------------------------------------------------------------------------------- -- 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/expat-2.2.8.txz Installing /packages/All/libffi-3.3_1.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/python27-2.7.18_1.txz ===== Message from python27-2.7.18_1: -- 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 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/libnghttp2-1.41.0.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/curl-7.72.0.txz Installing /packages/All/pcre2-10.35.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/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/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/pcre-8.44.txz Installing /packages/All/libxml2-2.9.10.txz Installing /packages/All/libiconv-1.16.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/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/graphite2-1.3.14.txz Installing /packages/All/harfbuzz-2.7.2.txz Installing /packages/All/fribidi-0.19.7.txz Installing /packages/All/libfontenc-1.1.4.txz Installing /packages/All/mkfontscale-1.2.1.txz Installing /packages/All/font-bh-ttf-1.0.3_4.txz Installing /packages/All/font-misc-meltho-1.0.3_4.txz Installing /packages/All/font-misc-ethiopic-1.0.4.txz Installing /packages/All/encodings-1.0.5,1.txz Installing /packages/All/dejavu-2.37_1.txz ===== Message from dejavu-2.37_1: -- Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Installing /packages/All/xorg-fonts-truetype-7.7_1.txz Installing /packages/All/libXft-2.3.3.txz Installing /packages/All/pango-1.42.4_4.txz Installing /packages/All/tcl86-8.6.10.txz Installing /packages/All/libXScrnSaver-1.2.3_2.txz Installing /packages/All/tk86-8.6.10_1.txz Installing /packages/All/libidn-1.35.txz Installing /packages/All/jbig2dec-0.18.txz Installing /packages/All/libpaper-1.1.24.4.txz Installing /packages/All/libdaemon-0.14_1.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/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/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/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/poppler-data-0.4.9_5.txz Installing /packages/All/ghostscript9-agpl-base-9.52_8.txz ===== Message from ghostscript9-agpl-base-9.52_8: -- 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. Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.33.1_3,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/libXt-1.2.0,1.txz Installing /packages/All/libXmu-1.1.3,1.txz Installing /packages/All/R-4.0.2.txz Installing /packages/All/R-cran-getopt-1.20.3_1.txz Installing /packages/All/R-cran-optparse-1.6.6.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:01:26 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- /!\ haplohseq-0.1.2_2: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- /!\ haplohseq-0.1.2_2: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. ===> haplohseq-0.1.2_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by haplohseq-0.1.2_2 for building SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- /!\ haplohseq-0.1.2_2: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. ===> haplohseq-0.1.2_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by haplohseq-0.1.2_2 for building => SHA256 Checksum OK for haplohseq-0.1.2.tar.xz. SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- /!\ haplohseq-0.1.2_2: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. ===> haplohseq-0.1.2_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by haplohseq-0.1.2_2 for building ===> Extracting for haplohseq-0.1.2_2 => SHA256 Checksum OK for haplohseq-0.1.2.tar.xz. Extracted Memory Use: 60.23M SUCCEEDED 00:00:13 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for haplohseq-0.1.2_2 ===> Applying ports patches for haplohseq-0.1.2_2 from /xports/biology/haplohseq/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_2 depends on package: gmake>=4.3 - found ===> haplohseq-0.1.2_2 depends on file: /usr/local/bin/python2.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_2 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_2 depends on package: gmake>=4.3 - found ===> haplohseq-0.1.2_2 depends on file: /usr/local/bin/python2.7 - found ===> haplohseq-0.1.2_2 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> Configuring for haplohseq-0.1.2_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for haplohseq-0.1.2_2 gmake[1]: Entering directory '/construction/biology/haplohseq/haplohseq-0.1.2' mkdir -p build build/bin build/obj mkdir -p build/test c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Hmm.o src/hmm/Hmm.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/DataStructures.o src/hmm/DataStructures.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/MathUtil.o src/hmm/MathUtil.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/StringUtil.o src/util/StringUtil.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/InputProcessor.o src/util/InputProcessor.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Reporter.o src/Reporter.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/FreqPhase.o src/FreqPhase.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/VcfUtil.o src/util/VcfUtil.cpp cp -r src/test/resources build/test c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/HaplohSeq.o src/HaplohSeq.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/FreqPhaseTest.o src/test/FreqPhaseTest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HaplohSeqTest.o src/test/HaplohSeqTest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HmmTest.o src/test/HmmTest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/InputProcessorTest.o src/test/InputProcessorTest.cpp c++ -o build/bin/haplohseq -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 build/obj/Hmm.o build/obj/DataStructures.o build/obj/MathUtil.o build/obj/StringUtil.o build/obj/InputProcessor.o build/obj/Reporter.o build/obj/FreqPhase.o build/obj/VcfUtil.o build/obj/HaplohSeq.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib c++ -o build/test/HmmTest -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include build/obj/Hmm.o build/obj/DataStructures.o build/obj/MathUtil.o build/obj/StringUtil.o build/test/HmmTest.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib c++ -o build/test/InputProcessorTest -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include build/obj/Hmm.o build/obj/DataStructures.o build/obj/MathUtil.o build/obj/StringUtil.o build/obj/InputProcessor.o build/test/InputProcessorTest.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib c++ -o build/test/HaplohSeqTest -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include build/obj/Hmm.o build/obj/DataStructures.o build/obj/MathUtil.o build/obj/StringUtil.o build/obj/InputProcessor.o build/test/HaplohSeqTest.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib c++ -o build/test/FreqPhaseTest -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include build/obj/StringUtil.o build/obj/InputProcessor.o build/obj/FreqPhase.o build/test/FreqPhaseTest.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib gmake[1]: Leaving directory '/construction/biology/haplohseq/haplohseq-0.1.2' SUCCEEDED 00:01:22 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_2 depends on package: R-cran-optparse>0 - found ===> haplohseq-0.1.2_2 depends on file: /usr/local/bin/python2.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for haplohseq-0.1.2_2 ===> haplohseq-0.1.2_2 depends on package: R-cran-optparse>0 - found ===> haplohseq-0.1.2_2 depends on file: /usr/local/bin/python2.7 - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/haplohseq/haplohseq-0.1.2' mkdir -p /construction/biology/haplohseq/stage/usr/local/bin install -c -s build/bin/* /construction/biology/haplohseq/stage/usr/local/bin gmake[1]: Leaving directory '/construction/biology/haplohseq/haplohseq-0.1.2' install -m 555 /construction/biology/haplohseq/haplohseq-example /construction/biology/haplohseq/stage/usr/local/bin (cd /construction/biology/haplohseq/haplohseq-0.1.2 && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE "example ldmap scripts" /construction/biology/haplohseq/stage/usr/local/share/examples/haplohseq) ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for haplohseq-0.1.2_2 file sizes/checksums [10]: 0% file sizes/checksums [10]: 100% packing files [10]: 0% packing files [10]: 100% packing directories [1]: 0% packing directories [1]: 100% SUCCEEDED 00:02:16 TOTAL TIME 00:05:52