------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/canu XDG_CONFIG_HOME=/construction/biology/canu HOME=/construction/biology/canu TMPDIR="/tmp" PATH=/construction/biology/canu/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- DESTDIR=/construction/biology/canu/canu-2.1/src CANU_BUILD_ENV=ports PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/canu XDG_CONFIG_HOME=/construction/biology/canu HOME=/construction/biology/canu TMPDIR="/tmp" PATH=/construction/biology/canu/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fopenmp " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS=" -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/canu/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 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/5.32 PROFILE="@comment " DOCSDIR="share/doc/canu" EXAMPLESDIR="share/examples/canu" DATADIR="share/canu" WWWDIR="www/canu" ETCDIR="etc/canu" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="1.8+" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/canu DOCSDIR=/usr/local/share/doc/canu EXAMPLESDIR=/usr/local/share/examples/canu WWWDIR=/usr/local/www/canu ETCDIR=/usr/local/etc/canu SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/perl5-5.32.1_1.txz Installing /packages/All/icu-68.2,1.txz Installing /packages/All/boost-libs-1.72.0_4.txz ===== Message from boost-libs-1.72.0_4: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/png-1.6.37_1.txz Installing /packages/All/freetype2-2.10.4.txz ===== Message from freetype2-2.10.4: -- 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/site/index.html, if documentation was installed). Installing /packages/All/expat-2.2.10.txz Installing /packages/All/fontconfig-2.13.93,1.txz Installing /packages/All/graphite2-1.3.14.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/pcre-8.44.txz Installing /packages/All/libxml2-2.9.10_3.txz Installing /packages/All/libiconv-1.16.txz Installing /packages/All/ncurses-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. Installing /packages/All/xkeyboard-config-2.31.txz Installing /packages/All/libxkbcommon-1.1.0.txz ===== Message from libxkbcommon-1.1.0: -- 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 Installing /packages/All/libXi-1.7.10,1.txz Installing /packages/All/libXtst-1.2.3_2.txz Installing /packages/All/at-spi2-core-2.36.0.txz Installing /packages/All/at-spi2-atk-2.34.2.txz Installing /packages/All/libdaemon-0.14_1.txz Installing /packages/All/dbus-glib-0.110.txz Installing /packages/All/gdbm-1.19.txz Installing /packages/All/libevent-2.1.12.txz Installing /packages/All/gnome_subr-1.0.txz Installing /packages/All/avahi-app-0.8.txz ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. Installing /packages/All/gmp-6.2.1.txz Installing /packages/All/nettle-3.7.2_1.txz Installing /packages/All/libtasn1-4.16.0_1.txz Installing /packages/All/libunistring-0.9.10_1.txz Installing /packages/All/libidn2-2.3.0_1.txz Installing /packages/All/ca_root_nss-3.63.txz ===== Message from ca_root_nss-3.63: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/p11-kit-0.23.22_1.txz Installing /packages/All/tpm-emulator-0.7.4_2.txz ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. Installing /packages/All/trousers-0.3.14_3.txz ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. ===== Message from trousers-0.3.14_3: -- To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Installing /packages/All/gnutls-3.6.15.txz Installing /packages/All/libpaper-1.1.24.4.txz Installing /packages/All/cups-2.3.3op2.txz ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. Installing /packages/All/libgsf-1.14.47_1.txz Installing /packages/All/libfontenc-1.1.4.txz Installing /packages/All/mkfontscale-1.2.1.txz Installing /packages/All/font-bh-ttf-1.0.3_4.txz Installing /packages/All/font-misc-meltho-1.0.3_4.txz Installing /packages/All/font-misc-ethiopic-1.0.4.txz Installing /packages/All/encodings-1.0.5,1.txz Installing /packages/All/dejavu-2.37_1.txz ===== Message from dejavu-2.37_1: -- 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. Installing /packages/All/xorg-fonts-truetype-7.7_1.txz Installing /packages/All/libXft-2.3.3.txz Installing /packages/All/pango-1.42.4_5.txz Installing /packages/All/hicolor-icon-theme-0.17.txz Installing /packages/All/gtk-update-icon-cache-3.24.26.txz Installing /packages/All/adwaita-icon-theme-3.38.0.txz Installing /packages/All/gsettings-desktop-schemas-3.38.0.txz Installing /packages/All/wayland-protocols-1.20.txz Installing /packages/All/libcroco-0.6.13.txz Installing /packages/All/librsvg2-2.40.21.txz Installing /packages/All/libXcomposite-0.4.5,1.txz Installing /packages/All/libXcursor-1.2.0.txz Installing /packages/All/libXinerama-1.1.4_2,1.txz Installing /packages/All/gtk3-3.24.27.txz Installing /packages/All/libedit-3.1.20210216,1.txz Installing /packages/All/lua53-5.3.6.txz Installing /packages/All/gnuplot-5.4.1.txz Installing /packages/All/libinotify-20180201_2.txz ===== Message from libinotify-20180201_2: -- Libinotify functionality on FreeBSD is missing support for - detecting a file being moved into or out of a directory within the same filesystem - certain modifications to a symbolic link (rather than the file it points to.) in addition to the known limitations on all platforms using kqueue(2) where various open and close notifications are unimplemented. This means the following regression tests will fail: Directory notifications: IN_MOVED_FROM IN_MOVED_TO Open/close notifications: IN_OPEN IN_CLOSE_NOWRITE IN_CLOSE_WRITE Symbolic Link notifications: IN_DONT_FOLLOW IN_ATTRIB IN_MOVE_SELF IN_DELETE_SELF Kernel patches to address the missing directory and symbolic link notifications are available from: https://github.com/libinotify-kqueue/libinotify-kqueue/tree/master/patches 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. Installing /packages/All/alsa-lib-1.1.2_2.txz ===== Message from alsa-lib-1.1.2_2: -- ===> NOTICE: The alsa-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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/javavmwrapper-2.7.7.txz Installing /packages/All/java-zoneinfo-2021.a.txz Installing /packages/All/libXt-1.2.1,1.txz Installing /packages/All/openjdk8-8.282.08.1.txz ===== Message from openjdk8-8.282.08.1: -- This OpenJDK implementation requires procfs(5) mounted on /proc. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 SUCCEEDED 00:01:40 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> canu-2.1_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> canu-2.1_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by canu-2.1_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> canu-2.1_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by canu-2.1_1 for building => SHA256 Checksum OK for canu-2.1.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> canu-2.1_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by canu-2.1_1 for building ===> Extracting for canu-2.1_1 ===> canu-2.1_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by canu-2.1_1 for building => SHA256 Checksum OK for canu-2.1.tar.gz. Extracted Memory Use: 14.98M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for canu-2.1_1 ===> Applying ports patches for canu-2.1_1 from /xports/biology/canu/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> canu-2.1_1 depends on package: gmake>=4.3 - found ===> canu-2.1_1 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> canu-2.1_1 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> canu-2.1_1 depends on package: gmake>=4.3 - found ===> canu-2.1_1 depends on package: perl5>=5.32.r0<5.33 - found ===> canu-2.1_1 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Configuring for canu-2.1_1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for canu-2.1_1 gmake[2]: Entering directory '/construction/biology/canu/canu-2.1/src' /bin/sh: git: not found Building release v2.1 For 'DragonFly' '9999999' as 'amd64' into '/construction/biology/canu/canu-2.1/src//build/{bin,obj}'. Using '/usr/bin/c++' version '8.3'. Using user-supplied CXXFLAGS ' -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include '. c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/runtime.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/runtime.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/align-ssw-driver.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/align-ssw-driver.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/align-ssw.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/align-ssw.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/files.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/edlib.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/edlib.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/files-buffered.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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 /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/files-memoryMapped.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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 /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/files-compressed.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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 /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/strings.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/strings.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/logging.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/logging.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/system.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/system.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/system-stackTrace.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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 /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/sequence.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sequence.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/types.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/types.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-exact.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-exact.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-files.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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 /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-histogram.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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 /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-reader.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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 /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-block.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer-block.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-stream.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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 /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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:52:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] #warning how to set prefix size for streaming operations? ^~~~~~~ c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/bits.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/hexDump.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/hexDump.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/md5.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/md5.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/mt19937ar.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/speedCounter.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sweatShop.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqCache.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqStore.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C stores/ovOverlap.C:201:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING ^~~~~~~ c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStore.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C stores/ovStoreWriter.C:33:2: warning: #warning not failing if a valid store [-Wcpp] #warning not failing if a valid store ^~~~~~~ c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/tgStore.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/tgTig.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -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 /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/objectStore.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/objectStore.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/gfa/gfa.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/gfa/bed.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/dumpBlob.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/ovStoreBuild.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/ovStoreConfig.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/ovStoreBucketizer.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/ovStoreSorter.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/ovStoreIndexer.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/ovStoreDump.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/ovStoreStats.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/sqStoreCreate.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Iseqrequester/src/seqrequester stores/sqStoreDumpMetaData.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/sqStoreDumpMetaData/seqrequester/src/seqrequester/summarize.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Iseqrequester/src/seqrequester seqrequester/src/seqrequester/summarize.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/tgStoreCompress.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/tgStoreDump.C stores/tgStoreDump.C:643:2: warning: #warning replace this with genericStatistics [-Wcpp] #warning replace this with genericStatistics ^~~~~~~ c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/tgTigSizeAnalysis.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/tgStoreLoad.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/tgTigDisplay.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/loadCorrectedReads.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/loadTrimmedReads.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/loadErates/stores/loadErates.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility stores/loadErates.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/meryl.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/meryl.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylCommandBuilder.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCommandBuilder.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylCountArray.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCountArray.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylInput.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylInput.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-count.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-count.C meryl/src/meryl/merylCommandBuilder.C:218:2: warning: #warning "-E not implemented." [-Wcpp] #warning "-E not implemented." ^~~~~~~ In file included from utgcns/libboost/boost/scoped_ptr.hpp:14, from utgcns/libboost/boost/graph/adjacency_list.hpp:31, from utgcns/libpbutgcns/AlnGraphBoost.C:59: utgcns/libboost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.C:59: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countSimple.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countSimple.C In file included from utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:28, from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.C:59: utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.C:59: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.C:59: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.C:59: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.C:59: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.C:59: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.C:59: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.C:59: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.C:59: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.C:59: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.C:59: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.C:59: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.C:59: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.C:59: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countThreads.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countThreads.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-histogram.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-histogram.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-nextMer.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-nextMer.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylOp.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/edalign/overlapInCore/edalign.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C overlapInCore/overlapPair.C:463:2: warning: #warning do we need to check for contained too? [-Wcpp] #warning do we need to check for contained too? ^~~~~~~ c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Imhap/liboverlap mhap/mhapConvert.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Iminimap/liboverlap minimap/mmapConvert.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores correction/filterCorrectionOverlaps.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Iutgcns correction/generateCorrectionLayouts.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores correction/filterCorrectionLayouts.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/falconsense/correction/falconsense.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Iutgcns correction/falconsense.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/falconsense/utgcns/stashContains.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -Iutgcns haplotyping/splitHaplotype.C c++ -o 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-Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/bogart.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/bogart.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_AssemblyGraph.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_BestOverlapGraph.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_ChunkGraph.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_DetectSpurs.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Instrumentation.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_FindCircular.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_FindCircular.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Logging.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_MarkRepeatReads.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_MergeOrphans.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_OptimizePositions.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Outputs.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_OverlapCache.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceContains.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_PopulateUnitig.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_PromoteToSingleton.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_ReadInfo.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_SetParentAndHang.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitDiscontinuous.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_SplitTig_AtReadEnds.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitTig_AtReadEnds.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_TigVector.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_AddRead.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/layoutReads.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/layoutReads.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Instrumentation.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Instrumentation.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Logging.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Logging.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_OptimizePositions.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_OptimizePositions.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Outputs.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Outputs.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_OverlapCache.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_OverlapCache.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceContains.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceContains.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_ReadInfo.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_ReadInfo.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_SetParentAndHang.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_SetParentAndHang.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_TigVector.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_TigVector.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_AddRead.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_AddRead.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogus/bogus/bogus.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogus/bogus.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogus/bogus/bogusUtil.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores bogus/bogusUtil.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/utgcns/utgcns/utgcns.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/utgcns/utgcns/stashContains.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -pipe -fopenmp -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -I/construction/biology/canu/canu-2.1/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C cp -pf pipelines/canu.pl /construction/biology/canu/canu-2.1/src//build/bin/canu cp -pf pipelines/canu-time.pl /construction/biology/canu/canu-2.1/src//build/bin/canu-time cp -pf pipelines/draw-tig.pl /construction/biology/canu/canu-2.1/src//build/bin/draw-tig cp -pf mhap/mhap-2.1.3.jar /construction/biology/canu/canu-2.1/src//build/share/java/classes/mhap-2.1.3.jar cp -pf pipelines/canu/Consensus.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/CorrectReads.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/HaplotypeReads.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Configure.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Defaults.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Execution.pm 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pipelines/canu/Output.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapBasedTrimming.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapErrorAdjustment.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapInCore.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMhap.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMMap.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapStore.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Report.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ cp -pf pipelines/canu/Unitig.pm /construction/biology/canu/canu-2.1/src//build/lib/site_perl/canu/ ar rv 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-L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /construction/biology/canu/canu-2.1/src//build/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/filterCorrectionLayouts -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/falconsense -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/falconsense/correction/falconsense.o /construction/biology/canu/canu-2.1/src//build/obj/bin/falconsense/utgcns/stashContains.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/errorEstimate -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/splitHaplotype -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/trimReads -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /construction/biology/canu/canu-2.1/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /construction/biology/canu/canu-2.1/src//build/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/splitReads -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /construction/biology/canu/canu-2.1/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /construction/biology/canu/canu-2.1/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /construction/biology/canu/canu-2.1/src//build/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /construction/biology/canu/canu-2.1/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /construction/biology/canu/canu-2.1/src//build/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/mergeRanges -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/overlapAlign -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapAlign/overlapAlign/trimRead.o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /construction/biology/canu/canu-2.1/src//build/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/findErrors -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /construction/biology/canu/canu-2.1/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /construction/biology/canu/canu-2.1/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /construction/biology/canu/canu-2.1/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /construction/biology/canu/canu-2.1/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /construction/biology/canu/canu-2.1/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /construction/biology/canu/canu-2.1/src//build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/fixErrors -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/fixErrors/overlapErrorAdjustment/fixErrors.o /construction/biology/canu/canu-2.1/src//build/obj/bin/fixErrors/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/findErrors-Dump -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/correctOverlaps -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /construction/biology/canu/canu-2.1/src//build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/bogart -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/bogart.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_FindCircular.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Logging.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Outputs.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_SplitTig_AtReadEnds.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_TigVector.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/layoutReads -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/layoutReads.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Instrumentation.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Logging.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_OptimizePositions.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Outputs.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_OverlapCache.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceContains.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_PlaceReadUsingOverlaps.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_ReadInfo.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_SetParentAndHang.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_TigVector.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_AddRead.o /construction/biology/canu/canu-2.1/src//build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/bogus -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/bogus/bogus/bogus.o /construction/biology/canu/canu-2.1/src//build/obj/bin/bogus/bogus/bogusUtil.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/alignGFA -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/alignGFA/gfa/alignGFA.o -lcanu In file included from utgcns/libboost/boost/scoped_ptr.hpp:14, from utgcns/libboost/boost/graph/adjacency_list.hpp:31, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: utgcns/libboost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr p ) BOOST_NOEXCEPT : px( p.release() ) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:28, from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from utgcns/libboost/boost/shared_ptr.hpp:17, from utgcns/libboost/boost/property_map/vector_property_map.hpp:14, from utgcns/libboost/boost/property_map/property_map.hpp:600, from utgcns/libboost/boost/graph/adjacency_list.hpp:36, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: utgcns/libboost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14, from utgcns/libboost/boost/unordered/unordered_set.hpp:17, from utgcns/libboost/boost/unordered_set.hpp:17, from utgcns/libboost/boost/graph/adjacency_list.hpp:21, from utgcns/libpbutgcns/AlnGraphBoost.H:57, from utgcns/unitigConsensus.C:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ c++ -o /construction/biology/canu/canu-2.1/src//build/bin/utgcns -fopenmp -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/utgcns/utgcns/utgcns.o /construction/biology/canu/canu-2.1/src//build/obj/bin/utgcns/utgcns/stashContains.o /construction/biology/canu/canu-2.1/src//build/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu Success! canu installed in /construction/biology/canu/canu-2.1/src//build/bin/canu gmake[2]: Leaving directory '/construction/biology/canu/canu-2.1/src' /bin/mv /construction/biology/canu/canu-2.1/src/build/lib/site_perl /construction/biology/canu/canu-2.1/src/build/lib/perl5 SUCCEEDED 00:00:36 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> canu-2.1_1 depends on executable: gnuplot - found ===> canu-2.1_1 depends on file: /usr/local/openjdk8/bin/java - found ===> canu-2.1_1 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for canu-2.1_1 ===> canu-2.1_1 depends on executable: gnuplot - found ===> canu-2.1_1 depends on file: /usr/local/openjdk8/bin/java - found ===> canu-2.1_1 depends on package: perl5>=5.32.r0<5.33 - found ===> Generating temporary packing list (cd /construction/biology/canu/canu-2.1/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 /construction/biology/canu/stage/usr/local) (cd /construction/biology/canu/canu-2.1/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" /construction/biology/canu/stage/usr/local) ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for canu-2.1_1 file sizes/checksums [77]: 0% file sizes/checksums [77]: 100% packing files [77]: 0% packing files [77]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:06 TOTAL TIME 00:02:27