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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy24/data/main-amd64-default/pe05e2042985b_s715cc25713/logs/vsearch-2.30.1.log Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=pe05e2042985b_s715cc25713 Log: =>> Building biology/vsearch build started at Tue Dec 16 14:28:18 -00 2025 port directory: /usr/ports/biology/vsearch package name: vsearch-2.30.1 building for: FreeBSD main-amd64-default-job-43 16.0-CURRENT FreeBSD 16.0-CURRENT 1600006 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 650 Oct 7 01:01 /usr/ports/biology/vsearch/Makefile Ports top last git commit: e05e2042985b2fb7ece06669592fd7618c9eae5f Ports top unclean checkout: no Port dir last git commit: f07bc6e23dc66bc4d886d148259f91ba93344cc3 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4-15-g61aba751 Host OSVERSION: 1600000 Jail OSVERSION: 1600006 Job Id: 43 !!! Jail is newer than host. (Jail: 1600006, Host: 1600000) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600006 UNAME_v=FreeBSD 16.0-CURRENT 1600006 UNAME_r=16.0-CURRENT 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=3.4.4-15-g61aba751 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/main-amd64-default/43/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4-15-g61aba751 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-2.30.1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- [email protected] --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=16.0 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--- # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### 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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vsearch-2.30.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [main-amd64-default-job-43] Installing pkg-2.4.2_1... [main-amd64-default-job-43] Extracting pkg-2.4.2_1: .......... done ===> vsearch-2.30.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vsearch-2.30.1 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by vsearch-2.30.1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by vsearch-2.30.1 for building => SHA256 Checksum OK for torognes-vsearch-v2.30.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by vsearch-2.30.1 for building ===> Extracting for vsearch-2.30.1 => SHA256 Checksum OK for torognes-vsearch-v2.30.1_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for vsearch-2.30.1 ===> Applying FreeBSD patches for vsearch-2.30.1 from /usr/ports/biology/vsearch/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vsearch-2.30.1 depends on package: ghostscript10>=10.02.0 - not found ===> Installing existing package /packages/All/ghostscript10-10.06.0_1.pkg [main-amd64-default-job-43] Installing ghostscript10-10.06.0_1... [main-amd64-default-job-43] `-- Installing cups-2.4.16... [main-amd64-default-job-43] | `-- Installing avahi-app-0.8_6... <snip> -- 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_1: -- 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-2.30.1 depends on package: ghostscript10>=10.02.0 - found ===> Returning to build of vsearch-2.30.1 ===> vsearch-2.30.1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [main-amd64-default-job-43] Installing gmake-4.4.1... [main-amd64-default-job-43] Extracting gmake-4.4.1: .......... done ===> vsearch-2.30.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of vsearch-2.30.1 ===> vsearch-2.30.1 depends on package: autoconf>=2.72_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [main-amd64-default-job-43] Installing autoconf-2.72_1... [main-amd64-default-job-43] `-- Installing autoconf-switch-20220527... [main-amd64-default-job-43] `-- Extracting autoconf-switch-20220527: .......... done [main-amd64-default-job-43] `-- Installing m4-1.4.20,1... [main-amd64-default-job-43] `-- Extracting m4-1.4.20,1: .......... done [main-amd64-default-job-43] `-- Installing perl5-5.42.0_1... [main-amd64-default-job-43] `-- Extracting perl5-5.42.0_1: .......... done [main-amd64-default-job-43] Extracting autoconf-2.72_1: .......... done ===> vsearch-2.30.1 depends on package: autoconf>=2.72_1 - found ===> Returning to build of vsearch-2.30.1 ===> vsearch-2.30.1 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [main-amd64-default-job-43] Installing automake-1.18.1... [main-amd64-default-job-43] Extracting automake-1.18.1: .......... done ===> vsearch-2.30.1 depends on package: automake>=1.18.1 - found ===> Returning to build of vsearch-2.30.1 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vsearch-2.30.1 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-freebsd16.0 checking host system type... amd64-portbld-freebsd16.0 checking target system type... amd64-portbld-freebsd16.0 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 =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for vsearch-2.30.1 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.1' Making all in src gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.1/src' depbase=`echo align_simd.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 align_simd.o -MD -MP -MF $depbase.Tpo -c -o align_simd.o align_simd.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo allpairs.o | sed 's|[^/]*$|.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 allpairs.o -MD -MP -MF $depbase.Tpo -c -o allpairs.o allpairs.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo arch.o | sed 's|[^/]*$|.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 arch.o -MD -MP -MF $depbase.Tpo -c -o arch.o arch.cc &&\ mv -f $depbase.Tpo $depbase.Po arch.cc:70:16: error: redefinition of 'memalignment' as different kind of symbol 70 | constexpr auto memalignment = 16; | ^ /usr/include/stdlib.h:175:8: note: previous definition is here 175 | size_t memalignment(const void *) __pure2; | ^ arch.cc:228:7: error: no matching function for call to 'posix_memalign' 228 | if (posix_memalign(&ptr, memalignment, size) != 0) | ^~~~~~~~~~~~~~ /usr/lib/clang/19/include/mm_malloc.h:25:16: note: candidate function not viable: no known conversion from 'size_t (const void *)' (aka 'unsigned long (const void *)') to 'size_t' (aka 'unsigned long') for 2nd argument 25 | extern "C" int posix_memalign(void **__memptr, size_t __alignment, size_t __size); | ^ ~~~~~~~~~~~~~~~~~~ 2 errors generated. gmake[2]: *** [Makefile:859: arch.o] Error 1 gmake[2]: *** Waiting for unfinished jobs.... gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.1/src' gmake[1]: *** [Makefile:381: all-recursive] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vsearch/work/vsearch-2.30.1' gmake: *** [Makefile:322: all] Error 2 ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped making "build" in /usr/ports/biology/vsearch
