------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/perl5-5.32.0.txz Installing /packages/All/icu-67.1,1.txz Installing /packages/All/boost-libs-1.72.0_2.txz ===== Message from boost-libs-1.72.0_2: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/freetype2-2.10.2.txz ===== Message from freetype2-2.10.2: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). Installing /packages/All/expat-2.2.8.txz Installing /packages/All/fontconfig-2.13.92_2,1.txz Running fc-cache to build fontconfig cache... Font directories: /usr/local/share/fonts /usr/local/lib/X11/fonts /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 /packages/All/graphite2-1.3.14.txz Installing /packages/All/pcre-8.44.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/libxml2-2.9.10.txz Installing /packages/All/libiconv-1.16.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.9.txz ===== Message from python37-3.7.9: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/glib-2.56.3_9,1.txz No schema files found: doing nothing. Installing /packages/All/harfbuzz-2.7.2.txz Installing /packages/All/png-1.6.37.txz Installing /packages/All/jbigkit-2.1_1.txz Installing /packages/All/jpeg-turbo-2.0.4.txz Installing /packages/All/tiff-4.1.0.txz Installing /packages/All/giflib-5.2.1.txz Installing /packages/All/webp-1.1.0.txz Installing /packages/All/libgd-2.3.0,1.txz Installing /packages/All/tex-kpathsea-6.2.1_2.txz Installing /packages/All/atk-2.36.0.txz Installing /packages/All/pixman-0.40.0_1.txz Installing /packages/All/libpthread-stubs-0.4.txz Installing /packages/All/libXau-1.0.9.txz Installing /packages/All/xorgproto-2020.1.txz Installing /packages/All/libXdmcp-1.1.3.txz Installing /packages/All/libxcb-1.13.1.txz Installing /packages/All/libX11-1.6.12,1.txz Installing /packages/All/libXext-1.3.4,1.txz Installing /packages/All/libXrender-0.9.10_2.txz Installing /packages/All/cairo-1.16.0,2.txz Installing /packages/All/shared-mime-info-2.0.txz Installing /packages/All/gdk-pixbuf2-2.40.0.txz Installing /packages/All/wayland-1.18.0.txz Installing /packages/All/pciids-20200819.txz Installing /packages/All/libpciaccess-0.16.txz Installing /packages/All/libdrm-2.4.101.txz Installing /packages/All/libXfixes-5.0.3_2.txz Installing /packages/All/libXdamage-1.1.5.txz Installing /packages/All/libxshmfence-1.3.txz Installing /packages/All/libXxf86vm-1.1.4_3.txz Installing /packages/All/libXrandr-1.5.2.txz Installing /packages/All/mesa-libs-19.0.8_2.txz Installing /packages/All/libepoxy-1.5.4.txz Installing /packages/All/fribidi-0.19.7.txz Installing /packages/All/libICE-1.0.10,1.txz Installing /packages/All/libSM-1.2.3,1.txz Installing /packages/All/dbus-1.12.20.txz ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. Installing /packages/All/xkeyboard-config-2.30.txz Installing /packages/All/libxkbcommon-0.10.0_2.txz ===== Message from libxkbcommon-0.10.0_2: -- If arrow keys don't work under X11 switch to legacy rules e.g., For sh/bash/ksh/zsh run and (optionally) add into ~/.profile: export XKB_DEFAULT_RULES=xorg For csh/tcsh run and (optionally) add into ~/.login: setenv XKB_DEFAULT_RULES xorg Installing /packages/All/libXi-1.7.10,1.txz Installing /packages/All/libXtst-1.2.3_2.txz Installing /packages/All/at-spi2-core-2.36.0.txz Installing /packages/All/at-spi2-atk-2.34.2.txz Installing /packages/All/nspr-4.28.txz Installing /packages/All/spidermonkey60-60.9.0_4.txz ===== Message from spidermonkey60-60.9.0_4: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/polkit-0.116.txz ===> Creating groups. Creating group 'polkitd' with gid '565'. ===> Creating users Creating user 'polkitd' with uid '565'. Installing /packages/All/lcms2-2.11_1.txz Installing /packages/All/libedit-3.1.20191231,1.txz Installing /packages/All/sqlite3-3.33.0,1.txz Installing /packages/All/libXinerama-1.1.4_2,1.txz Installing /packages/All/libXScrnSaver-1.2.3_2.txz Installing /packages/All/argyllcms-1.9.2_5.txz Installing /packages/All/colord-1.3.5.txz ===> Creating groups. Creating group 'colord' with gid '970'. ===> Creating users Creating user 'colord' with uid '970'. Installing /packages/All/libdaemon-0.14_1.txz Installing /packages/All/dbus-glib-0.110.txz Installing /packages/All/gdbm-1.18.1_1.txz Installing /packages/All/gobject-introspection-1.56.1_1,1.txz Installing /packages/All/gnome_subr-1.0.txz Installing /packages/All/avahi-app-0.7_3.txz ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/nettle-3.6.txz Installing /packages/All/libtasn1-4.16.0.txz Installing /packages/All/libunistring-0.9.10_1.txz Installing /packages/All/libidn2-2.3.0_1.txz Installing /packages/All/ca_root_nss-3.56.txz ===== Message from ca_root_nss-3.56: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/bash-5.0.18_3.txz Installing /packages/All/bash-completion-2.11,2.txz ===== Message from bash-completion-2.11,2: -- To enable the bash completion library, add the following to your .bashrc file: [[ $PS1 && -f /usr/local/share/bash-completion/bash_completion.sh ]] && \ source /usr/local/share/bash-completion/bash_completion.sh See /usr/local/share/doc/bash-completion/README.md for more information. Installing /packages/All/p11-kit-0.23.21.txz Installing /packages/All/tpm-emulator-0.7.4_2.txz ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. Installing /packages/All/trousers-0.3.14_3.txz ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. ===== Message from trousers-0.3.14_3: -- To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Installing /packages/All/gnutls-3.6.15.txz Installing /packages/All/libpaper-1.1.24.4.txz Installing /packages/All/cups-2.3.3_1.txz ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. Installing /packages/All/libfontenc-1.1.4.txz Installing /packages/All/mkfontscale-1.2.1.txz Installing /packages/All/font-bh-ttf-1.0.3_4.txz Installing /packages/All/font-misc-meltho-1.0.3_4.txz Installing /packages/All/font-misc-ethiopic-1.0.4.txz Installing /packages/All/encodings-1.0.5,1.txz Installing /packages/All/dejavu-2.37_1.txz ===== Message from dejavu-2.37_1: -- Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Installing /packages/All/xorg-fonts-truetype-7.7_1.txz Installing /packages/All/libXft-2.3.3.txz Installing /packages/All/pango-1.42.4_4.txz Installing /packages/All/hicolor-icon-theme-0.17.txz Installing /packages/All/gtk-update-icon-cache-3.24.20.txz Installing /packages/All/adwaita-icon-theme-3.28.0.txz Installing /packages/All/libcroco-0.6.13.txz Installing /packages/All/libgsf-1.14.47_1.txz Installing /packages/All/librsvg2-2.40.21.txz Installing /packages/All/wayland-protocols-1.20.txz Installing /packages/All/libXcomposite-0.4.5,1.txz Installing /packages/All/libXcursor-1.2.0.txz Installing /packages/All/gtk3-3.24.20.txz Installing /packages/All/lua53-5.3.5_3.txz Installing /packages/All/gnuplot-5.4.0.txz Installing /packages/All/alsa-lib-1.1.2_2.txz ===== Message from alsa-lib-1.1.2_2: -- ===> NOTICE: The alsa-lib port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/javavmwrapper-2.7.5.txz Installing /packages/All/java-zoneinfo-2020.a.txz Installing /packages/All/libXt-1.2.0,1.txz Installing /packages/All/openjdk8-8.181.13_1.txz ===== Message from openjdk8-8.181.13_1: -- ====================================================================== This OpenJDK implementation requires procfs(5) mounted on /proc. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following line in /etc/fstab: proc /proc procfs rw 0 0 ====================================================================== SUCCEEDED 00:00:55 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> canu-2.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> canu-2.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by canu-2.0 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> canu-2.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by canu-2.0 for building => SHA256 Checksum OK for marbl-canu-v2.0_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> canu-2.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by canu-2.0 for building ===> Extracting for canu-2.0 => SHA256 Checksum OK for marbl-canu-v2.0_GH0.tar.gz. Extracted Memory Use: 17.03M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for canu-2.0 ===> Applying ports patches for canu-2.0 from /xports/biology/canu/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> canu-2.0 depends on package: gmake>=4.3 - found ===> canu-2.0 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> canu-2.0 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> canu-2.0 depends on package: gmake>=4.3 - found ===> canu-2.0 depends on package: perl5>=5.32.r0<5.33 - found ===> canu-2.0 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Configuring for canu-2.0 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for canu-2.0 gmake[1]: Entering directory '/construction/biology/canu/canu-2.0/src' Building for 'DragonFly' '9999999' as 'amd64' into '/construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/{bin,obj}'. Using '/usr/bin/c++' version '8.3'. Using user-supplied CXXFLAGS ' -pipe -O2 -fno-strict-aliasing '. c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/edlib.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C Building release v2.0 c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/files.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/logging.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/strings.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/system.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/sequence.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/kmers.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] #warning how to set prefix size for streaming operations? ^~~~~~~ c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-statistics.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-exact.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/bits.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/hexDump.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/md5.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/sqCache.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C utility/objectStore.C: In function 'bool fetchFromObjectStore(char*)': utility/objectStore.C:257:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] args[1] = "download"; ^~~~~~~~~~ utility/objectStore.C:258:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] args[2] = "--overwrite"; ^~~~~~~~~~~~~ utility/objectStore.C:259:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] args[3] = "--no-progress"; ^~~~~~~~~~~~~~~ utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] args[4] = "--output"; ^~~~~~~~~~ c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C stores/sqReadDataWriter.C: In member function 'void sqReadDataWriter::sqReadDataWriter_writeBlob(writeBuffer*)': stores/sqReadDataWriter.C:109:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] buffer->writeIFFchunk("BLOB"); ^ stores/sqReadDataWriter.C:110:48: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] buffer->writeIFFchunk("NAME", _name, _nameLen); ^ stores/sqReadDataWriter.C:115:49: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] buffer->writeIFFchunk("2SQR", rseq, rseq2Len); // Two-bit encoded sequence (ACGT only) ^ stores/sqReadDataWriter.C:117:49: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] buffer->writeIFFchunk("3SQR", rseq, rseq3Len); // Three-bit encoded sequence (ACGTN) ^ stores/sqReadDataWriter.C:119:49: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] buffer->writeIFFchunk("USQR", rseq, rseqULen); // Unencoded sequence ^ stores/sqReadDataWriter.C:124:49: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] buffer->writeIFFchunk("2SQC", cseq, cseq2Len); // Two-bit encoded sequence (ACGT only) ^ stores/sqReadDataWriter.C:126:49: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] buffer->writeIFFchunk("3SQC", cseq, cseq3Len); // Three-bit encoded sequence (ACGTN) ^ stores/sqReadDataWriter.C:128:49: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] buffer->writeIFFchunk("USQC", cseq, cseqULen); // Unencoded sequence ^ stores/sqReadDataWriter.C:132:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] buffer->closeIFFchunk("BLOB"); ^ c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING ^~~~~~~ c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp] #warning not failing if a valid store ^~~~~~~ c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C stores/sqStoreInfo.C: In member function 'void sqStoreInfo::writeInfo(char*)': stores/sqStoreInfo.C:333:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("MAGC", _sqMagic); ^ stores/sqStoreInfo.C:334:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("VERS", _sqVersion); ^ stores/sqStoreInfo.C:336:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("LSIZ", _sqLibrarySize); ^ stores/sqStoreInfo.C:337:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("RSIZ", _sqReadSize); ^ stores/sqStoreInfo.C:338:48: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("MLB ", _sqMaxLibrariesBits); ^ stores/sqStoreInfo.C:339:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("LNS ", _sqLibraryNameSize); ^ stores/sqStoreInfo.C:340:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("MRB ", _sqMaxReadBits); ^ stores/sqStoreInfo.C:341:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("MRLB", _sqMaxReadLenBits); ^ stores/sqStoreInfo.C:343:42: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("NLIB", _numLibraries); ^ stores/sqStoreInfo.C:344:38: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("NREA", _numReads); ^ stores/sqStoreInfo.C:345:38: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFobject("NBLO", _numBlobs); ^ stores/sqStoreInfo.C:347:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFarray("READ", _reads, sqRead_largest); ^ stores/sqStoreInfo.C:348:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] B->writeIFFarray("BASE", _bases, sqRead_largest); ^ c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': stores/tgTigSizeAnalysis.C:140:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); ^ stores/tgTigSizeAnalysis.C:141:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] printSummary(out, "lenSuggestCircular", lenSuggestCircular); ^ stores/tgTigSizeAnalysis.C:143:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] printSummary(out, "lenUnassembled", lenUnassembled); ^ stores/tgTigSizeAnalysis.C:144:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] printSummary(out, "lenBubble", lenBubble); ^ stores/tgTigSizeAnalysis.C:145:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] printSummary(out, "lenContig", lenContig); ^ stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)': stores/tgTig.C:813:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] _suggestCircular ? "yes" : "no"); ^ stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)': stores/tgTig.C:833:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] _suggestCircular ? "yes" : "no"); ^ c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C c++ -o /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -pipe -O2 -fno-strict-aliasing -DNOBACKTRACE -I/construction/biology/canu/canu-2.0/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C In file included from utgcns/libboost/boost/config.hpp:53, from utgcns/libboost/boost/graph/graph_traits.hpp:13, from utgcns/libpbutgcns/AlnGraphBoost.C:70: utgcns/libboost/boost/config/select_platform_config.hpp:22:33: fatal error: boost/config/platform/bsd.hpp: No such file or directory # define BOOST_PLATFORM_CONFIG "boost/config/platform/bsd.hpp" ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:716: /construction/biology/canu/canu-2.0/src/usr/local/DragonFly-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o] Error 1 gmake[1]: *** Waiting for unfinished jobs.... utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::processHits()': utgcns/libNDalign/NDalign.C:660:49: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] display("NDalign::processHits()-- ", false); ^ utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::scanDeltaForBadness(bool, bool)': utgcns/libNDalign/NDalign.C:724:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] display("NDalign::scanForDeltaBadness()-- ", true); ^ utgcns/libNDalign/NDalign.C: In member function 'void NDalign::realignForward(bool, bool)': utgcns/libNDalign/NDalign.C:774:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] display("NDalign::realignForward()-- ", displayAlign); ^ utgcns/libNDalign/NDalign.C: In member function 'void NDalign::realignBackward(bool, bool)': utgcns/libNDalign/NDalign.C:838:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] display("NDalign::realignBackward()-- ", displayAlign); ^ gfa/gfa.C: In member function 'void gfaSequence::load(char*)': gfa/gfa.C:123:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] findGFAtokenI(_features, "LN:i:", _length); ^ gmake[1]: Leaving directory '/construction/biology/canu/canu-2.0/src' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /xports/biology/canu FAILED 00:00:09