sqStoreDumpMetaData -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/sqStoreDumpMetaData/seqrequester/src/seqrequester/summarize.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgStoreCompress.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/tgStoreCompress -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgStoreDump.C stores/tgStoreDump.C:643:2: warning: replace this with genericStatistics [-W#warnings] 643 | #warning replace this with genericStatistics | ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgTigSizeAnalysis.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/tgStoreDump -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreDump/stores/tgStoreDump.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgStoreLoad.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/tgStoreLoad -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/tgTigDisplay.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/tgTigDisplay -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/loadCorrectedReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/loadCorrectedReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/loadTrimmedReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/loadTrimmedReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadErates/stores/loadErates.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility stores/loadErates.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/loadErates -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/loadErates/stores/loadErates.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/meryl.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/meryl.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylCommandBuilder.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCommandBuilder.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylCountArray.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCountArray.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylInput.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylInput.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-count.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-count.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countSimple.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countSimple.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countThreads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countThreads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-histogram.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-histogram.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-nextMer.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-nextMer.C meryl/src/meryl/merylOp-nextMer.C:234:8: warning: comparison of array 'name' equal to a null pointer is always false [-Wtautological-pointer-compare] 234 | if ((name == NULL) || // If there is no name, we've | ^~~~ ~~~~ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/meryl -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/meryl.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylCommandBuilder.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylCountArray.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylInput.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-count.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countSimple.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countThreads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-histogram.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-nextMer.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/meryl/meryl/src/meryl/merylOp.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapCheck/overlapCheck/overlapCheck.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapCheck/overlapCheck.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapCheck -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapCheck/overlapCheck/overlapCheck.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapInCore -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapInCorePartition -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapConvert -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapImport -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C overlapInCore/overlapPair.C:463:2: warning: do we need to check for contained too? [-W#warnings] 463 | #warning do we need to check for contained too? | ^ 1 warning generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapPair -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/edalign/overlapInCore/edalign.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/edalign -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/edalign/overlapInCore/edalign.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/prefixEditDistance-matchLimitGenerate -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Imhap/liboverlap mhap/mhapConvert.C mhap/mhapConvert.C:151:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 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 %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, 152 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ^~~~~~~~~~~~~~~ mhap/mhapConvert.C:152:34: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 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, 152 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ^~~~~~~~~~~~~~~ 4 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/mhapConvert -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iminimap/liboverlap minimap/mmapConvert.C minimap/mmapConvert.C:130:17: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] 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, | ^~~~~~~~~~~~~~~ minimap/mmapConvert.C:130:34: 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, | ^~~~~~~~~~~~~~~ minimap/mmapConvert.C:131:17: 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, | ^~~~~~~~~~~~~~~ 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/bin/mmapConvert -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores correction/filterCorrectionOverlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/filterCorrectionOverlaps -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns correction/generateCorrectionLayouts.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/generateCorrectionLayouts -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores correction/filterCorrectionLayouts.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/filterCorrectionLayouts -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/falconsense/correction/falconsense.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns correction/falconsense.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/falconsense/utgcns/stashContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/falconsense -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/falconsense/correction/falconsense.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/falconsense/utgcns/stashContains.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/errorEstimate -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -Iutgcns haplotyping/splitHaplotype.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/splitHaplotype -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-bestEdge.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-largestCovered.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/trimReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-workUnit.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-subReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-trimBad.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustNormal.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustFlipped.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/splitReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapBasedTrimming/mergeRanges.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/mergeRanges -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/overlapAlign -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/trimRead.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/computeDiff.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/computeDiff.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/findErrors -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/computeDiff.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/fixErrors/overlapErrorAdjustment/fixErrors.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapErrorAdjustment/fixErrors.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/fixErrors/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores overlapErrorAdjustment/correctOverlaps-Correct_Frags.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/fixErrors -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/fixErrors/overlapErrorAdjustment/fixErrors.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/fixErrors/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/findErrors-Dump -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/computeDiff.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/computeDiff.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/correctOverlaps -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/computeDiff.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/bogart.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/bogart.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_AssemblyGraph.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_BestOverlapGraph.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_ChunkGraph.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_DetectSpurs.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Instrumentation.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_FindCircular.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_FindCircular.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Logging.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_MarkRepeatReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_MergeOrphans.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_OptimizePositions.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Outputs.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_OverlapCache.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PopulateUnitig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PromoteToSingleton.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_ReadInfo.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_SetParentAndHang.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitDiscontinuous.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SplitTig_AtReadEnds.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitTig_AtReadEnds.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_TigVector.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_AddRead.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/bogart -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/bogart.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_FindCircular.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Logging.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Outputs.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_SplitTig_AtReadEnds.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_TigVector.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/layoutReads.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/layoutReads.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Instrumentation.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Instrumentation.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Logging.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Logging.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_OptimizePositions.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_OptimizePositions.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Outputs.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Outputs.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_OverlapCache.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_OverlapCache.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_ReadInfo.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_ReadInfo.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_SetParentAndHang.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_SetParentAndHang.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_TigVector.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_TigVector.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_AddRead.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_AddRead.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/layoutReads -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/layoutReads.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Instrumentation.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Logging.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_OptimizePositions.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Outputs.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_OverlapCache.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceContains.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceReadUsingOverlaps.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_ReadInfo.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_SetParentAndHang.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_TigVector.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_AddRead.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/utgcns.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/stashContains.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C In file included from utgcns/unitigConsensus.C:23: In file included from utgcns/libpbutgcns/AlnGraphBoost.H:57: In file included from utgcns/libboost/boost/graph/adjacency_list.hpp: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:18: 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) | ^ 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: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] 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/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:19: 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 | 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/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_NOTHROW_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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 29 warnings generated. c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/utgcns -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/utgcns.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/stashContains.o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/alignGFA -fstack-protector-strong -pthread -fopenmp -L/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/bin/alignGFA/gfa/alignGFA.o -lcanu cp -pf pipelines/canu.pl /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/canu cp -pf pipelines/canu-time.pl /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/canu-time cp -pf pipelines/draw-tig.pl /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/draw-tig cp -pf mhap/mhap-2.1.3.jar /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/share/java/classes/mhap-2.1.3.jar cp -pf pipelines/canu/Consensus.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/CorrectReads.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/HaplotypeReads.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Configure.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Defaults.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Execution.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/SequenceStore.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Cloud.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_DNANexus.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_LSF.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Local.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_PBSTorque.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_SGE.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Slurm.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Meryl.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Output.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapBasedTrimming.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapErrorAdjustment.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapInCore.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMhap.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMMap.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapStore.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Report.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Unitig.pm /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/lib/site_perl/canu/ Success! canu installed in /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/bin/canu /bin/mv /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src/build/lib/site_perl /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src/build/lib/perl5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> canu-2.2_6 depends on executable: gnuplot - not found ===> Installing existing package /packages/All/gnuplot-5.4.10_2.pkg [pkg-builder.dan.net.uk] Installing gnuplot-5.4.10_2... [pkg-builder.dan.net.uk] `-- Installing at-spi2-core-2.54.1_1... [pkg-builder.dan.net.uk] | `-- Installing dbus-1.16.2_2,1... [pkg-builder.dan.net.uk] | | `-- Installing libxml2-2.11.9... [pkg-builder.dan.net.uk] | | `-- Extracting libxml2-2.11.9: .......... done ===> Creating groups Creating group 'messagebus' with gid '556' ===> Creating users Creating user 'messagebus' with uid '556' [pkg-builder.dan.net.uk] | `-- Extracting dbus-1.16.2_2,1: ......... done [pkg-builder.dan.net.uk] `-- Extracting at-spi2-core-2.54.1_1: .......... done [pkg-builder.dan.net.uk] `-- Installing cairo-1.18.2,3... [pkg-builder.dan.net.uk] | `-- Installing lzo2-2.10_1... [pkg-builder.dan.net.uk] | `-- Extracting lzo2-2.10_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing pixman-0.44.2... [pkg-builder.dan.net.uk] | `-- Extracting pixman-0.44.2: ...... done [pkg-builder.dan.net.uk] `-- Extracting cairo-1.18.2,3: .......... done [pkg-builder.dan.net.uk] `-- Installing gdk-pixbuf2-2.42.12_1... [pkg-builder.dan.net.uk] | `-- Installing shared-mime-info-2.4_1... [pkg-builder.dan.net.uk] | `-- Extracting shared-mime-info-2.4_1: ......... done [pkg-builder.dan.net.uk] `-- Extracting gdk-pixbuf2-2.42.12_1: .......... done [pkg-builder.dan.net.uk] `-- Installing gtk3-3.24.48... [pkg-builder.dan.net.uk] | `-- Installing adwaita-icon-theme-42.0... [pkg-builder.dan.net.uk] | | `-- Installing gtk-update-icon-cache-3.24.42... [pkg-builder.dan.net.uk] | | `-- Extracting gtk-update-icon-cache-3.24.42: .......... done [pkg-builder.dan.net.uk] | `-- Extracting adwaita-icon-theme-42.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing colord-1.4.7_3... [pkg-builder.dan.net.uk] | | `-- Installing hwdata-0.394,1... [pkg-builder.dan.net.uk] | | `-- Extracting hwdata-0.394,1: ...... done [pkg-builder.dan.net.uk] | | `-- Installing libgudev-237... [pkg-builder.dan.net.uk] | | `-- Installing libudev-devd-0.6.0... [pkg-builder.dan.net.uk] | | `-- Extracting libudev-devd-0.6.0: ..... done [pkg-builder.dan.net.uk] | | `-- Extracting libgudev-237: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libgusb-0.4.9_1... [pkg-builder.dan.net.uk] | | `-- Installing json-glib-1.10.6... [pkg-builder.dan.net.uk] | | | `-- Installing gobject-introspection-1.84.0,1... [pkg-builder.dan.net.uk] | | | `-- Extracting gobject-introspection-1.84.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting json-glib-1.10.6: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libgusb-0.4.9_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing polkit-125_1... [pkg-builder.dan.net.uk] | | `-- Installing duktape-lib-2.7.0... [pkg-builder.dan.net.uk] | | `-- Extracting duktape-lib-2.7.0: ...... done ===> Creating groups Creating group 'polkitd' with gid '565' ===> Creating users Creating user 'polkitd' with uid '565' [pkg-builder.dan.net.uk] | | `-- Extracting polkit-125_1: ......... done [pkg-builder.dan.net.uk] | | `-- Installing sqlite3-3.46.1_1,1... [pkg-builder.dan.net.uk] | | `-- Installing libedit-3.1.20250104,1... [pkg-builder.dan.net.uk] | | `-- Extracting libedit-3.1.20250104,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting sqlite3-3.46.1_1,1: ......... done ===> Creating groups Creating group 'colord' with gid '970' ===> Creating users Creating user 'colord' with uid '970' [pkg-builder.dan.net.uk] | `-- Extracting colord-1.4.7_3: .......... done [pkg-builder.dan.net.uk] | `-- Installing cups-2.4.11_1... [pkg-builder.dan.net.uk] | | `-- Installing avahi-app-0.8_6... [pkg-builder.dan.net.uk] | | `-- Installing dbus-glib-0.114... [pkg-builder.dan.net.uk] | | `-- Extracting dbus-glib-0.114: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gdbm-1.25... [pkg-builder.dan.net.uk] | | `-- Extracting gdbm-1.25: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gnome_subr-1.0... [pkg-builder.dan.net.uk] | | `-- Extracting gnome_subr-1.0: . done [pkg-builder.dan.net.uk] | | `-- Installing libdaemon-0.14_1... [pkg-builder.dan.net.uk] | | `-- Extracting libdaemon-0.14_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libevent-2.1.12... [pkg-builder.dan.net.uk] | | `-- Extracting libevent-2.1.12: .......... done ===> Creating groups Creating group 'avahi' with gid '558' ===> Creating users Creating user 'avahi' with uid '558' [pkg-builder.dan.net.uk] | | `-- Extracting avahi-app-0.8_6: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gnutls-3.8.9... [pkg-builder.dan.net.uk] | | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | | | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | | | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libtasn1-4.20.0_1... [pkg-builder.dan.net.uk] | | `-- Extracting libtasn1-4.20.0_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing nettle-3.10.1... [pkg-builder.dan.net.uk] | | `-- Extracting nettle-3.10.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing p11-kit-0.25.5... [pkg-builder.dan.net.uk] | | `-- Extracting p11-kit-0.25.5: .......... done [pkg-builder.dan.net.uk] | | `-- Installing unbound-1.23.0... [pkg-builder.dan.net.uk] | | | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | | | `-- Extracting libnghttp2-1.65.0: ....... done ===> Creating groups Using existing group 'unbound' ===> Creating users Using existing user 'unbound' [pkg-builder.dan.net.uk] | | `-- Extracting unbound-1.23.0: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting gnutls-3.8.9: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libpaper-1.1.28_1... [pkg-builder.dan.net.uk] | | `-- Extracting libpaper-1.1.28_1: .......... done ===> Creating groups Creating group 'cups' with gid '193' ===> Creating users Creating user 'cups' with uid '193' [pkg-builder.dan.net.uk] | `-- Extracting cups-2.4.11_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing fribidi-1.0.16... [pkg-builder.dan.net.uk] | `-- Extracting fribidi-1.0.16: .......... done [pkg-builder.dan.net.uk] | `-- Installing gsettings-desktop-schemas-47.1_1... [pkg-builder.dan.net.uk] | `-- Extracting gsettings-desktop-schemas-47.1_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing hicolor-icon-theme-0.18... [pkg-builder.dan.net.uk] | `-- Extracting hicolor-icon-theme-0.18: . done [pkg-builder.dan.net.uk] | `-- Installing libXcomposite-0.4.6_1,1... [pkg-builder.dan.net.uk] | `-- Extracting libXcomposite-0.4.6_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXcursor-1.2.2... [pkg-builder.dan.net.uk] | `-- Extracting libXcursor-1.2.2: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXdamage-1.1.6... [pkg-builder.dan.net.uk] | `-- Extracting libXdamage-1.1.6: ...... done [pkg-builder.dan.net.uk] | `-- Installing libXinerama-1.1.5,1... [pkg-builder.dan.net.uk] | `-- Extracting libXinerama-1.1.5,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libepoxy-1.5.10... [pkg-builder.dan.net.uk] | | `-- Installing libglvnd-1.7.0... [pkg-builder.dan.net.uk] | | `-- Extracting libglvnd-1.7.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libepoxy-1.5.10: .......... done [pkg-builder.dan.net.uk] | `-- Installing librsvg2-rust-2.60.0_1... [pkg-builder.dan.net.uk] | | `-- Installing dav1d-1.5.1... [pkg-builder.dan.net.uk] | | `-- Extracting dav1d-1.5.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing pango-1.56.1... [pkg-builder.dan.net.uk] | | `-- Installing libXft-2.3.8... [pkg-builder.dan.net.uk] | | `-- Extracting libXft-2.3.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libthai-0.1.29_1... [pkg-builder.dan.net.uk] | | | `-- Installing libdatrie-0.2.13_2... [pkg-builder.dan.net.uk] | | | `-- Extracting libdatrie-0.2.13_2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libthai-0.1.29_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting pango-1.56.1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting librsvg2-rust-2.60.0_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libxkbcommon-1.8.1_2... [pkg-builder.dan.net.uk] | | `-- Installing wayland-1.23.1... [pkg-builder.dan.net.uk] | | `-- Installing libepoll-shim-0.0.20240608... [pkg-builder.dan.net.uk] | | `-- Extracting libepoll-shim-0.0.20240608: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting wayland-1.23.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing xkeyboard-config-2.41_4... [pkg-builder.dan.net.uk] | | `-- Extracting xkeyboard-config-2.41_4: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libxkbcommon-1.8.1_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting gtk3-3.24.48: .......... done [pkg-builder.dan.net.uk] `-- Installing libgd-2.3.3_13,1... [pkg-builder.dan.net.uk] | `-- Installing libXpm-3.5.17_1... [pkg-builder.dan.net.uk] | `-- Extracting libXpm-3.5.17_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libimagequant-4.3.4_2... [pkg-builder.dan.net.uk] | `-- Extracting libimagequant-4.3.4_2: ...... done [pkg-builder.dan.net.uk] | `-- Installing webp-1.5.0... [pkg-builder.dan.net.uk] | | `-- Installing freeglut-3.2.1... [pkg-builder.dan.net.uk] | | `-- Installing libGLU-9.0.3... [pkg-builder.dan.net.uk] | | `-- Extracting libGLU-9.0.3: ..... done [pkg-builder.dan.net.uk] | | `-- Installing libXxf86vm-1.1.5... [pkg-builder.dan.net.uk] | | `-- Extracting libXxf86vm-1.1.5: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting freeglut-3.2.1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting webp-1.5.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting libgd-2.3.3_13,1: .......... done [pkg-builder.dan.net.uk] `-- Installing lua53-5.3.6_1... [pkg-builder.dan.net.uk] `-- Extracting lua53-5.3.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing tex-kpathsea-6.4.1... [pkg-builder.dan.net.uk] `-- Extracting tex-kpathsea-6.4.1: .......... done [pkg-builder.dan.net.uk] `-- Installing wx30-gtk3-3.0.5.1_6... [pkg-builder.dan.net.uk] | `-- Installing gstreamer1-1.26.0_1... [pkg-builder.dan.net.uk] | | `-- Installing libunwind-20240221_2... [pkg-builder.dan.net.uk] | | `-- Extracting libunwind-20240221_2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting gstreamer1-1.26.0_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing gstreamer1-plugins-1.26.0... [pkg-builder.dan.net.uk] | | `-- Installing iso-codes-4.15.0... [pkg-builder.dan.net.uk] | | `-- Extracting iso-codes-4.15.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libdrm-2.4.123,1... [pkg-builder.dan.net.uk] | | `-- Installing libpciaccess-0.18.1_1... [pkg-builder.dan.net.uk] | | `-- Extracting libpciaccess-0.18.1_1: ..... done [pkg-builder.dan.net.uk] | | `-- Extracting libdrm-2.4.123,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing orc-0.4.41... [pkg-builder.dan.net.uk] | | `-- Extracting orc-0.4.41: .......... done [pkg-builder.dan.net.uk] | `-- Extracting gstreamer1-plugins-1.26.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing libmspack-0.11alpha... [pkg-builder.dan.net.uk] | `-- Extracting libmspack-0.11alpha: ...... done [pkg-builder.dan.net.uk] | `-- Installing libsoup-2.74.3... [pkg-builder.dan.net.uk] | | `-- Installing glib-networking-2.80.1_1... [pkg-builder.dan.net.uk] | | `-- Installing libproxy-0.5.9_1... [pkg-builder.dan.net.uk] | | | `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | | | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | | | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | | | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] | | | `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libproxy-0.5.9_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting glib-networking-2.80.1_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libgcrypt-1.11.0... [pkg-builder.dan.net.uk] | | `-- Installing libgpg-error-1.55... [pkg-builder.dan.net.uk] | | `-- Extracting libgpg-error-1.55: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libgcrypt-1.11.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libpsl-0.21.5_2... [pkg-builder.dan.net.uk] | | `-- Extracting libpsl-0.21.5_2: ........ done [pkg-builder.dan.net.uk] | `-- Extracting libsoup-2.74.3: .......... done [pkg-builder.dan.net.uk] | `-- Installing webkit2-gtk_40-2.46.6... [pkg-builder.dan.net.uk] | | `-- Installing enchant2-2.2.15_6... [pkg-builder.dan.net.uk] | | `-- Installing hunspell-1.7.2_1... [pkg-builder.dan.net.uk] | | `-- Extracting hunspell-1.7.2_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting enchant2-2.2.15_6: .......... done [pkg-builder.dan.net.uk] | | `-- Installing geoclue-2.7.2... [pkg-builder.dan.net.uk] | | `-- Installing libsoup3-3.6.5_2... [pkg-builder.dan.net.uk] | | `-- Extracting libsoup3-3.6.5_2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting geoclue-2.7.2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing graphene-1.10.8_1... [pkg-builder.dan.net.uk] | | `-- Installing py311-pygobject-3.50.0... [pkg-builder.dan.net.uk] | | | `-- Installing py311-cairo-1.28.0,1... [pkg-builder.dan.net.uk] | | | `-- Extracting py311-cairo-1.28.0,1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing pygobject-common-3.50.0... [pkg-builder.dan.net.uk] | | | `-- Extracting pygobject-common-3.50.0: .. done [pkg-builder.dan.net.uk] | | `-- Extracting py311-pygobject-3.50.0: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting graphene-1.10.8_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gstreamer1-plugins-bad-1.26.0... [pkg-builder.dan.net.uk] | | `-- Extracting gstreamer1-plugins-bad-1.26.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gstreamer1-plugins-gl-1.26.0... [pkg-builder.dan.net.uk] | | `-- Extracting gstreamer1-plugins-gl-1.26.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing harfbuzz-icu-10.3.0... [pkg-builder.dan.net.uk] | | `-- Extracting harfbuzz-icu-10.3.0: ..... done [pkg-builder.dan.net.uk] | | `-- Installing hyphen-2.8.8... [pkg-builder.dan.net.uk] | | `-- Extracting hyphen-2.8.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libavif-1.2.1... [pkg-builder.dan.net.uk] | | `-- Installing libyuv-0.0.1789_2... [pkg-builder.dan.net.uk] | | `-- Extracting libyuv-0.0.1789_2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing svt-av1-3.0.2... [pkg-builder.dan.net.uk] | | `-- Extracting svt-av1-3.0.2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libavif-1.2.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libjxl-0.11.1_1... [pkg-builder.dan.net.uk] | | `-- Installing highway-1.2.0... [pkg-builder.dan.net.uk] | | `-- Extracting highway-1.2.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openexr-3.3.3... [pkg-builder.dan.net.uk] | | | `-- Installing Imath-3.1.12... [pkg-builder.dan.net.uk] | | | `-- Extracting Imath-3.1.12: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting openexr-3.3.3: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libjxl-0.11.1_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libsecret-0.20.5_3... [pkg-builder.dan.net.uk] | | `-- Extracting libsecret-0.20.5_3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libsysinfo-0.0.3_3... [pkg-builder.dan.net.uk] | | `-- Extracting libsysinfo-0.0.3_3: ...... done [pkg-builder.dan.net.uk] | | `-- Installing libxslt-1.1.42... [pkg-builder.dan.net.uk] | | `-- Extracting libxslt-1.1.42: .......... done [pkg-builder.dan.net.uk] | | `-- Installing mesa-libs-24.1.7_1... [pkg-builder.dan.net.uk] | | `-- Installing libxshmfence-1.3.2... [pkg-builder.dan.net.uk] | | `-- Extracting libxshmfence-1.3.2: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting mesa-libs-24.1.7_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing woff2-1.0.2_5... [pkg-builder.dan.net.uk] | | `-- Extracting woff2-1.0.2_5: .......... done [pkg-builder.dan.net.uk] | `-- Extracting webkit2-gtk_40-2.46.6: .......... done [pkg-builder.dan.net.uk] `-- Extracting wx30-gtk3-3.0.5.1_6: .......... done [pkg-builder.dan.net.uk] Extracting gnuplot-5.4.10_2: .......... 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 ==> 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 duktape-lib-2.7.0: -- ===> NOTICE: The duktape-lib port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from wayland-1.23.1: -- 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-1.8.1_2: -- If arrow keys don't work under X11 switch to legacy rules e.g., For sh/bash/ksh/zsh run and (optionally) add into ~/.profile: export XKB_DEFAULT_RULES=xorg For csh/tcsh run and (optionally) add into ~/.login: setenv XKB_DEFAULT_RULES xorg ===== Message from libimagequant-4.3.4_2: -- ===> NOTICE: The libimagequant port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from freeglut-3.2.1: -- Joystick support is untested and it is unknown if it works. Do not hesitate to contact x11@FreeBSD.org if this causes issues. ===== Message from libsoup-2.74.3: -- libsoup can use NTLM authentication if it is compiled with the SMB option. To use it, you must install a port that provides NTLM, like net/samba412 or net/samba413. ===== Message from libjxl-0.11.1_1: -- 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_6 depends on executable: gnuplot - found ===> Returning to build of canu-2.2_6 ===> canu-2.2_6 depends on file: /usr/local/openjdk21/bin/java - found ===> canu-2.2_6 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for canu-2.2_6 ===> 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=2025-05-07T14:14:56+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=fa53920e72' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for canu-2.2_6 ===> Building canu-2.2_6 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for canu-2.2_6 build of biology/canu | canu-2.2_6 ended at Wed May 7 15:23:51 BST 2025 build time: 00:08:55