------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=5.9 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 -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS=" -pipe -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=5.9 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=500908 OSVERSION=9999999 OSREL=5.9 _OSRELEASE=5.9-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_3.txz ===== Message from boost-libs-1.72.0_3: -- 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-6.2.20210213.txz Installing /packages/All/readline-8.1.0.txz Installing /packages/All/openssl-1.1.1j_1,1.txz Installing /packages/All/python37-3.7.9_1.txz ===== Message from python37-3.7.9_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/glib-2.66.7,1.txz No schema files found: doing nothing. Installing /packages/All/harfbuzz-2.7.4.txz Installing /packages/All/jbigkit-2.1_1.txz Installing /packages/All/jpeg-turbo-2.0.6.txz Installing /packages/All/tiff-4.2.0.txz Installing /packages/All/giflib-5.2.1.txz Installing /packages/All/webp-1.2.0.txz Installing /packages/All/libgd-2.3.1,1.txz Installing /packages/All/tex-kpathsea-6.2.1_2.txz Installing /packages/All/atk-2.36.0.txz Installing /packages/All/pixman-0.40.0_1.txz Installing /packages/All/libpthread-stubs-0.4.txz Installing /packages/All/libXau-1.0.9.txz Installing /packages/All/xorgproto-2020.1.txz Installing /packages/All/libXdmcp-1.1.3.txz Installing /packages/All/libxcb-1.14_1.txz Installing /packages/All/libX11-1.6.12,1.txz Installing /packages/All/libXext-1.3.4,1.txz Installing /packages/All/libXrender-0.9.10_2.txz Installing /packages/All/cairo-1.16.0_1,3.txz Installing /packages/All/shared-mime-info-2.0.txz Installing /packages/All/gdk-pixbuf2-2.40.0.txz Installing /packages/All/wayland-1.18.0.txz Installing /packages/All/liblz4-1.9.3,1.txz Installing /packages/All/zstd-1.4.8.txz Installing /packages/All/pciids-20210131.txz Installing /packages/All/libpciaccess-0.16.txz Installing /packages/All/libdrm-2.4.101.txz Installing /packages/All/libunwind-20201110.txz Installing /packages/All/libXfixes-5.0.3_2.txz Installing /packages/All/libXdamage-1.1.5.txz Installing /packages/All/libxshmfence-1.3.txz Installing /packages/All/libXxf86vm-1.1.4_3.txz Installing /packages/All/libXrandr-1.5.2.txz Installing /packages/All/mesa-libs-20.2.3.txz Installing /packages/All/libepoxy-1.5.4.txz Installing /packages/All/fribidi-1.0.10.txz Installing /packages/All/libICE-1.0.10,1.txz Installing /packages/All/libSM-1.2.3,1.txz Installing /packages/All/dbus-1.12.20_3.txz ===> 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-1.0.3.txz ===== Message from libxkbcommon-1.0.3: -- 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-3.6.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-3.61.txz ===== Message from ca_root_nss-3.61: -- 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/bash-5.1.4_1.txz Installing /packages/All/bash-completion-2.11,2.txz ===== Message from bash-completion-2.11,2: -- To enable the bash completion library, add the following to your .bashrc file: [[ $PS1 && -f /usr/local/share/bash-completion/bash_completion.sh ]] && \ source /usr/local/share/bash-completion/bash_completion.sh See /usr/local/share/doc/bash-completion/README.md for more information. Installing /packages/All/p11-kit-0.23.22.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-3.24.24.txz Installing /packages/All/adwaita-icon-theme-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/gtk3-3.24.24.txz Installing /packages/All/libedit-3.1.20191231,1.txz Installing /packages/All/lua53-5.3.6.txz Installing /packages/All/gnuplot-5.4.0.txz 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-2.7.6.txz Installing /packages/All/java-zoneinfo-2021.a.txz Installing /packages/All/libXt-1.2.1,1.txz Installing /packages/All/openjdk8-8.181.13_1.txz ===== Message from openjdk8-8.181.13_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 line in /etc/fstab: proc /proc procfs rw 0 0 ====================================================================== SUCCEEDED 00:01:06 ------------------------------------------------------------------------------- -- 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 => SHA256 Checksum OK for canu-2.1.tar.gz. Extracted Memory Use: 14.98M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- 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 00:00:00 ------------------------------------------------------------------------------- -- 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[1]: 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 -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 -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.o -c -MD -pipe -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/align-ssw-driver.o -c -MD -pipe -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/edlib.o -c -MD -pipe -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 -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 -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/strings.o -c -MD -pipe -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 -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/files.o -c -MD -pipe -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/files-compressed.o -c -MD -pipe -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/system.o -c -MD -pipe -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 c++ -o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStore.o -c -MD -pipe -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 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/ovStoreWriter.o -c -MD -pipe -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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-reverse.o -c -MD -pipe -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/gfa/gfa.o -c -MD -pipe -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/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -pipe -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/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -pipe -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/gfa/bed.o -c -MD -pipe -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -pipe -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 -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 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/tgTigDisplay/stores/tgTigDisplay.o -c -MD -pipe -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 -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 -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 -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 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; ^~~~~~~~ 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/meryl.o -c -MD -pipe -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 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCommandBuilder.C meryl/src/meryl/merylCommandBuilder.C:218:2: warning: #warning "-E not implemented." [-Wcpp] #warning "-E not implemented." ^~~~~~~ c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylCountArray.o -c -MD -pipe -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 -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 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-count.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countSimple.o -c -MD -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNOBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countSimple.C c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/meryl/meryl/src/meryl/merylOp-countThreads.o -c -MD -pipe -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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/edalign/overlapInCore/edalign.o -c -MD -pipe -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 c++ -o /construction/biology/canu/canu-2.1/src//build/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -pipe -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 -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 -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 -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 -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 -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 -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 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include 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/construction/biology/canu/canu-2.1/src//build/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -pipe -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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/construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/gfa/gfa.o /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/gfa/bed.o /usr/libexec/binutils234/elf/ar: creating /construction/biology/canu/canu-2.1/src//build/lib/libcanu.a a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/runtime.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/align-ssw.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/align-ssw-driver.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/edlib.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/files.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/files-buffered.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/files-compressed.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/files-memoryMapped.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/logging.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/strings.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/system.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/system-stackTrace.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/sequence.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/types.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-exact.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-files.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-histogram.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-reader.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-block.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-stream.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/kmers.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/bits.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/hexDump.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/md5.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/correction/computeGlobalScore.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/correction/falconConsensus.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqCache.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqLibrary.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqReadData.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqReadDataWriter.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqStore.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqStoreBlob.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqStoreConstructor.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/sqStoreInfo.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovOverlap.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStore.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStoreWriter.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStoreFilter.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStoreFile.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/ovStoreHistogram.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/tgStore.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/tgTig.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/libsnappy/snappy.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/stores/objectStore.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/gfa/gfa.o a - /construction/biology/canu/canu-2.1/src//build/obj/lib/libcanu.a/gfa/bed.o c++ -o /construction/biology/canu/canu-2.1/src//build/bin/dumpBlob -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu c++ -o /construction/biology/canu/canu-2.1/src//build/bin/ovStoreBuild -L/construction/biology/canu/canu-2.1/src//build/lib /construction/biology/canu/canu-2.1/src//build/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu /construction/biology/canu/canu-2.1/src//build/lib/libcanu.a(runtime.o):runtime.C:function AS_configure(int, char**): error: undefined reference to 'omp_set_num_threads' /construction/biology/canu/canu-2.1/src//build/lib/libcanu.a(runtime.o):runtime.C:function AS_configure(int, char**): error:collect2: error: ld returned 1 exit status undefined reference to 'omp_set_num_threads' /construction/biology/canu/canu-gmake[1]: *** [Makefile:754: /construction/biology/canu/canu-2.1/src//build/bin/dumpBlob] Error 1 gmake[1]: *** Waiting for unfinished jobs.... 2.1/src//build/lib/libcanu.a(files-compressed.o):files-compressed.C:function compressedFileWriter::compressedFileWriter(char const*, int): error: undefined reference to 'omp_get_max_threads' collect2: error: ld returned 1 exit status gmake[1]: *** [Makefile:754: /construction/biology/canu/canu-2.1/src//build/bin/ovStoreBuild] Error 1 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; ^~~~~~~~ gmake[1]: Leaving directory '/construction/biology/canu/canu-2.1/src' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /xports/biology/canu FAILED 00:00:42