[package - main-amd64-default][biology/cufflinks] Failed for cufflinks-2.2.1.89_13 in configure
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Date: Wed, 22 Oct 2025 08:27:29 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy24/data/main-amd64-default/pb14ef2e3a017_s1cc316727e/logs/cufflinks-2.2.1.89_13.log
Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=pb14ef2e3a017_s1cc316727e
Log:
=>> Building biology/cufflinks
build started at Wed Oct 22 08:27:10 -00 2025
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.89_13
building for: FreeBSD main-amd64-default-job-12 16.0-CURRENT FreeBSD 16.0-CURRENT 1600002 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1328 Oct 21 01:01 /usr/ports/biology/cufflinks/Makefile
Ports top last git commit: b14ef2e3a
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: 1600002
Job Id: 12
!!! Jail is newer than host. (Jail: 1600002, Host: 1600000) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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--MAINTAINER--
yuri@FreeBSD.org
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--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--
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--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd16 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
[main-amd64-default-job-12] Installing pkg-2.3.1...
[main-amd64-default-job-12] 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
[main-amd64-default-job-12] Installing eigen-3.4.0_4...
[main-amd64-default-job-12] `-- Installing blas-3.12.1...
[main-amd64-default-job-12] | `-- Installing gcc13-13.3.0_3...
<snip>
[main-amd64-default-job-12] | | `-- Extracting libunistring-1.4.1: .......... done
[main-amd64-default-job-12] | `-- Extracting libidn2-2.3.8: .......... done
[main-amd64-default-job-12] | `-- Installing libnghttp2-1.67.1...
[main-amd64-default-job-12] | `-- Extracting libnghttp2-1.67.1: .......... done
[main-amd64-default-job-12] | `-- Installing libpsl-0.21.5_2...
[main-amd64-default-job-12] | `-- Extracting libpsl-0.21.5_2: .......... done
[main-amd64-default-job-12] | `-- Installing libssh2-1.11.1,3...
[main-amd64-default-job-12] | `-- Extracting libssh2-1.11.1,3: .......... done
[main-amd64-default-job-12] `-- Extracting curl-8.16.0: .......... done
[main-amd64-default-job-12] `-- Installing libdeflate-1.24...
[main-amd64-default-job-12] `-- Extracting libdeflate-1.24: .......... done
[main-amd64-default-job-12] 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... freebsd16
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-freebsd16.0
checking host system type... amd64-portbld-freebsd16.0
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 yuri@FreeBSD.org [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