=> Building biology/abyss Started : Thursday, 7 MAR 2019 at 18:07:09 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for abyss-2.1.5: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/abyss XDG_CONFIG_HOME=/construction/biology/abyss HOME=/construction/biology/abyss TMPDIR="/tmp" PATH=/construction/biology/abyss/.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" CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --without-sparsehash --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/abyss XDG_CONFIG_HOME=/construction/biology/abyss HOME=/construction/biology/abyss TMPDIR="/tmp" PATH=/construction/biology/abyss/.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=" -L/usr/local/lib " LIBS="" 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/abyss/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/abyss" EXAMPLESDIR="share/examples/abyss" DATADIR="share/abyss" WWWDIR="www/abyss" ETCDIR="etc/abyss" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/abyss DOCSDIR=/usr/local/share/doc/abyss EXAMPLESDIR=/usr/local/share/examples/abyss WWWDIR=/usr/local/www/abyss ETCDIR=/usr/local/etc/abyss -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> abyss-2.1.5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> abyss-2.1.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of abyss-2.1.5 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user => abyss-2.1.5.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.5/abyss-2.1.5.tar.gz abyss-2.1.5.tar.gz 1173 kB 0 Bps ===> Fetching all distfiles required by abyss-2.1.5 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.1.5 for building => SHA256 Checksum OK for abyss-2.1.5.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.1.5 for building ===> Extracting for abyss-2.1.5 => SHA256 Checksum OK for abyss-2.1.5.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for abyss-2.1.5 ===> Applying ports patches for abyss-2.1.5 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> abyss-2.1.5 depends on file: /usr/local/include/boost/version.hpp - not found ===> Installing existing package /packages/All/boost-libs-1.69.0_1.txz Installing boost-libs-1.69.0_1... `-- Installing icu-63.1_1,1... `-- Extracting icu-63.1_1,1: .......... done Extracting boost-libs-1.69.0_1: .......... done Message from boost-libs-1.69.0_1: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> abyss-2.1.5 depends on file: /usr/local/include/boost/version.hpp - found ===> Returning to build of abyss-2.1.5 ===> abyss-2.1.5 depends on executable: ghc - not found ===> Installing existing package /packages/All/ghc-8.6.3.txz Installing ghc-8.6.3... `-- Installing gmp-6.1.2_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gmp-6.1.2_1: .......... done `-- Installing libffi-3.2.1_3... `-- Extracting libffi-3.2.1_3: .......... done `-- Installing libiconv-1.14_11... `-- Extracting libiconv-1.14_11: .......... done `-- Installing ncurses-6.1.20190112... `-- Extracting ncurses-6.1.20190112: .......... done Extracting ghc-8.6.3: .......... done ===> abyss-2.1.5 depends on executable: ghc - found ===> Returning to build of abyss-2.1.5 ===> abyss-2.1.5 depends on executable: pandoc - not found ===> Installing existing package /packages/All/hs-pandoc-2.5_2.txz Installing hs-pandoc-2.5_2... `-- Installing texlive-texmf-20150523_4... | `-- Installing python27-2.7.15... | | `-- Installing expat-2.2.6_1... | | `-- Extracting expat-2.2.6_1: .......... done | | `-- Installing gettext-runtime-0.19.8.1_2... | | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done | | `-- Installing libressl-2.8.3... | | `-- Extracting libressl-2.8.3: .......... done | | `-- Installing readline-7.0.5... | | `-- Extracting readline-7.0.5: .......... done | `-- Extracting python27-2.7.15: .......... done | `-- Installing texlive-base-20150521_32... | | `-- Installing freetype2-2.9.1... | | `-- Extracting freetype2-2.9.1: .......... done | | `-- Installing ghostscript9-agpl-base-9.26... | | `-- Installing cups-2.2.10... | | | `-- Installing avahi-app-0.7_2... | | | `-- Installing dbus-1.12.12... | | | | `-- Installing libICE-1.0.9_3,1... | | | | `-- Extracting libICE-1.0.9_3,1: .......... done | | | | `-- Installing libSM-1.2.3,1... | | | | `-- Extracting libSM-1.2.3,1: .......... done | | | | `-- Installing libX11-1.6.7,1... | | | | `-- Installing libXau-1.0.8_5... | | | | `-- Extracting libXau-1.0.8_5: .......... done | | | | `-- Installing libXdmcp-1.1.2_2... | | | | | `-- Installing xorgproto-2018.4... | | | | | `-- Extracting xorgproto-2018.4: .......... done | | | | `-- Extracting libXdmcp-1.1.2_2: ......... done | | | | `-- Installing libxcb-1.13.1... | | | | | `-- Installing libpthread-stubs-0.4... | | | | | `-- Extracting libpthread-stubs-0.4: .... done | | | | | `-- Installing libxml2-2.9.8... | | | | | `-- Extracting libxml2-2.9.8: .......... done | | | | `-- Extracting libxcb-1.13.1: .......... done | | | | `-- Extracting libX11-1.6.7,1: .......... done ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. | | | `-- Extracting dbus-1.12.12: ......... done | | | `-- Installing dbus-glib-0.110... | | | | `-- Installing glib-2.56.3_3,1... | | | | `-- Installing pcre-8.42_1... | | | | `-- Extracting pcre-8.42_1: .......... done | | | | `-- Extracting glib-2.56.3_3,1: .......... done No schema files found: doing nothing. | | | `-- Extracting dbus-glib-0.110: .......... done | | | `-- Installing gdbm-1.18.1... | | | `-- Extracting gdbm-1.18.1: .......... done | | | `-- Installing gnome_subr-1.0... | | | `-- Extracting gnome_subr-1.0: .... done | | | `-- Installing gobject-introspection-1.56.1,1... | | | | `-- Installing python36-3.6.8... | | | | `-- Extracting python36-3.6.8: .......... done | | | `-- Extracting gobject-introspection-1.56.1,1: .......... done | | | `-- Installing libdaemon-0.14_1... | | | `-- Extracting libdaemon-0.14_1: .......... done ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. | | | `-- Extracting avahi-app-0.7_2: .......... done | | | `-- Installing gnutls-3.6.6_2... | | | `-- Installing ca_root_nss-3.42.1... | | | `-- Extracting ca_root_nss-3.42.1: ........ done | | | `-- Installing libidn2-2.1.1... | | | | `-- Installing libunistring-0.9.10_1... | | | | `-- Extracting libunistring-0.9.10_1: .......... done | | | `-- Extracting libidn2-2.1.1: .......... done | | | `-- Installing libtasn1-4.13_1... | | | `-- Extracting libtasn1-4.13_1: .......... done | | | `-- Installing nettle-3.4.1_1... | | | `-- Extracting nettle-3.4.1_1: .......... done | | | `-- Installing p11-kit-0.23.15... | | | `-- Extracting p11-kit-0.23.15: .......... done | | | `-- Installing trousers-0.3.14_2... | | | | `-- Installing tpm-emulator-0.7.4_2... ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | | | `-- Extracting tpm-emulator-0.7.4_2: ......... done ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | | `-- Extracting trousers-0.3.14_2: .......... done | | | `-- Extracting gnutls-3.6.6_2: .......... done | | | `-- Installing libpaper-1.1.24.4... | | | `-- Extracting libpaper-1.1.24.4: .......... done ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. | | `-- Extracting cups-2.2.10: .......... done | | `-- Installing fontconfig-2.12.6,1... | | `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded | | `-- Installing jbig2dec-0.15... | | | `-- Installing png-1.6.36... | | | `-- Extracting png-1.6.36: .......... done | | `-- Extracting jbig2dec-0.15: .......... done | | `-- Installing jpeg-turbo-2.0.2... | | `-- Extracting jpeg-turbo-2.0.2: .......... done | | `-- Installing libidn-1.34_1... | | `-- Extracting libidn-1.34_1: .......... done | | `-- Installing poppler-data-0.4.9... | | `-- Extracting poppler-data-0.4.9: .......... done | | `-- Installing tiff-4.0.10... | | | `-- Installing jbigkit-2.1_1... | | | `-- Extracting jbigkit-2.1_1: .......... done | | `-- Extracting tiff-4.0.10: .......... done | | `-- Extracting ghostscript9-agpl-base-9.26: .......... done | | `-- Installing graphite2-1.3.13... | | `-- Extracting graphite2-1.3.13: .......... done | | `-- Installing harfbuzz-2.3.1... | | `-- Installing cairo-1.15.12,2... | | | `-- Installing libXext-1.3.3_3,1... | | | `-- Extracting libXext-1.3.3_3,1: .......... done | | | `-- Installing libXrender-0.9.10_2... | | | `-- Extracting libXrender-0.9.10_2: .......... done | | | `-- Installing mesa-libs-18.3.2... | | | `-- Installing libXdamage-1.1.4_5... | | | | `-- Installing libXfixes-5.0.3_2... | | | | `-- Extracting libXfixes-5.0.3_2: .......... done | | | `-- Extracting libXdamage-1.1.4_5: ......... done | | | `-- Installing libXrandr-1.5.1_2... | | | `-- Extracting libXrandr-1.5.1_2: .......... done | | | `-- Installing libXxf86vm-1.1.4_3... | | | `-- Extracting libXxf86vm-1.1.4_3: .......... done | | | `-- Installing libdrm-2.4.96,1... | | | | `-- Installing libpciaccess-0.13.5... | | | | `-- Installing pciids-20190213... | | | | `-- Extracting pciids-20190213: ..... done | | | | `-- Extracting libpciaccess-0.13.5: ......... done | | | `-- Extracting libdrm-2.4.96,1: .......... done | | | `-- Installing libelf-0.8.13_3... | | | `-- Extracting libelf-0.8.13_3: .......... done | | | `-- Installing libxshmfence-1.2_4... | | | `-- Extracting libxshmfence-1.2_4: ......... done | | | `-- Installing wayland-1.16.0... | | | `-- Extracting wayland-1.16.0: .......... done | | | `-- Extracting mesa-libs-18.3.2: .......... done | | | `-- Installing pixman-0.34.0_1... | | | `-- Extracting pixman-0.34.0_1: .......... done | | | `-- Installing xcb-util-renderutil-0.3.9_1... | | | `-- Installing xcb-util-0.4.0_2,1... | | | `-- Extracting xcb-util-0.4.0_2,1: .......... done | | | `-- Extracting xcb-util-renderutil-0.3.9_1: ......... done | | `-- Extracting cairo-1.15.12,2: .......... done | | `-- Extracting harfbuzz-2.3.1: .......... done | | `-- Installing harfbuzz-icu-2.3.1... | | `-- Extracting harfbuzz-icu-2.3.1: ..... done | | `-- Installing libgd-2.2.5_1,1... | | `-- Installing webp-1.0.2... | | | `-- Installing giflib-5.1.4... | | | `-- Extracting giflib-5.1.4: .......... done | | `-- Extracting webp-1.0.2: .......... done | | `-- Extracting libgd-2.2.5_1,1: .......... done | | `-- Installing libpotrace-1.12... | | `-- Extracting libpotrace-1.12: ........ done | | `-- Installing perl5-5.28.1... | | `-- Extracting perl5-5.28.1: .......... done | | `-- Installing poppler-0.74.0... | | `-- Installing lcms2-2.9... | | `-- Extracting lcms2-2.9: .......... done | | `-- Installing nspr-4.20... | | `-- Extracting nspr-4.20: .......... done | | `-- Installing nss-3.42.1... | | | `-- Installing sqlite3-3.27.1... | | | `-- Extracting sqlite3-3.27.1: .......... done | | `-- Extracting nss-3.42.1: .......... done | | `-- Installing openjpeg-2.3.0_3... | | `-- Extracting openjpeg-2.3.0_3: .......... done | | `-- Extracting poppler-0.74.0: .......... done | | `-- Installing psutils-1.17_5... | | `-- Extracting psutils-1.17_5: .......... done | | `-- Installing t1lib-5.1.2_4,1... | | `-- Installing libXaw-1.0.13_2,2... | | | `-- Installing libXmu-1.1.2_5,1... | | | `-- Installing libXt-1.1.5_2,1... | | | `-- Extracting libXt-1.1.5_2,1: .......... done | | | `-- Extracting libXmu-1.1.2_5,1: .......... done | | | `-- Installing libXp-1.0.3_2,1... | | | `-- Extracting libXp-1.0.3_2,1: .......... done | | | `-- Installing libXpm-3.5.12_2... | | | `-- Extracting libXpm-3.5.12_2: .......... done | | `-- Extracting libXaw-1.0.13_2,2: .......... done | | `-- Extracting t1lib-5.1.2_4,1: .......... done | | `-- Installing teckit-2.5.7... | | `-- Extracting teckit-2.5.7: .......... done | | `-- Installing tex-kpathsea-6.2.1_2... | | `-- Extracting tex-kpathsea-6.2.1_2: .......... done | | `-- Installing tex-ptexenc-1.3.3_2... | | `-- Extracting tex-ptexenc-1.3.3_2: .......... done | | `-- Installing tex-web2c-20150521_3... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | | `-- Installing openjpeg15-1.5.2_1... | | `-- Extracting openjpeg15-1.5.2_1: .......... done | | `-- Installing zziplib-0.13.69_1... | | `-- Extracting zziplib-0.13.69_1: .......... done | | `-- Extracting tex-web2c-20150521_3: .......... done | | `-- Installing texlive-tlmgr-20150523_2... | | `-- Extracting texlive-tlmgr-20150523_2: ......... done | | `-- Installing xpdfopen-0.86... | | `-- Extracting xpdfopen-0.86: .... done | `-- Extracting texlive-base-20150521_32: .......... done mktexlsr: Updating /usr/local/share/texmf/ls-R... mktexlsr: Updating /usr/local/share/texmf-config/ls-R... mktexlsr: Updating /usr/local/share/texmf-dist/ls-R... mktexlsr: Updating /usr/local/share/texmf-local/ls-R... mktexlsr: Updating /usr/local/share/texmf-var/ls-R... mktexlsr: Done. `-- Extracting texlive-texmf-20150523_4: .......... done mktexlsr: Updating /usr/local/share/texmf/ls-R... mktexlsr: Done. mktexlsr: Updating /usr/local/share/texmf-dist/ls-R... mktexlsr: Done. Extracting hs-pandoc-2.5_2: .......... done Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from freetype2-2.9.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from python36-3.6.8: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Message from ca_root_nss-3.42.1: ********************************* WARNING ********************************* 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. *********************************** NOTE ********************************** 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 *************************************************************************** Message from trousers-0.3.14_2: 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 Message from ghostscript9-agpl-base-9.26: This package installs a script named dvipdf that depends on dvips. If you want to use this script you need to install print/tex-dvipsk. Message from perl5-5.28.1: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Message from zziplib-0.13.69_1: ===> NOTICE: The zziplib 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 ===> abyss-2.1.5 depends on executable: pandoc - found ===> Returning to build of abyss-2.1.5 ===> abyss-2.1.5 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... Extracting gmake-4.2.1_3: .......... done ===> abyss-2.1.5 depends on executable: gmake - found ===> Returning to build of abyss-2.1.5 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> abyss-2.1.5 depends on shared library: libffi.so - found (/usr/local/lib/libffi.so) ===> abyss-2.1.5 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so) ===> abyss-2.1.5 depends on shared library: libomp.so - not found ===> Installing existing package /packages/All/openmp-7.0.1.txz Installing openmp-7.0.1... Extracting openmp-7.0.1: .......... done ===> abyss-2.1.5 depends on shared library: libomp.so - found (/usr/local/lib/libomp.so) ===> Returning to build of abyss-2.1.5 ===> abyss-2.1.5 depends on shared library: libiconv.so - found (/usr/local/lib/libiconv.so) ===> abyss-2.1.5 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for abyss-2.1.5 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking for gawk... (cached) /usr/bin/awk checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by gmake... GNU checking dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking for ranlib... ranlib checking for ghc... ghc The Glorious Glasgow Haskell Compilation System, version 8.6.3 checking for pandoc... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for fcntl.h... (cached) yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for stddef.h... (cached) yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for sys/param.h... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... (cached) yes checking for mode_t... (cached) yes checking for pid_t... (cached) yes checking for size_t... (cached) yes checking for ssize_t... (cached) yes checking for int64_t... (cached) yes checking for uint8_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint64_t... (cached) yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... (cached) yes checking for gethostname... (cached) yes checking for getopt_long... yes checking for getpagesize... (cached) yes checking for memset... (cached) yes checking for strdup... (cached) yes checking for strerror... (cached) yes checking for strtoul... (cached) yes checking for vfork.h... (cached) no checking for fork... (cached) yes checking for vfork... (cached) yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... (cached) yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... no checking build system type... x86_64-portbld-dragonfly5.5 checking host system type... x86_64-portbld-dragonfly5.5 checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking mpi.h usability... no checking mpi.h presence... no checking for mpi.h... no checking for MPI_Init in -lmpi... no checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking how to run the C++ preprocessor... c++ -E checking functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... no checking google/sparse_hash_map presence... no checking for google/sparse_hash_map... no checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for c++ option to support OpenMP... -fopenmp configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Misc/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating lib/gtest-1.7.0/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating lib/bloomfilter/Makefile config.status: creating lib/nthash/Makefile config.status: creating config.h config.status: executing depfiles commands -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for abyss-2.1.5 gmake[1]: Entering directory '/construction/biology/abyss/abyss-2.1.5' gmake all-recursive gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5' Making all in bin gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/bin' cp ../bin/abyss-nompi ABYSS-P gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/bin' Making all in doc gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/doc' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/doc' Making all in Common gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Common' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-ContigID.o -MD -MP -MF .deps/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Fcontrol.o -MD -MP -MF .deps/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Histogram.o -MD -MP -MF .deps/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Kmer.o -MD -MP -MF .deps/libcommon_a-Kmer.Tpo -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Log.o -MD -MP -MF .deps/libcommon_a-Log.Tpo -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Options.o -MD -MP -MF .deps/libcommon_a-Options.Tpo -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp mv -f .deps/libcommon_a-Options.Tpo .deps/libcommon_a-Options.Po c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Sequence.o -MD -MP -MF .deps/libcommon_a-Sequence.Tpo -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp mv -f .deps/libcommon_a-Log.Tpo .deps/libcommon_a-Log.Po c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-SignalHandler.o -MD -MP -MF .deps/libcommon_a-SignalHandler.Tpo -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp mv -f .deps/libcommon_a-SignalHandler.Tpo .deps/libcommon_a-SignalHandler.Po c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Timer.o -MD -MP -MF .deps/libcommon_a-Timer.Tpo -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp mv -f .deps/libcommon_a-Sequence.Tpo .deps/libcommon_a-Sequence.Po c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Uncompress.o -MD -MP -MF .deps/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp mv -f .deps/libcommon_a-Histogram.Tpo .deps/libcommon_a-Histogram.Po c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-city.o -MD -MP -MF .deps/libcommon_a-city.Tpo -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc mv -f .deps/libcommon_a-ContigID.Tpo .deps/libcommon_a-ContigID.Po mv -f .deps/libcommon_a-Uncompress.Tpo .deps/libcommon_a-Uncompress.Po mv -f .deps/libcommon_a-city.Tpo .deps/libcommon_a-city.Po mv -f .deps/libcommon_a-Kmer.Tpo .deps/libcommon_a-Kmer.Po mv -f .deps/libcommon_a-Timer.Tpo .deps/libcommon_a-Timer.Po rm -f libcommon.a ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcommon.a gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Common' Making all in Graph gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Graph' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_gc-gc.o -MD -MP -MF .deps/abyss_gc-gc.Tpo -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_todot-todot.o -MD -MP -MF .deps/abyss_todot-todot.Tpo -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc mv -f .deps/abyss_gc-gc.Tpo .deps/abyss_gc-gc.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_todot-todot.Tpo .deps/abyss_todot-todot.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L. -L/usr/local/lib -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Graph' Making all in DataLayer gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DataLayer' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdatalayer_a-FastaReader.o -MD -MP -MF .deps/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdatalayer_a-FastaWriter.o -MD -MP -MF .deps/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fac-fac.o -MD -MP -MF .deps/abyss_fac-fac.Tpo -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_tofastq-abyss-tofastq.o -MD -MP -MF .deps/abyss_tofastq-abyss-tofastq.Tpo -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc mv -f .deps/libdatalayer_a-FastaWriter.Tpo .deps/libdatalayer_a-FastaWriter.Po mv -f .deps/abyss_tofastq-abyss-tofastq.Tpo .deps/abyss_tofastq-abyss-tofastq.Po mv -f .deps/abyss_fac-fac.Tpo .deps/abyss_fac-fac.Po mv -f .deps/libdatalayer_a-FastaReader.Tpo .deps/libdatalayer_a-FastaReader.Po rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DataLayer' Making all in DataBase gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DataBase' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdb_a-DB.o -MD -MP -MF .deps/libdb_a-DB.Tpo -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_db_csv-DB.o -MD -MP -MF .deps/abyss_db_csv-DB.Tpo -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_db_csv-db-csv.o -MD -MP -MF .deps/abyss_db_csv-db-csv.Tpo -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc mv -f .deps/abyss_db_csv-db-csv.Tpo .deps/abyss_db_csv-db-csv.Po mv -f .deps/libdb_a-DB.Tpo .deps/libdb_a-DB.Po rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a mv -f .deps/abyss_db_csv-DB.Tpo .deps/abyss_db_csv-DB.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DataBase' Making all in FMIndex gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/FMIndex' c++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libfmindex_a-bit_array.o -MD -MP -MF .deps/libfmindex_a-bit_array.Tpo -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_count-count.o -MD -MP -MF .deps/abyss_count-count.Tpo -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_dawg-abyss-dawg.o -MD -MP -MF .deps/abyss_dawg-abyss-dawg.Tpo -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc mv -f .deps/libfmindex_a-bit_array.Tpo .deps/libfmindex_a-bit_array.Po rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfmindex.a mv -f .deps/abyss_dawg-abyss-dawg.Tpo .deps/abyss_dawg-abyss-dawg.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_count-count.Tpo .deps/abyss_count-count.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/FMIndex' Making all in Assembly gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Assembly' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libassembly_a-AssemblyAlgorithms.o -MD -MP -MF .deps/libassembly_a-AssemblyAlgorithms.Tpo -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libassembly_a-Options.o -MD -MP -MF .deps/libassembly_a-Options.Tpo -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc mv -f .deps/libassembly_a-Options.Tpo .deps/libassembly_a-Options.Po mv -f .deps/libassembly_a-AssemblyAlgorithms.Tpo .deps/libassembly_a-AssemblyAlgorithms.Po rm -f libassembly.a ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libassembly.a gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Assembly' Making all in dialign gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/dialign' depbase=`echo alig.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT alig.o -MD -MP -MF $depbase.Tpo -c -o alig.o alig.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo assemble.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT assemble.o -MD -MP -MF $depbase.Tpo -c -o assemble.o assemble.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo diag.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT diag.o -MD -MP -MF $depbase.Tpo -c -o diag.o diag.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT io.o -MD -MP -MF $depbase.Tpo -c -o io.o io.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo orf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT orf.o -MD -MP -MF $depbase.Tpo -c -o orf.o orf.c &&\ mv -f $depbase.Tpo $depbase.Po assemble.c:40:20: warning: inline function 'align_diag' declared but never defined extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ^~~~~~~~~~ assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); ^~~~~~~~ assemble.c:25:39: warning: inline function 'find_diags_guided' declared but never defined extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function 'calc_weight' declared but never defined extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); ^~~~~~~~~~~~~~~~ depbase=`echo parameters.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT parameters.o -MD -MP -MF $depbase.Tpo -c -o parameters.o parameters.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo prob.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT prob.o -MD -MP -MF $depbase.Tpo -c -o prob.o prob.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo translate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT translate.o -MD -MP -MF $depbase.Tpo -c -o translate.o translate.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo museq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT museq.o -MD -MP -MF $depbase.Tpo -c -o museq.o museq.c &&\ mv -f $depbase.Tpo $depbase.Po museq.c: In function 'main': museq.c:168:2: warning: implicit declaration of function 'free_diag'; did you mean 'free_diag_col'? [-Wimplicit-function-declaration] free_diag(adcol.diags[i]); ^~~~~~~~~ free_diag_col museq.c:278:27: warning: implicit declaration of function 'free_alignment' [-Wimplicit-function-declaration] if(! para->FAST_MODE) free_alignment(algn); ^~~~~~~~~~~~~~ rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdialign.a cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -L/usr/local/lib -o dialign museq.o libdialign.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/dialign' Making all in Align gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Align' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-alignGlobal.o -MD -MP -MF .deps/libalign_a-alignGlobal.Tpo -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-dialign.o -MD -MP -MF .deps/libalign_a-dialign.Tpo -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-dna_diag_prob.o -MD -MP -MF .deps/libalign_a-dna_diag_prob.Tpo -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-smith_waterman.o -MD -MP -MF .deps/libalign_a-smith_waterman.Tpo -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_align-align.o -MD -MP -MF .deps/abyss_align-align.Tpo -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc mv -f .deps/libalign_a-dna_diag_prob.Tpo .deps/libalign_a-dna_diag_prob.Po c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_mergepairs-mergepairs.o -MD -MP -MF .deps/abyss_mergepairs-mergepairs.Tpo -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc mv -f .deps/libalign_a-alignGlobal.Tpo .deps/libalign_a-alignGlobal.Po mv -f .deps/libalign_a-dialign.Tpo .deps/libalign_a-dialign.Po mv -f .deps/libalign_a-smith_waterman.Tpo .deps/libalign_a-smith_waterman.Po rm -f libalign.a ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalign.a mv -f .deps/abyss_align-align.Tpo .deps/abyss_align-align.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_mergepairs-mergepairs.Tpo .deps/abyss_mergepairs-mergepairs.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Align' Making all in ABYSS gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/ABYSS' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ABYSS-abyss.o -MD -MP -MF .deps/ABYSS-abyss.Tpo -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc mv -f .deps/ABYSS-abyss.Tpo .deps/ABYSS-abyss.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/ABYSS' Making all in Bloom gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Bloom' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_bloom-bloom.o -MD -MP -MF .deps/abyss_bloom-bloom.Tpo -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc mv -f .deps/abyss_bloom-bloom.Tpo .deps/abyss_bloom-bloom.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Bloom' Making all in BloomDBG gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/BloomDBG' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_bloom_dbg-bloom-dbg.o -MD -MP -MF .deps/abyss_bloom_dbg-bloom-dbg.Tpo -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc mv -f .deps/abyss_bloom_dbg-bloom-dbg.Tpo .deps/abyss_bloom_dbg-bloom-dbg.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/BloomDBG' Making all in Konnector gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Konnector' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT konnector-konnector.o -MD -MP -MF .deps/konnector-konnector.Tpo -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc mv -f .deps/konnector-konnector.Tpo .deps/konnector-konnector.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Konnector' Making all in Consensus gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Consensus' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Consensus-Consensus.o -MD -MP -MF .deps/Consensus-Consensus.Tpo -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp mv -f .deps/Consensus-Consensus.Tpo .deps/Consensus-Consensus.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Consensus' Making all in DAssembler gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DAssembler' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DAssembler-DAssembler.o -MD -MP -MF .deps/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DAssembler-RotatedRead.o -MD -MP -MF .deps/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp mv -f .deps/DAssembler-RotatedRead.Tpo .deps/DAssembler-RotatedRead.Po mv -f .deps/DAssembler-DAssembler.Tpo .deps/DAssembler-DAssembler.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DAssembler' Making all in DistanceEst gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DistanceEst' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst-DistanceEst.o -MD -MP -MF .deps/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst-MLE.o -MD -MP -MF .deps/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst_ssq-DistanceEst.o -MD -MP -MF .deps/DistanceEst_ssq-DistanceEst.Tpo -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst_ssq-MLE.o -MD -MP -MF .deps/DistanceEst_ssq-MLE.Tpo -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp mv -f .deps/DistanceEst-MLE.Tpo .deps/DistanceEst-MLE.Po mv -f .deps/DistanceEst_ssq-MLE.Tpo .deps/DistanceEst_ssq-MLE.Po mv -f .deps/DistanceEst-DistanceEst.Tpo .deps/DistanceEst-DistanceEst.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm mv -f .deps/DistanceEst_ssq-DistanceEst.Tpo .deps/DistanceEst_ssq-DistanceEst.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DistanceEst' Making all in KAligner gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/KAligner' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT KAligner-KAligner.o -MD -MP -MF .deps/KAligner-KAligner.Tpo -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT KAligner-Aligner.o -MD -MP -MF .deps/KAligner-Aligner.Tpo -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp mv -f .deps/KAligner-KAligner.Tpo .deps/KAligner-KAligner.Po mv -f .deps/KAligner-Aligner.Tpo .deps/KAligner-Aligner.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/KAligner' Making all in Layout gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Layout' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_layout-layout.o -MD -MP -MF .deps/abyss_layout-layout.Tpo -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc mv -f .deps/abyss_layout-layout.Tpo .deps/abyss_layout-layout.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Layout' Making all in LogKmerCount gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/LogKmerCount' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT logcounter-logcounter.o -MD -MP -MF .deps/logcounter-logcounter.Tpo -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc mv -f .deps/logcounter-logcounter.Tpo .deps/logcounter-logcounter.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/LogKmerCount' Making all in Map gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Map' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_index-index.o -MD -MP -MF .deps/abyss_index-index.Tpo -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_map-map.o -MD -MP -MF .deps/abyss_map-map.Tpo -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_map_ssq-map.o -MD -MP -MF .deps/abyss_map_ssq-map.Tpo -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_overlap-overlap.o -MD -MP -MF .deps/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc mv -f .deps/abyss_index-index.Tpo .deps/abyss_index-index.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_map-map.Tpo .deps/abyss_map-map.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm mv -f .deps/abyss_overlap-overlap.Tpo .deps/abyss_overlap-overlap.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_map_ssq-map.Tpo .deps/abyss_map_ssq-map.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Map' Making all in MergePaths gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/MergePaths' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT MergePaths-MergePaths.o -MD -MP -MF .deps/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT MergeContigs-MergeContigs.o -MD -MP -MF .deps/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT PathConsensus-PathConsensus.o -MD -MP -MF .deps/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp mv -f .deps/MergeContigs-MergeContigs.Tpo .deps/MergeContigs-MergeContigs.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm mv -f .deps/PathConsensus-PathConsensus.Tpo .deps/PathConsensus-PathConsensus.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm mv -f .deps/MergePaths-MergePaths.Tpo .deps/MergePaths-MergePaths.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/MergePaths' Making all in Misc gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Misc' ghc --make -O2 -hidir ./ -odir ./ -o abyss-samtobreak samtobreak.hs [1 of 1] Compiling Main ( samtobreak.hs, Main.o ) Linking abyss-samtobreak ... gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Misc' Making all in Overlap gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Overlap' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Overlap-Overlap.o -MD -MP -MF .deps/Overlap-Overlap.Tpo -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp mv -f .deps/Overlap-Overlap.Tpo .deps/Overlap-Overlap.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Overlap' Making all in PairedDBG gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/PairedDBG' depbase=`echo KmerPair.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT KmerPair.o -MD -MP -MF $depbase.Tpo -c -o KmerPair.o KmerPair.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg-abyss-paired-dbg.o -MD -MP -MF .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc c++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg-KmerPair.o -MD -MP -MF .deps/abyss_paired_dbg-KmerPair.Tpo -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpaireddbg.a mv -f .deps/abyss_paired_dbg-KmerPair.Tpo .deps/abyss_paired_dbg-KmerPair.Po mv -f .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo .deps/abyss_paired_dbg-abyss-paired-dbg.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/PairedDBG' Making all in ParseAligns gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/ParseAligns' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fixmate-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fixmate_ssq-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ParseAligns-ParseAligns.o -MD -MP -MF .deps/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp mv -f .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo .deps/abyss_fixmate_ssq-abyss-fixmate.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm mv -f .deps/ParseAligns-ParseAligns.Tpo .deps/ParseAligns-ParseAligns.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_fixmate-abyss-fixmate.Tpo .deps/abyss_fixmate-abyss-fixmate.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/ParseAligns' Making all in PathOverlap gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/PathOverlap' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT PathOverlap-PathOverlap.o -MD -MP -MF .deps/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp mv -f .deps/PathOverlap-PathOverlap.Tpo .deps/PathOverlap-PathOverlap.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/PathOverlap' Making all in PopBubbles gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/PopBubbles' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT PopBubbles-PopBubbles.o -MD -MP -MF .deps/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp mv -f .deps/PopBubbles-PopBubbles.Tpo .deps/PopBubbles-PopBubbles.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/PopBubbles' Making all in Scaffold gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Scaffold' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_scaffold-scaffold.o -MD -MP -MF .deps/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_junction-junction.o -MD -MP -MF .deps/abyss_junction-junction.Tpo -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_longseqdist-longseqdist.o -MD -MP -MF .deps/abyss_longseqdist-longseqdist.Tpo -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_drawgraph-drawgraph.o -MD -MP -MF .deps/abyss_drawgraph-drawgraph.Tpo -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc mv -f .deps/abyss_longseqdist-longseqdist.Tpo .deps/abyss_longseqdist-longseqdist.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_junction-junction.Tpo .deps/abyss_junction-junction.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_drawgraph-drawgraph.Tpo .deps/abyss_drawgraph-drawgraph.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_scaffold-scaffold.Tpo .deps/abyss_scaffold-scaffold.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Scaffold' Making all in SimpleGraph gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/SimpleGraph' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-strict-aliasing -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT SimpleGraph-SimpleGraph.o -MD -MP -MF .deps/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp mv -f .deps/SimpleGraph-SimpleGraph.Tpo .deps/SimpleGraph-SimpleGraph.Po c++ -Wall -Wextra -Wno-strict-aliasing -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/SimpleGraph' Making all in kmerprint gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/kmerprint' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT kmerprint-kmerprint.o -MD -MP -MF .deps/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc mv -f .deps/kmerprint-kmerprint.Tpo .deps/kmerprint-kmerprint.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/kmerprint' Making all in FilterGraph gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/FilterGraph' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_filtergraph-FilterGraph.o -MD -MP -MF .deps/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc mv -f .deps/abyss_filtergraph-FilterGraph.Tpo .deps/abyss_filtergraph-FilterGraph.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/FilterGraph' Making all in GapFiller gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/GapFiller' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_gapfill-gapfill.o -MD -MP -MF .deps/abyss_gapfill-gapfill.Tpo -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp mv -f .deps/abyss_gapfill-gapfill.Tpo .deps/abyss_gapfill-gapfill.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/GapFiller' Making all in Sealer gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Sealer' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_sealer-sealer.o -MD -MP -MF .deps/abyss_sealer-sealer.Tpo -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc mv -f .deps/abyss_sealer-sealer.Tpo .deps/abyss_sealer-sealer.Po c++ -Wall -Wextra -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Sealer' Making all in AdjList gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/AdjList' c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/construction/biology/abyss/abyss-2.1.5 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT AdjList-AdjList.o -MD -MP -MF .deps/AdjList-AdjList.Tpo -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp mv -f .deps/AdjList-AdjList.Tpo .deps/AdjList-AdjList.Po c++ -Wall -Wextra -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/AdjList' Making all in lib/bloomfilter gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/lib/bloomfilter' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/lib/bloomfilter' Making all in lib/nthash gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/lib/nthash' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/lib/nthash' Making all in lib/gtest-1.7.0 gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/lib/gtest-1.7.0' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/lib/gtest-1.7.0' Making all in Unittest gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Unittest' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Unittest' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5' gmake[1]: Leaving directory '/construction/biology/abyss/abyss-2.1.5' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> abyss-2.1.5 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.0.2.txz Installing bash-5.0.2... Extracting bash-5.0.2: .......... done ===> abyss-2.1.5 depends on executable: bash - found ===> Returning to build of abyss-2.1.5 ===> abyss-2.1.5 depends on executable: gmake - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for abyss-2.1.5 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/abyss/abyss-2.1.5' Making install in bin gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/bin' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/bin' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -m 555 abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size ABYSS-P '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/bin' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/bin' Making install in doc gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/doc' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/doc' gmake[3]: Nothing to be done for 'install-exec-am'. test -z "/usr/local/share/doc/abyss" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/share/doc/abyss" install -m 0644 flowchart.pdf flowchart_simplified.pdf '/construction/biology/abyss/stage/usr/local/share/doc/abyss' test -z "/usr/local/man/man1" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/man/man1" install -m 0644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/construction/biology/abyss/stage/usr/local/man/man1' gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/doc' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/doc' Making install in Common gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Common' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Common' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Common' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Common' Making install in Graph gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Graph' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Graph' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-gc abyss-todot '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Graph' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Graph' Making install in DataLayer gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DataLayer' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DataLayer' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-fac abyss-tofastq '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DataLayer' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DataLayer' Making install in DataBase gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DataBase' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DataBase' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-db-csv '/construction/biology/abyss/stage/usr/local/bin' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -m 555 abyss-db-txt '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DataBase' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DataBase' Making install in FMIndex gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/FMIndex' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/FMIndex' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/FMIndex' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/FMIndex' Making install in Assembly gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Assembly' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Assembly' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Assembly' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Assembly' Making install in dialign gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/dialign' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/dialign' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/dialign' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/dialign' Making install in Align gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Align' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Align' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-align abyss-mergepairs '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Align' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Align' Making install in ABYSS gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/ABYSS' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/ABYSS' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 ABYSS '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/ABYSS' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/ABYSS' Making install in Bloom gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Bloom' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Bloom' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-bloom '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Bloom' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Bloom' Making install in BloomDBG gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/BloomDBG' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/BloomDBG' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-bloom-dbg '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/BloomDBG' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/BloomDBG' Making install in Konnector gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Konnector' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Konnector' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 konnector '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Konnector' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Konnector' Making install in Consensus gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Consensus' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Consensus' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 Consensus '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Consensus' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Consensus' Making install in DAssembler gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DAssembler' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DAssembler' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 DAssembler '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DAssembler' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DAssembler' Making install in DistanceEst gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DistanceEst' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/DistanceEst' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 DistanceEst DistanceEst-ssq '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DistanceEst' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/DistanceEst' Making install in KAligner gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/KAligner' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/KAligner' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 KAligner '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/KAligner' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/KAligner' Making install in Layout gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Layout' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Layout' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-layout '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Layout' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Layout' Making install in LogKmerCount gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/LogKmerCount' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/LogKmerCount' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 logcounter '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/LogKmerCount' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/LogKmerCount' Making install in Map gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Map' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Map' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-index abyss-map abyss-map-ssq abyss-overlap '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Map' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Map' Making install in MergePaths gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/MergePaths' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/MergePaths' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 MergePaths MergeContigs PathConsensus '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/MergePaths' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/MergePaths' Making install in Misc gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Misc' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Misc' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-samtobreak '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Misc' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Misc' Making install in Overlap gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Overlap' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Overlap' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 Overlap '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Overlap' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Overlap' Making install in PairedDBG gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/PairedDBG' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/PairedDBG' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-paired-dbg '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/PairedDBG' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/PairedDBG' Making install in ParseAligns gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/ParseAligns' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/ParseAligns' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-fixmate abyss-fixmate-ssq ParseAligns '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/ParseAligns' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/ParseAligns' Making install in PathOverlap gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/PathOverlap' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/PathOverlap' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 PathOverlap '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/PathOverlap' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/PathOverlap' Making install in PopBubbles gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/PopBubbles' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/PopBubbles' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 PopBubbles '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/PopBubbles' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/PopBubbles' Making install in Scaffold gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Scaffold' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Scaffold' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-scaffold abyss-junction abyss-longseqdist '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Scaffold' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Scaffold' Making install in SimpleGraph gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/SimpleGraph' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/SimpleGraph' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 SimpleGraph '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/SimpleGraph' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/SimpleGraph' Making install in kmerprint gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/kmerprint' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/kmerprint' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/kmerprint' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/kmerprint' Making install in FilterGraph gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/FilterGraph' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/FilterGraph' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-filtergraph '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/FilterGraph' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/FilterGraph' Making install in GapFiller gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/GapFiller' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/GapFiller' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-gapfill '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/GapFiller' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/GapFiller' Making install in Sealer gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Sealer' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Sealer' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 abyss-sealer '/construction/biology/abyss/stage/usr/local/bin' test -z "/usr/local/man/man1" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/man/man1" install -m 0644 abyss-sealer.1 '/construction/biology/abyss/stage/usr/local/man/man1' gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Sealer' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Sealer' Making install in AdjList gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/AdjList' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/AdjList' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/bin" install -s -m 555 AdjList '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/AdjList' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/AdjList' Making install in lib/bloomfilter gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/lib/bloomfilter' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/lib/bloomfilter' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/lib/bloomfilter' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/lib/bloomfilter' Making install in lib/nthash gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/lib/nthash' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/lib/nthash' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/lib/nthash' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/lib/nthash' Making install in lib/gtest-1.7.0 gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/lib/gtest-1.7.0' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/lib/gtest-1.7.0' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/lib/gtest-1.7.0' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/lib/gtest-1.7.0' Making install in Unittest gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Unittest' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5/Unittest' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Unittest' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5/Unittest' gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.1.5' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.1.5' gmake[3]: Nothing to be done for 'install-exec-am'. test -z "/usr/local/share/doc/abyss" || /bin/mkdir -p "/construction/biology/abyss/stage/usr/local/share/doc/abyss" install -m 0644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md README.html '/construction/biology/abyss/stage/usr/local/share/doc/abyss' gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.1.5' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.1.5' gmake[1]: Leaving directory '/construction/biology/abyss/abyss-2.1.5' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for abyss-2.1.5 file sizes/checksums [72]: . done packing files [72]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 18:21:44 UTC Duration: 00:14:34