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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy23/data/150releng-amd64-default/5beafd729224/logs/cufflinks-2.2.1.89_13.log Build URL: https://pkg-status.freebsd.org/beefy23/build.html?mastername=150releng-amd64-default&build=5beafd729224 Log: =>> Building biology/cufflinks build started at Tue Oct 21 05:06:56 -00 2025 port directory: /usr/ports/biology/cufflinks package name: cufflinks-2.2.1.89_13 building for: FreeBSD 150releng-amd64-default-job-18 15.0-BETA2 FreeBSD 15.0-BETA2 1500067 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 1328 Oct 21 01:01 /usr/ports/biology/cufflinks/Makefile Ports top last git commit: 5beafd729 Ports top unclean checkout: no Port dir last git commit: 67fb95fb3 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1600000 Jail OSVERSION: 1500067 Job Id: 18 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500067 UNAME_v=FreeBSD 15.0-BETA2 1500067 UNAME_r=15.0-BETA2 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=/usr/local/poudriere/data/.m/150releng-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/150releng-amd64-default/18/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=150releng-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/150releng-amd64-default/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-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/cufflinks/work/.cache HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/cufflinks/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 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/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/cufflinks/work/.cache HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/cufflinks/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 -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/eigen3 " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="ins tall -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=freebsd15 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=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cufflinks" EXAMPLESDIR="share/examples/cufflinks" DATADIR="share/cufflinks" WWWDIR="www/cufflinks" ETCDIR="etc/cufflinks" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 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/cufflinks DOCSDIR=/usr/local/share/doc/cufflinks EXAMPLESDIR=/usr/local/share/examples/cufflinks WWWDIR=/usr/local/www/cufflinks ETCDIR=/usr/local/etc/cufflinks --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 BSL accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cufflinks-2.2.1.89_13 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1.pkg [150releng-amd64-default-job-18] Installing pkg-2.3.1... [150releng-amd64-default-job-18] Extracting pkg-2.3.1: .......... done ===> cufflinks-2.2.1.89_13 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cufflinks-2.2.1.89_13 =========================================================================== =======================<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 BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.89_13 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.89_13 for building => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz. => SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch. =========================================================================== =======================<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 BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.89_13 for building ===> Extracting for cufflinks-2.2.1.89_13 => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz. => SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch. =========================================================================== =======================<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 cufflinks-2.2.1.89_13 ===> Applying distribution patches for cufflinks-2.2.1.89_13 ===> Applying FreeBSD patches for cufflinks-2.2.1.89_13 from /usr/ports/biology/cufflinks/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cufflinks-2.2.1.89_13 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.4.0_4.pkg [150releng-amd64-default-job-18] Installing eigen-3.4.0_4... [150releng-amd64-default-job-18] `-- Installing blas-3.12.1... [150releng-amd64-default-job-18] | `-- Installing gcc13-13.3.0_3... [150releng-amd64-default-job-18] | | `-- Installing binutils-2.44,1... [150releng-amd64-default-job-18] | | `-- Installing indexinfo-0.3.1_1... [150releng-amd64-default-job-18] | | `-- Extracting indexinfo-0.3.1_1: .... done [150releng-amd64-default-job-18] | | `-- Installing zstd-1.5.7... [150releng-amd64-default-job-18] | | | `-- Installing liblz4-1.10.0,1... [150releng-amd64-default-job-18] | | | `-- Extracting liblz4-1.10.0,1: .......... done [150releng-amd64-default-job-18] | | `-- Extracting zstd-1.5.7: .......... done [150releng-amd64-default-job-18] | | `-- Extracting binutils-2.44,1: .......... done [150releng-amd64-default-job-18] | | `-- Installing gmp-6.3.0... [150releng-amd64-default-job-18] | | `-- Extracting gmp-6.3.0: .......... done <snip> [150releng-amd64-default-job-18] | | `-- Extracting libunistring-1.4.1: .......... done [150releng-amd64-default-job-18] | `-- Extracting libidn2-2.3.8: .......... done [150releng-amd64-default-job-18] | `-- Installing libnghttp2-1.67.1... [150releng-amd64-default-job-18] | `-- Extracting libnghttp2-1.67.1: .......... done [150releng-amd64-default-job-18] | `-- Installing libpsl-0.21.5_2... [150releng-amd64-default-job-18] | `-- Extracting libpsl-0.21.5_2: .......... done [150releng-amd64-default-job-18] | `-- Installing libssh2-1.11.1,3... [150releng-amd64-default-job-18] | `-- Extracting libssh2-1.11.1,3: .......... done [150releng-amd64-default-job-18] `-- Extracting curl-8.16.0: .......... done [150releng-amd64-default-job-18] `-- Installing libdeflate-1.24... [150releng-amd64-default-job-18] `-- Extracting libdeflate-1.24: .......... done [150releng-amd64-default-job-18] Extracting htslib-1.22: .......... done ===> cufflinks-2.2.1.89_13 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of cufflinks-2.2.1.89_13 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for cufflinks-2.2.1.89_13 sh: svnversion: not found sh: svnversion: not found sh: svnversion: not found configure.ac:44: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... ax_check_zlib.m4:62: AX_CHECK_ZLIB is expanded from... configure.ac:44: the top level sh: svnversion: not found sh: svnversion: not found configure.ac:36: installing 'build-aux/ar-lib' configure.ac:32: installing 'build-aux/compile' configure.ac:38: installing 'build-aux/config.guess' configure.ac:38: installing 'build-aux/config.sub' configure.ac:17: installing 'build-aux/install-sh' configure.ac:17: installing 'build-aux/missing' src/Makefile.am:113: warning: source file 'locfit/adap.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibility. src/Makefile.am:113: warning: source file 'locfit/ar_funs.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/arith.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/band.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_args.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_plot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/cmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_haz.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_int.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_odi.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/density.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dist.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_atree.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_interp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_kdtre.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_main.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_trian.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/family.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/fitted.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/frend.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/help.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_dercor.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_fitfun.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_robust.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_vari.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfstr.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/linalg.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/locfit.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_chol.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_eigen.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_jacob.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_max.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/makecmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/math.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/minmax.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/nbhd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pcomp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pout.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/preplot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/random.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/readfile.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb_cons.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/simul.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/solve.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/startlf.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/strings.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/vari.cpp' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/wdiag.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/weight.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am: installing 'build-aux/depcomp' configure: loading site script /usr/ports/Templates/config.site 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 how to create a pax tar archive... gnutar checking for gawk... (cached) /usr/bin/awk 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 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 whether /usr/local/bin/gmake sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking whether /usr/local/bin/python3.11 version is >= 2.4... yes checking for /usr/local/bin/python3.11 version... 3.11 checking for /usr/local/bin/python3.11 platform... freebsd15 checking for GNU default /usr/local/bin/python3.11 prefix... ${prefix} checking for GNU default /usr/local/bin/python3.11 exec_prefix... ${exec_prefix} checking for /usr/local/bin/python3.11 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.11/site-packages checking for /usr/local/bin/python3.11 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.11/site-packages checking build system type... amd64-portbld-freebsd15.0 checking host system type... amd64-portbld-freebsd15.0 checking for boostlib >= 1.47.0 (104700)... yes checking for htslib or bamlib... yes checking whether the Boost::System library is available... yes configure: error: Could not find a version of the library! ===> Script "configure" failed unexpectedly. Please report the problem to [email protected] [maintainer] and attach the "/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/config.log" including the output of the failure of your make command. Also, it might be a good idea to provide an overview of all packages installed on your system (e.g. a /usr/local/sbin/pkg-static info -g -Ea). *** Error code 1 Stop. make: stopped making "configure" in /usr/ports/biology/cufflinks
