=>> Building biology/rna-seq build started at Tue Dec 30 17:24:37 EST 2025 port directory: /usr/ports/biology/rna-seq package name: rna-seq-0.1.4_1 building for: FreeBSD 143amd64-deluxe-desktop-job-02 14.3-RELEASE-p2 FreeBSD 14.3-RELEASE-p2 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 720 Dec 16 05:29 /usr/ports/biology/rna-seq/Makefile Ports top last git commit: 3dd9e2202282 Ports top unclean checkout: yes Port dir last git commit: b304d8ab18ac Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1403000 Jail OSVERSION: 1403000 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p2 UNAME_r=14.3-RELEASE-p2 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.4 MASTERMNT=/mnt/data/.m/143amd64-deluxe-desktop/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/mnt/data/.m/143amd64-deluxe-desktop/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=143amd64-deluxe-desktop SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/mnt/data/.m/143amd64-deluxe-desktop/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/rna-seq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/rna-seq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/rna-seq/work/.cache HOME=/wrkdirs/usr/ports/biology/rna-seq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/rna-seq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/rna-seq/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/rna-seq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/rna-seq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/rna-seq/work/.cache HOME=/wrkdirs/usr/ports/biology/rna-seq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/rna-seq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/rna-seq/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/rna-seq" EXAMPLESDIR="share/examples/rna-seq" DATADIR="share/rna-seq" WWWDIR="www/rna-seq" ETCDIR="etc/rna-seq" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/rna-seq DOCSDIR=/usr/local/share/doc/rna-seq EXAMPLESDIR=/usr/local/share/examples/rna-seq WWWDIR=/usr/local/www/rna-seq ETCDIR=/usr/local/etc/rna-seq --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # Work around some weirdness when fetching golang modules GO_TAGS+=netcgo .if ${.CURDIR:M*/www/chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/www/ungoogled-chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/lang/rust*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/lang/gcc*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/www/iridium*} MAKE_JOBS_NUMBER=16 .endif .if ${.CURDIR:M*/devel/electron*} MAKE_JOBS_NUMBER=20 .endif .if ${.CURDIR:M*/databases/mongodb*} MAKE_JOBS_NUMBER=12 .endif .if ${.CURDIR:M*/devel/llvm*} MAKE_JOBS_NUMBER=16 .endif # Speed things up a bit MAKE_JOBS_NUMBER?=8 #### #### #MAKE_JOBS_NUMBER?=4 # Alows us to build ports non-interactivly DISABLE_LICENSES=yes LICENSES_ACCEPTED+= DCC # Enable SNDIO on anything that supports it #OPTIONS_SET+=PULSEAUDIO OPTIONS_SET+=SNDIO # Yes we have MS Windows x11-fonts_webfonts_SET+=EXTRAFONTS CLEARTYPE # Desktop Specific Options sysutils_gksu_UNSET+=NAUTILUS x11-wm_compiz-fusion_UNSET+=EMERALD accessibility_redshift_SET+=GUI VIDMODE # These ports default to other audio servers, audio_espeak_UNSET+=PORTAUDIO www_qt5-webengine_UNSET+=ALSA www_qt6-webengine_UNSET+=ALSA audio_rhvoice_UNSET+=AO comms_morse_UNSET+=OSS audio_harp_UNSET+=OSS # Somehow these options are being set and result in ports being rebuilt needlessly becuase they are actually turned off audio_alsa-plugins_SET+=FFMPEG JACK PULSEAUDIO SAMPLERATE SPEEX #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> rna-seq-0.1.4_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [143amd64-deluxe-desktop-job-02] Installing pkg-2.5.1... [143amd64-deluxe-desktop-job-02] Extracting pkg-2.5.1: .......... done ===> rna-seq-0.1.4_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rna-seq-0.1.4_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by rna-seq-0.1.4_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by rna-seq-0.1.4_1 for building =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Fetching all distfiles required by rna-seq-0.1.4_1 for building ===> Extracting for rna-seq-0.1.4_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for rna-seq-0.1.4_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> rna-seq-0.1.4_1 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.14.pkg [143amd64-deluxe-desktop-job-02] Installing python311-3.11.14... [143amd64-deluxe-desktop-job-02] `-- Installing gettext-runtime-0.26... [143amd64-deluxe-desktop-job-02] | `-- Installing indexinfo-0.3.1_1... [143amd64-deluxe-desktop-job-02] | `-- Extracting indexinfo-0.3.1_1: . done [143amd64-deluxe-desktop-job-02] `-- Extracting gettext-runtime-0.26: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing libffi-3.5.1... [143amd64-deluxe-desktop-job-02] `-- Extracting libffi-3.5.1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing mpdecimal-4.0.1... [143amd64-deluxe-desktop-job-02] `-- Extracting mpdecimal-4.0.1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing readline-8.3.1... [143amd64-deluxe-desktop-job-02] `-- Extracting readline-8.3.1: .......... done [143amd64-deluxe-desktop-job-02] Extracting python311-3.11.14: .......... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> rna-seq-0.1.4_1 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of rna-seq-0.1.4_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for rna-seq-0.1.4_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> rna-seq-0.1.4_1 depends on package: sra-tools>0 - not found ===> Installing existing package /packages/All/sra-tools-3.3.0.pkg [143amd64-deluxe-desktop-job-02] Installing sra-tools-3.3.0... [143amd64-deluxe-desktop-job-02] `-- Installing hdf5-1.12.2_2,1... [143amd64-deluxe-desktop-job-02] | `-- Installing gcc14-14.2.0_4... [143amd64-deluxe-desktop-job-02] | | `-- Installing binutils-2.44,1... [143amd64-deluxe-desktop-job-02] | | `-- Installing zstd-1.5.7_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting zstd-1.5.7_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting binutils-2.44,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing gmp-6.3.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting gmp-6.3.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing mpc-1.3.1_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing mpfr-4.2.2,1... 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[143amd64-deluxe-desktop-job-02] | | `-- Installing brotli-1.2.0,1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting brotli-1.2.0,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing png-1.6.53... [143amd64-deluxe-desktop-job-02] | | `-- Extracting png-1.6.53: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting freetype2-2.14.1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting fontconfig-2.17.1,1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing giflib-5.2.2... [143amd64-deluxe-desktop-job-02] | `-- Extracting giflib-5.2.2: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing harfbuzz-12.2.0... [143amd64-deluxe-desktop-job-02] | | `-- Installing glib-2.84.4,2... [143amd64-deluxe-desktop-job-02] | | `-- Installing libiconv-1.18_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libiconv-1.18_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libinotify-20240724_3... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libinotify-20240724_3: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing pcre2-10.47_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting pcre2-10.47_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-packaging-25.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-packaging-25.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting glib-2.84.4,2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing graphite2-1.3.14... [143amd64-deluxe-desktop-job-02] | | `-- Extracting graphite2-1.3.14: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting harfbuzz-12.2.0: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing javavmwrapper-2.7.10... [143amd64-deluxe-desktop-job-02] | `-- Extracting javavmwrapper-2.7.10: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing jpeg-turbo-3.1.3... [143amd64-deluxe-desktop-job-02] | `-- Extracting jpeg-turbo-3.1.3: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing lcms2-2.17... [143amd64-deluxe-desktop-job-02] | | `-- Installing tiff-4.7.1... [143amd64-deluxe-desktop-job-02] | | `-- Installing jbigkit-2.1_3... [143amd64-deluxe-desktop-job-02] | | `-- Extracting jbigkit-2.1_3: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing lerc-4.0.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting lerc-4.0.0: ..... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libdeflate-1.25... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libdeflate-1.25: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting tiff-4.7.1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting lcms2-2.17: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libX11-1.8.12,1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libxcb-1.17.0... [143amd64-deluxe-desktop-job-02] | | `-- Installing libXau-1.0.12... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libXau-1.0.12: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libXdmcp-1.1.5... [143amd64-deluxe-desktop-job-02] | | | `-- Installing xorgproto-2024.1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting xorgproto-2024.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libXdmcp-1.1.5: ...... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting libxcb-1.17.0: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting libX11-1.8.12,1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXext-1.3.6,1... [143amd64-deluxe-desktop-job-02] | `-- Extracting libXext-1.3.6,1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXi-1.8.2,1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libXfixes-6.0.1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libXfixes-6.0.1: ....... done [143amd64-deluxe-desktop-job-02] | `-- Extracting libXi-1.8.2,1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXrandr-1.5.4... [143amd64-deluxe-desktop-job-02] | | `-- Installing libXrender-0.9.12... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libXrender-0.9.12: ....... done [143amd64-deluxe-desktop-job-02] | `-- Extracting libXrandr-1.5.4: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXt-1.3.0,1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libICE-1.1.2,1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libICE-1.1.2,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libSM-1.2.6,1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libSM-1.2.6,1: ........ done [143amd64-deluxe-desktop-job-02] | `-- Extracting libXt-1.3.0,1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libXtst-1.2.5... [143amd64-deluxe-desktop-job-02] | `-- Extracting libXtst-1.2.5: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing xorg-fonts-truetype-7.7_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing dejavu-2.37_3... [143amd64-deluxe-desktop-job-02] | | `-- Installing mkfontscale-1.2.3... [143amd64-deluxe-desktop-job-02] | | | `-- Installing libfontenc-1.1.8... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libfontenc-1.1.8: ...... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting mkfontscale-1.2.3: .... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting dejavu-2.37_3: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing encodings-1.1.0,1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting encodings-1.1.0,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing font-bh-ttf-1.0.3_5... [143amd64-deluxe-desktop-job-02] | | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing font-misc-ethiopic-1.0.4... [143amd64-deluxe-desktop-job-02] | | `-- Extracting font-misc-ethiopic-1.0.4: ... done [143amd64-deluxe-desktop-job-02] | | `-- Installing font-misc-meltho-1.0.3_5... [143amd64-deluxe-desktop-job-02] | | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting openjdk17-17.0.17+10.1: .......... done [143amd64-deluxe-desktop-job-02] Extracting sra-tools-3.3.0: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from gcc14-14.2.0_4: -- 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/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from freetype2-2.14.1: -- 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. 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/index.html, if documentation was installed). ===== Message from libinotify-20240724_3: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from dejavu-2.37_3: -- 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. ===== Message from openjdk17-17.0.17+10.1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> rna-seq-0.1.4_1 depends on package: sra-tools>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: fastq-trim>0 - not found ===> Installing existing package /packages/All/fastq-trim-0.1.4.pkg [143amd64-deluxe-desktop-job-02] Installing fastq-trim-0.1.4... [143amd64-deluxe-desktop-job-02] `-- Installing biolibc-0.2.7... [143amd64-deluxe-desktop-job-02] | `-- Installing libxtend-0.2.1.10... [143amd64-deluxe-desktop-job-02] | `-- Extracting libxtend-0.2.1.10: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting biolibc-0.2.7: .......... done [143amd64-deluxe-desktop-job-02] Extracting fastq-trim-0.1.4: .......... done ===> rna-seq-0.1.4_1 depends on package: fastq-trim>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: fastqc>0 - not found ===> Installing existing package /packages/All/fastqc-0.12.1.pkg [143amd64-deluxe-desktop-job-02] Installing fastqc-0.12.1... [143amd64-deluxe-desktop-job-02] `-- Installing openjdk8-8.472.08.1... [143amd64-deluxe-desktop-job-02] | `-- Installing java-zoneinfo-2021.e... [143amd64-deluxe-desktop-job-02] | `-- Extracting java-zoneinfo-2021.e: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting openjdk8-8.472.08.1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing perl5-5.42.0_1... [143amd64-deluxe-desktop-job-02] `-- Extracting perl5-5.42.0_1: .......... done [143amd64-deluxe-desktop-job-02] Extracting fastqc-0.12.1: .......... done ===== Message from openjdk8-8.472.08.1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> rna-seq-0.1.4_1 depends on package: fastqc>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: py311-multiqc>0 - not found ===> Installing existing package /packages/All/py311-multiqc-1.25.2_3.pkg [143amd64-deluxe-desktop-job-02] Installing py311-multiqc-1.25.2_3... [143amd64-deluxe-desktop-job-02] `-- Installing py311-Jinja2-3.1.6... [143amd64-deluxe-desktop-job-02] | `-- Installing py311-Babel-2.17.0_1... [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-Babel-2.17.0_1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing py311-markupsafe-3.0.3... [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-markupsafe-3.0.3: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting py311-Jinja2-3.1.6: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-coloredlogs-15.0.1_1... [143amd64-deluxe-desktop-job-02] | `-- Installing py311-humanfriendly-10.0_1... [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-humanfriendly-10.0_1: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting py311-coloredlogs-15.0.1_1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-humanize-4.14.0... [143amd64-deluxe-desktop-job-02] `-- Extracting py311-humanize-4.14.0: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-importlib-metadata-8.7.0... [143amd64-deluxe-desktop-job-02] | `-- Installing py311-zipp-3.21.0... [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-zipp-3.21.0: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting py311-importlib-metadata-8.7.0: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-markdown-3.10... [143amd64-deluxe-desktop-job-02] `-- Extracting py311-markdown-3.10: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-natsort-8.4.0_1... [143amd64-deluxe-desktop-job-02] `-- Extracting py311-natsort-8.4.0_1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-numpy-1.26.4_11,1... [143amd64-deluxe-desktop-job-02] | `-- Installing openblas-0.3.30,2... [143amd64-deluxe-desktop-job-02] | `-- Extracting openblas-0.3.30,2: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing suitesparse-umfpack-6.3.7... [143amd64-deluxe-desktop-job-02] | | `-- Installing suitesparse-amd-3.3.4... [143amd64-deluxe-desktop-job-02] | | `-- Installing suitesparse-config-7.12.1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting suitesparse-config-7.12.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting suitesparse-amd-3.3.4: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing suitesparse-camd-3.3.5... [143amd64-deluxe-desktop-job-02] | | `-- Extracting suitesparse-camd-3.3.5: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing suitesparse-ccolamd-3.3.5... [143amd64-deluxe-desktop-job-02] | | `-- Extracting suitesparse-ccolamd-3.3.5: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing suitesparse-cholmod-5.3.4... [143amd64-deluxe-desktop-job-02] | | `-- Installing suitesparse-colamd-3.3.5... [143amd64-deluxe-desktop-job-02] | | `-- Extracting suitesparse-colamd-3.3.5: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting suitesparse-cholmod-5.3.4: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting suitesparse-umfpack-6.3.7: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting py311-numpy-1.26.4_11,1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-orca-1.8_2... [143amd64-deluxe-desktop-job-02] | `-- Installing py311-pandas-2.3.3,1... [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-bottleneck-1.3.8_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-bottleneck-1.3.8_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-numexpr-2.14.1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-numexpr-2.14.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-python-dateutil-2.9.0... [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-six-1.17.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-six-1.17.0: ........ done [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-python-dateutil-2.9.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-pytz-2025.2_1,1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-pytz-2025.2_1,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-sqlite3-3.11.14_10... [143amd64-deluxe-desktop-job-02] | | `-- Installing sqlite3-3.50.4_2,1... [143amd64-deluxe-desktop-job-02] | | | `-- Installing libedit-3.1.20251016_1,1... 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[143amd64-deluxe-desktop-job-02] | | `-- Extracting lzo2-2.10_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-mock-5.2.0_1... [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-mock-5.2.0_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-py-cpuinfo-9.0.0_1... [143amd64-deluxe-desktop-job-02] | | `-- Installing lscpu-1.3.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting lscpu-1.3.0: .. done [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-py-cpuinfo-9.0.0_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing ucl-1.03_5... [143amd64-deluxe-desktop-job-02] | | `-- Extracting ucl-1.03_5: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-tables-3.10.2_2: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing py311-toolz-1.0.0_1... [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-toolz-1.0.0_1: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting py311-orca-1.8_2: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-pillow-11.3.0_1... [143amd64-deluxe-desktop-job-02] | `-- Installing libavif-1.3.0_2... [143amd64-deluxe-desktop-job-02] | | `-- Installing aom-3.13.1... [143amd64-deluxe-desktop-job-02] | | `-- Installing vmaf-3.0.0... [143amd64-deluxe-desktop-job-02] | | `-- Extracting vmaf-3.0.0: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting aom-3.13.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing dav1d-1.5.2... [143amd64-deluxe-desktop-job-02] | | `-- Extracting dav1d-1.5.2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing gdk-pixbuf2-2.44.1... [143amd64-deluxe-desktop-job-02] | | `-- Installing libxml2-2.14.6... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libxml2-2.14.6: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing shared-mime-info-2.4_2... [143amd64-deluxe-desktop-job-02] | | `-- Extracting shared-mime-info-2.4_2: ......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting gdk-pixbuf2-2.44.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing libyuv-0.0.1903... [143amd64-deluxe-desktop-job-02] | | `-- Extracting libyuv-0.0.1903: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting libavif-1.3.0_2: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing libimagequant-4.4.1_1... [143amd64-deluxe-desktop-job-02] | `-- Extracting libimagequant-4.4.1_1: ...... done [143amd64-deluxe-desktop-job-02] | `-- Installing libraqm-0.10.3... [143amd64-deluxe-desktop-job-02] | | `-- Installing fribidi-1.0.16... 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[143amd64-deluxe-desktop-job-02] | `-- Extracting py311-certifi-2025.11.12_1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing py311-charset-normalizer-3.4.4... [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-charset-normalizer-3.4.4: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing py311-idna-3.11... [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-idna-3.11: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing py311-pysocks-1.7.1_1... [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-pysocks-1.7.1_1: .......... done [143amd64-deluxe-desktop-job-02] | `-- Installing py311-urllib3-2.6.2,1... [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-urllib3-2.6.2,1: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting py311-requests-2.32.5: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-rich-14.2.0... [143amd64-deluxe-desktop-job-02] | `-- Installing py311-markdown-it-py-4.0.0... 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[143amd64-deluxe-desktop-job-02] | | `-- Installing py311-networkx-3.5_3,2... [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-gdal-3.11.5... [143amd64-deluxe-desktop-job-02] | | | `-- Installing gdal-3.11.5_2... [143amd64-deluxe-desktop-job-02] | | | `-- Installing curl-8.17.0... [143amd64-deluxe-desktop-job-02] | | | | `-- Installing libidn2-2.3.8... [143amd64-deluxe-desktop-job-02] | | | | `-- Installing libunistring-1.4.1... [143amd64-deluxe-desktop-job-02] | | | | `-- Extracting libunistring-1.4.1: .......... done [143amd64-deluxe-desktop-job-02] | | | | `-- Extracting libidn2-2.3.8: .......... done [143amd64-deluxe-desktop-job-02] | | | | `-- Installing libnghttp2-1.68.0... [143amd64-deluxe-desktop-job-02] | | | | `-- Extracting libnghttp2-1.68.0: ....... done [143amd64-deluxe-desktop-job-02] | | | | `-- Installing libpsl-0.21.5_2... 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[143amd64-deluxe-desktop-job-02] | | | `-- Installing libxslt-1.1.43_1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libxslt-1.1.43_1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-lxml-6.0.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-matplotlib-3.8.0_2... [143amd64-deluxe-desktop-job-02] | | | `-- Installing py311-contourpy-1.3.3... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting py311-contourpy-1.3.3: .......... done [143amd64-deluxe-desktop-job-02] | | | `-- Installing py311-cycler-0.12.1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting py311-cycler-0.12.1: ......... done [143amd64-deluxe-desktop-job-02] | | | `-- Installing py311-fonttools-4.61.1... [143amd64-deluxe-desktop-job-02] | | | `-- Installing py311-brotli-1.2.0... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting py311-brotli-1.2.0: ......... done [143amd64-deluxe-desktop-job-02] | | | `-- Installing py311-unicodedata2-17.0.0... 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[143amd64-deluxe-desktop-job-02] | | | | `-- Extracting libXmu-1.1.4,1: .......... done [143amd64-deluxe-desktop-job-02] | | | | `-- Installing libXpm-3.5.17_1... [143amd64-deluxe-desktop-job-02] | | | | `-- Extracting libXpm-3.5.17_1: .......... done [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libXaw-1.0.16,2: .......... done [143amd64-deluxe-desktop-job-02] | | | `-- Installing libgd-2.3.3_13,1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libgd-2.3.3_13,1: .......... done [143amd64-deluxe-desktop-job-02] | | | `-- Installing libltdl-2.5.4... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting libltdl-2.5.4: ......... done [143amd64-deluxe-desktop-job-02] | | | `-- Installing pango-1.56.4... [143amd64-deluxe-desktop-job-02] | | | | `-- Installing libthai-0.1.29_2... [143amd64-deluxe-desktop-job-02] | | | | `-- Installing libdatrie-0.2.14_1... [143amd64-deluxe-desktop-job-02] | | | | `-- Extracting libdatrie-0.2.14_1: .......... done [143amd64-deluxe-desktop-job-02] | | | | `-- Extracting libthai-0.1.29_2: .......... done [143amd64-deluxe-desktop-job-02] | | | `-- Extracting pango-1.56.4: .......... done [143amd64-deluxe-desktop-job-02] | | | `-- Extracting graphviz-14.1.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-pydot-4.0.1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-pygraphviz-1.6_2... [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-pygraphviz-1.6_2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Installing py311-scikit-sparse-0.4.16_2... [143amd64-deluxe-desktop-job-02] | | | `-- Installing py311-scipy-1.11.1_4,1... [143amd64-deluxe-desktop-job-02] | | | `-- Installing blas-3.12.1... [143amd64-deluxe-desktop-job-02] | | | `-- Extracting blas-3.12.1: ..... done [143amd64-deluxe-desktop-job-02] | | | `-- Extracting py311-scipy-1.11.1_4,1: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-scikit-sparse-0.4.16_2: .......... done [143amd64-deluxe-desktop-job-02] | | `-- Extracting py311-networkx-3.5_3,2: .......... done [143amd64-deluxe-desktop-job-02] | `-- Extracting py311-colormath-3.0.0_4: .......... done [143amd64-deluxe-desktop-job-02] `-- Extracting py311-spectra-0.0.11_3: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-tqdm-4.67.1... [143amd64-deluxe-desktop-job-02] `-- Extracting py311-tqdm-4.67.1: .......... done [143amd64-deluxe-desktop-job-02] `-- Installing py311-typeguard-4.4.4... [143amd64-deluxe-desktop-job-02] `-- Extracting py311-typeguard-4.4.4: .......... done [143amd64-deluxe-desktop-job-02] Extracting py311-multiqc-1.25.2_3: .......... done ==> Running trigger: gdk-pixbuf-query-loaders.ucl Generating gdk-pixbuf modules cache ==> Running trigger: shared-mime-info.ucl Building the Shared MIME-Info database cache ===== Message from py311-pandas-2.3.3,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. ===== Message from libraqm-0.10.3: -- ===> NOTICE: The libraqm 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from py311-urllib3-2.6.2,1: -- Since version 1.25 HTTPS connections are now verified by default which is done via "cert_reqs = 'CERT_REQUIRED'". While certificate verification can be disabled via "cert_reqs = 'CERT_NONE'", it's highly recommended to leave it on. Various consumers of net/py-urllib3 already have implemented routines that either explicitly enable or disable HTTPS certificate verification (e.g. via configuration settings, CLI arguments, etc.). Yet it may happen that there are still some consumers which don't explicitly enable/disable certificate verification for HTTPS connections which could then lead to errors (as is often the case with self-signed certificates). In case of an error one should try first to temporarily disable certificate verification of the problematic urllib3 consumer to see if that approach will remedy the issue. ===== Message from boost-libs-1.89.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===== Message from postgresql17-client-17.7_2: -- The PostgreSQL port has a collection of "side orders": postgresql-docs For all of the html documentation p5-Pg A perl5 API for client access to PostgreSQL databases. postgresql-tcltk If you want tcl/tk client support. postgresql-jdbc For Java JDBC support. postgresql-odbc For client access from unix applications using ODBC as access method. Not needed to access unix PostgreSQL servers from Win32 using ODBC. See below. ruby-postgres, py-psycopg For client access to PostgreSQL databases using the ruby & python languages. postgresql-plperl, postgresql-pltcl & postgresql-plruby For using perl5, tcl & ruby as procedural languages. postgresql-contrib Lots of contributed utilities, postgresql functions and datatypes. There you find pg_standby, pgcrypto and many other cool things. etc... ===== Message from py311-kiwisolver-1.4.9,1: -- ===> NOTICE: The py311-kiwisolver 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> rna-seq-0.1.4_1 depends on package: py311-multiqc>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: biolibc-tools>0 - not found ===> Installing existing package /packages/All/biolibc-tools-0.1.5.pkg [143amd64-deluxe-desktop-job-02] Installing biolibc-tools-0.1.5... [143amd64-deluxe-desktop-job-02] `-- Installing xxhash-0.8.3... [143amd64-deluxe-desktop-job-02] `-- Extracting xxhash-0.8.3: .......... done [143amd64-deluxe-desktop-job-02] Extracting biolibc-tools-0.1.5: .......... done ===> rna-seq-0.1.4_1 depends on package: biolibc-tools>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: gffread>0 - not found ===> Installing existing package /packages/All/gffread-0.12.7.pkg [143amd64-deluxe-desktop-job-02] Installing gffread-0.12.7... [143amd64-deluxe-desktop-job-02] Extracting gffread-0.12.7: . done ===> rna-seq-0.1.4_1 depends on package: gffread>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: kallisto>0 - not found ===> Installing existing package /packages/All/kallisto-0.51.1_1,1.pkg [143amd64-deluxe-desktop-job-02] Installing kallisto-0.51.1_1,1... [143amd64-deluxe-desktop-job-02] `-- Installing htslib-1.22... [143amd64-deluxe-desktop-job-02] `-- Extracting htslib-1.22: .......... done [143amd64-deluxe-desktop-job-02] Extracting kallisto-0.51.1_1,1: .......... done ===> rna-seq-0.1.4_1 depends on package: kallisto>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: hisat2>0 - not found ===> Installing existing package /packages/All/hisat2-2.2.1_2.pkg [143amd64-deluxe-desktop-job-02] Installing hisat2-2.2.1_2... [143amd64-deluxe-desktop-job-02] Extracting hisat2-2.2.1_2: .......... done ===> rna-seq-0.1.4_1 depends on package: hisat2>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: rna-STAR>0 - not found ===> Installing existing package /packages/All/rna-STAR-2.7.11.a_1.pkg [143amd64-deluxe-desktop-job-02] Installing rna-STAR-2.7.11.a_1... [143amd64-deluxe-desktop-job-02] Extracting rna-STAR-2.7.11.a_1: . done ===> rna-seq-0.1.4_1 depends on package: rna-STAR>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: samtools>0 - not found ===> Installing existing package /packages/All/samtools-1.22.pkg [143amd64-deluxe-desktop-job-02] Installing samtools-1.22... [143amd64-deluxe-desktop-job-02] Extracting samtools-1.22: .......... done ===> rna-seq-0.1.4_1 depends on package: samtools>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: fasda>0 - not found ===> Installing existing package /packages/All/fasda-0.2.0.1.pkg [143amd64-deluxe-desktop-job-02] Installing fasda-0.2.0.1... [143amd64-deluxe-desktop-job-02] `-- Installing stringtie-2.1.1... [143amd64-deluxe-desktop-job-02] `-- Extracting stringtie-2.1.1: . done [143amd64-deluxe-desktop-job-02] Extracting fasda-0.2.0.1: .......... done ===> rna-seq-0.1.4_1 depends on package: fasda>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: webbrowser>0 - not found ===> Installing existing package /packages/All/webbrowser-0.4.0.pkg [143amd64-deluxe-desktop-job-02] Installing webbrowser-0.4.0... [143amd64-deluxe-desktop-job-02] Extracting webbrowser-0.4.0: .. done ===> rna-seq-0.1.4_1 depends on package: webbrowser>0 - found ===> Returning to build of rna-seq-0.1.4_1 ===> rna-seq-0.1.4_1 depends on package: curl>0 - found ===> rna-seq-0.1.4_1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for rna-seq-0.1.4_1 ===> Generating temporary packing list ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-30T22:24:37+0000' 'PKG_NOTE_ports_top_git_hash=3dd9e2202282' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=b304d8ab18ac' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.4' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for rna-seq-0.1.4_1 ===> Building rna-seq-0.1.4_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for rna-seq-0.1.4_1 build of biology/rna-seq | rna-seq-0.1.4_1 ended at Tue Dec 30 17:24:57 EST 2025 build time: 00:00:21