=>> Building biology/vsearch build started at Thu Mar 12 02:12:50 EDT 2026 port directory: /usr/ports/biology/vsearch package name: vsearch-2.30.4 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 650 Feb 17 19:06 /usr/ports/biology/vsearch/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: e14df5e88aa2 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE 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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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--- ===> The following configuration options are available for vsearch-2.30.4: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vsearch/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vsearch/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vsearch/work/.cache HOME=/wrkdirs/usr/ports/biology/vsearch/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vsearch/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vsearch/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vsearch/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vsearch/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vsearch/work/.cache HOME=/wrkdirs/usr/ports/biology/vsearch/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vsearch/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vsearch/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 DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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-- PORTDOCS="" DOCS="" NO_DOCS="@comment " OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/vsearch" EXAMPLESDIR="share/examples/vsearch" DATADIR="share/vsearch" WWWDIR="www/vsearch" ETCDIR="etc/vsearch" --End PLIST_SUB-- --SUB_LIST-- DOCS="" NO_DOCS="@comment " PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vsearch DOCSDIR=/usr/local/share/doc/vsearch EXAMPLESDIR=/usr/local/share/examples/vsearch WWWDIR=/usr/local/www/vsearch ETCDIR=/usr/local/etc/vsearch --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vsearch-2.30.4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> vsearch-2.30.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vsearch-2.30.4 =========================================================================== =================================================== ===== 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 vsearch-2.30.4 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vsearch-2.30.4 for building => SHA256 Checksum OK for torognes-vsearch-v2.30.4_GH0.tar.gz. =========================================================================== =================================================== ===== 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 vsearch-2.30.4 for building ===> Extracting for vsearch-2.30.4 => SHA256 Checksum OK for torognes-vsearch-v2.30.4_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for vsearch-2.30.4 ===> Applying FreeBSD patches for vsearch-2.30.4 from /usr/ports/biology/vsearch/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vsearch-2.30.4 depends on package: ghostscript10>=10.02.0 - not found ===> Installing existing package /packages/All/ghostscript10-10.06.0_2.pkg [pkg.DaveG.ca] Installing ghostscript10-10.06.0_2... [pkg.DaveG.ca] `-- Installing cups-2.4.16... [pkg.DaveG.ca] | `-- Installing avahi-app-0.8_6... [pkg.DaveG.ca] | | `-- Installing dbus-1.16.2_4,1... [pkg.DaveG.ca] | | `-- Installing expat-2.7.4... [pkg.DaveG.ca] | | `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] | | `-- Installing libICE-1.1.2,1... [pkg.DaveG.ca] | | `-- Extracting libICE-1.1.2,1: .......... done [pkg.DaveG.ca] | | `-- Installing libSM-1.2.6,1... [pkg.DaveG.ca] | | `-- Extracting libSM-1.2.6,1: ........ done [pkg.DaveG.ca] | | `-- Installing libX11-1.8.12,1... [pkg.DaveG.ca] | | | `-- Installing libxcb-1.17.0... [pkg.DaveG.ca] | | | `-- Installing libXau-1.0.12... [pkg.DaveG.ca] | | | `-- Extracting libXau-1.0.12: .......... done [pkg.DaveG.ca] | | | `-- Installing libXdmcp-1.1.5... [pkg.DaveG.ca] | | | | `-- Installing xorgproto-2024.1... [pkg.DaveG.ca] | | | | `-- Extracting xorgproto-2024.1: .......... done [pkg.DaveG.ca] | | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg.DaveG.ca] | | | `-- Extracting libxcb-1.17.0: .......... done [pkg.DaveG.ca] | | `-- Extracting libX11-1.8.12,1: .......... done [pkg.DaveG.ca] | | `-- Installing libxml2-2.15.2... [pkg.DaveG.ca] | | | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] | | `-- Extracting libxml2-2.15.2: .......... done ===> Creating groups Creating group 'messagebus' with gid '556' ===> Creating users Creating user 'messagebus' with uid '556' [pkg.DaveG.ca] | | `-- Extracting dbus-1.16.2_4,1: ......... done [pkg.DaveG.ca] | | `-- Installing dbus-glib-0.114... [pkg.DaveG.ca] | | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] | | `-- Installing glib-2.84.4,2... [pkg.DaveG.ca] | | | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | | | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | | | `-- Installing libiconv-1.18_1... [pkg.DaveG.ca] | | | `-- Extracting libiconv-1.18_1: .......... done [pkg.DaveG.ca] | | | `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] | | | `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] | | | `-- Installing pcre2-10.47_1... [pkg.DaveG.ca] | | | `-- Extracting pcre2-10.47_1: .......... done [pkg.DaveG.ca] | | | `-- Installing py311-packaging-26.0... [pkg.DaveG.ca] | | | `-- Installing python311-3.11.15... [pkg.DaveG.ca] | | | | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | | | | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | | | `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] | | | `-- Extracting py311-packaging-26.0: .......... done [pkg.DaveG.ca] | | `-- Extracting glib-2.84.4,2: .......... done [pkg.DaveG.ca] | | `-- Extracting dbus-glib-0.114: .......... done [pkg.DaveG.ca] | | `-- Installing gdbm-1.26... [pkg.DaveG.ca] | | `-- Extracting gdbm-1.26: .......... done [pkg.DaveG.ca] | | `-- Installing gnome_subr-1.0... [pkg.DaveG.ca] | | `-- Extracting gnome_subr-1.0: . done [pkg.DaveG.ca] | | `-- Installing libdaemon-0.14_1... [pkg.DaveG.ca] | | `-- Extracting libdaemon-0.14_1: .......... done [pkg.DaveG.ca] | | `-- Installing libevent-2.1.12... [pkg.DaveG.ca] | | `-- Extracting libevent-2.1.12: .......... done ===> Creating groups Creating group 'avahi' with gid '558' ===> Creating users Creating user 'avahi' with uid '558' [pkg.DaveG.ca] | `-- Extracting avahi-app-0.8_6: .......... done [pkg.DaveG.ca] | `-- Installing gnutls-3.8.12... [pkg.DaveG.ca] | | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] | | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | | `-- Installing libtasn1-4.21.0... [pkg.DaveG.ca] | | `-- Extracting libtasn1-4.21.0: .......... done [pkg.DaveG.ca] | | `-- Installing nettle-3.10.2... [pkg.DaveG.ca] | | `-- Extracting nettle-3.10.2: .......... done [pkg.DaveG.ca] | | `-- Installing p11-kit-0.26.2... [pkg.DaveG.ca] | | `-- Extracting p11-kit-0.26.2: .......... done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting gnutls-3.8.12: .......... done [pkg.DaveG.ca] | `-- Installing libpaper-1.1.28_1... [pkg.DaveG.ca] | `-- Extracting libpaper-1.1.28_1: .......... done ===> Creating groups Creating group 'cups' with gid '193' ===> Creating users Creating user 'cups' with uid '193' [pkg.DaveG.ca] `-- Extracting cups-2.4.16: .......... done [pkg.DaveG.ca] `-- Installing fontconfig-2.17.1,1... [pkg.DaveG.ca] | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | `-- Installing png-1.6.55... [pkg.DaveG.ca] | | `-- Extracting png-1.6.55: .......... done [pkg.DaveG.ca] | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] `-- Extracting fontconfig-2.17.1,1: .......... done [pkg.DaveG.ca] `-- Installing jbig2dec-0.20_1... [pkg.DaveG.ca] `-- Extracting jbig2dec-0.20_1: ........ done [pkg.DaveG.ca] `-- Installing jpeg-turbo-3.1.3... [pkg.DaveG.ca] `-- Extracting jpeg-turbo-3.1.3: .......... done [pkg.DaveG.ca] `-- Installing lcms2-2.18... [pkg.DaveG.ca] | `-- Installing tiff-4.7.1... [pkg.DaveG.ca] | | `-- Installing jbigkit-2.1_3... [pkg.DaveG.ca] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg.DaveG.ca] | | `-- Installing lerc-4.0.0... [pkg.DaveG.ca] | | `-- Extracting lerc-4.0.0: ..... done [pkg.DaveG.ca] | | `-- Installing libdeflate-1.25... [pkg.DaveG.ca] | | `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] | `-- Extracting tiff-4.7.1: .......... done [pkg.DaveG.ca] `-- Extracting lcms2-2.18: .......... done [pkg.DaveG.ca] `-- Installing libXext-1.3.6,1... [pkg.DaveG.ca] `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] `-- Installing libXt-1.3.0,1... [pkg.DaveG.ca] `-- Extracting libXt-1.3.0,1: .......... done [pkg.DaveG.ca] `-- Installing libidn-1.43... [pkg.DaveG.ca] `-- Extracting libidn-1.43: .......... done [pkg.DaveG.ca] `-- Installing openjpeg-2.5.4_2... [pkg.DaveG.ca] `-- Extracting openjpeg-2.5.4_2: .......... done [pkg.DaveG.ca] `-- Installing poppler-data-0.4.12... [pkg.DaveG.ca] `-- Extracting poppler-data-0.4.12: .......... done [pkg.DaveG.ca] `-- Installing urw-base35-fonts-20200910... [pkg.DaveG.ca] | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | `-- Installing libfontenc-1.1.8... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg.DaveG.ca] | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] `-- Extracting urw-base35-fonts-20200910: .......... done [pkg.DaveG.ca] Extracting ghostscript10-10.06.0_2: .......... 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 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 python311-3.11.15: -- 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 ===== 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 ghostscript10-10.06.0_2: -- 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. ===> vsearch-2.30.4 depends on package: ghostscript10>=10.02.0 - found ===> Returning to build of vsearch-2.30.4 ===> vsearch-2.30.4 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> vsearch-2.30.4 depends on package: gmake>=4.4.1 - found ===> Returning to build of vsearch-2.30.4 ===> vsearch-2.30.4 depends on package: autoconf>=2.72_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [pkg.DaveG.ca] Installing autoconf-2.72_1... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing m4-1.4.20,1... [pkg.DaveG.ca] `-- Extracting m4-1.4.20,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72_1: .......... done ===> vsearch-2.30.4 depends on package: autoconf>=2.72_1 - found ===> Returning to build of vsearch-2.30.4 ===> vsearch-2.30.4 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [pkg.DaveG.ca] Installing automake-1.18.1... [pkg.DaveG.ca] Extracting automake-1.18.1: .......... done ===> vsearch-2.30.4 depends on package: automake>=1.18.1 - found ===> Returning to build of vsearch-2.30.4 ===> vsearch-2.30.4 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> vsearch-2.30.4 depends on file: /usr/local/bin/ccache - found ===> Returning to build of vsearch-2.30.4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vsearch-2.30.4 configure.ac:103: installing './compile' configure.ac:6: installing './config.guess' configure.ac:6: installing './config.sub' configure.ac:7: installing './install-sh' configure.ac:7: installing './missing' src/Makefile.am: installing './depcomp' configure: loading site script /usr/ports/Templates/config.site checking build system type... amd64-portbld-freebsd14.4 checking host system type... amd64-portbld-freebsd14.4 checking target system type... amd64-portbld-freebsd14.4 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports nested variables... yes checking xargs -n works... yes checking whether UID '0' is supported by ustar format... yes checking whether GID '0' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for ranlib... ranlib checking for pthread_create in -lpthread... yes checking for dlopen in -ldl... yes checking for GetProcessMemoryInfo in -lpsapi... no checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for getopt.h... (cached) yes checking for fcntl.h... (cached) yes checking for regex.h... yes checking for string.h... (cached) yes checking for sys/time.h... (cached) yes checking for dlfcn.h... (cached) yes checking for pthread.h... (cached) yes checking for inline... inline checking for size_t... (cached) yes checking for uint32_t... (cached) yes checking for int64_t... (cached) yes checking for uint64_t... (cached) yes checking for uint8_t... (cached) yes checking for memmove... (cached) yes checking for memcpy... (cached) yes checking for posix_memalign... yes checking for gettimeofday... (cached) yes checking for localtime... (cached) yes checking for memchr... (cached) yes checking for memset... (cached) yes checking for pow... yes checking for regcomp... yes checking for strchr... (cached) yes checking for strcspn... (cached) yes checking for sysinfo... no checking for bzlib.h... yes checking for zlib.h... (cached) yes checking for ps2pdf... yes checking for windows.h... no checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for vsearch-2.30.4 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4' Making all in src gmake[2]: Entering directory 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$depbase.Po depbase=`echo showalign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT showalign.o -MD -MP -MF $depbase.Tpo -c -o showalign.o showalign.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo shuffle.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT shuffle.o -MD -MP -MF $depbase.Tpo -c -o shuffle.o shuffle.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sintax.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sintax.o -MD -MP -MF $depbase.Tpo -c -o sintax.o sintax.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sortbylength.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sortbylength.o -MD -MP -MF $depbase.Tpo -c -o sortbylength.o sortbylength.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sortbysize.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sortbysize.o -MD -MP -MF $depbase.Tpo -c -o sortbysize.o sortbysize.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo subsample.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT subsample.o -MD -MP -MF $depbase.Tpo -c -o subsample.o subsample.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo tax.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT tax.o -MD -MP -MF $depbase.Tpo -c -o tax.o tax.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo udb.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT udb.o -MD -MP -MF $depbase.Tpo -c -o udb.o udb.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo unique.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT unique.o -MD -MP -MF $depbase.Tpo -c -o unique.o unique.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo userfields.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT userfields.o -MD -MP -MF $depbase.Tpo -c -o userfields.o userfields.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo util.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT util.o -MD -MP -MF $depbase.Tpo -c -o util.o util.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo vsearch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT vsearch.o -MD -MP -MF $depbase.Tpo -c -o vsearch.o vsearch.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -Wno-sign-compare -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcityhash_a-city.o -MD -MP -MF .deps/libcityhash_a-city.Tpo -c -o libcityhash_a-city.o `test -f 'city.cc' || echo './'`city.cc depbase=`echo cpu.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cpu.o -MD -MP -MF $depbase.Tpo -c -o cpu.o cpu.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo utils/fatal.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT utils/fatal.o -MD -MP -MF $depbase.Tpo -c -o utils/fatal.o utils/fatal.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo utils/maps.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT utils/maps.o -MD -MP -MF $depbase.Tpo -c -o utils/maps.o utils/maps.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo utils/check_output_filehandle.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT utils/check_output_filehandle.o -MD -MP -MF $depbase.Tpo -c -o utils/check_output_filehandle.o utils/check_output_filehandle.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo utils/cigar.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT utils/cigar.o -MD -MP -MF $depbase.Tpo -c -o utils/cigar.o utils/cigar.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo utils/compare_strings_nocase.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT utils/compare_strings_nocase.o -MD -MP -MF $depbase.Tpo -c -o utils/compare_strings_nocase.o utils/compare_strings_nocase.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo utils/open_file.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT utils/open_file.o -MD -MP -MF $depbase.Tpo -c -o utils/open_file.o utils/open_file.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo utils/os_byteswap.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT utils/os_byteswap.o -MD -MP -MF $depbase.Tpo -c -o utils/os_byteswap.o utils/os_byteswap.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo utils/xpthread.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT utils/xpthread.o -MD -MP -MF $depbase.Tpo -c -o utils/xpthread.o utils/xpthread.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo utils/seqcmp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT utils/seqcmp.o -MD -MP -MF $depbase.Tpo -c -o utils/seqcmp.o utils/seqcmp.cpp &&\ mv -f $depbase.Tpo $depbase.Po mv -f .deps/libcityhash_a-city.Tpo .deps/libcityhash_a-city.Po rm -f libcityhash.a ar cr libcityhash.a libcityhash_a-city.o ranlib libcityhash.a rm -f libcpu.a ar cr libcpu.a cpu.o ranlib libcpu.a c++ -Wall -Wextra -Wpedantic -Wno-ignored-attributes -DNDEBUG -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -o ../bin/vsearch align_simd.o allpairs.o arch.o attributes.o bitmap.o chimera.o cluster.o cut.o db.o dbhash.o dbindex.o derep.o derep_prefix.o derep_smallmem.o dynlibs.o eestats.o fasta2fastq.o fasta.o fastq.o fastq_chars.o fastq_join.o fastq_mergepairs.o fastq_stats.o fastqops.o fastx.o filter.o getseq.o kmerhash.o linmemalign.o mask.o md5.o minheap.o msa.o orient.o otutable.o rereplicate.o results.o search.o searchcore.o search_exact.o sff_convert.o sha1.o showalign.o shuffle.o sintax.o sortbylength.o sortbysize.o subsample.o tax.o udb.o unique.o userfields.o util.o utils/fatal.o utils/maps.o utils/check_output_filehandle.o utils/cigar.o utils/compare_strings_nocase.o utils/open_file.o utils/os_byteswap.o utils/xpthread.o utils/seqcmp.o vsearch.o libcityhash.a libcpu.a -ldl -lpthread -L/usr/local/lib gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/src' Making all in man gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/man' sed -e 's/\\-/-/g' vsearch.1 | \ iconv -f UTF-8 -t ISO-8859-1 | \ groff -W space -t -m mandoc -T ps -P -pa4 | ps2pdf - vsearch_manual.pdf /bin/sh: groff: not found gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/man' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for vsearch-2.30.4 ===> Generating temporary packing list Making install in src gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/src' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/src' /bin/mkdir -p '/wrkdirs/usr/ports/biology/vsearch/work/stage/usr/local/bin' install -s -m 555 ../bin/vsearch '/wrkdirs/usr/ports/biology/vsearch/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/src' Making install in man gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/man' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/man' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/vsearch/work/stage/usr/local/share/doc/vsearch' install -m 0644 vsearch_manual.pdf '/wrkdirs/usr/ports/biology/vsearch/work/stage/usr/local/share/doc/vsearch' /bin/mkdir -p '/wrkdirs/usr/ports/biology/vsearch/work/stage/usr/local/share/man/man1' install -m 0644 vsearch.1 '/wrkdirs/usr/ports/biology/vsearch/work/stage/usr/local/share/man/man1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/man' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4/man' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.4' ====> 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=2026-03-12T06:12:50+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=e14df5e88aa2' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for vsearch-2.30.4 ===> Building vsearch-2.30.4 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for vsearch-2.30.4 build of biology/vsearch | vsearch-2.30.4 ended at Thu Mar 12 02:13:58 EDT 2026 build time: 00:01:09