[package - 124i386-quarterly][biology/cufflinks] Failed for cufflinks-2.2.1.89_4 in lib-depends
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Thu, 25 May 2023 15:23:11 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/beefy4/data/124i386-quarterly/56368df6bdde/logs/cufflinks-2.2.1.89_4.log
Build URL: https://pkg-status.freebsd.org/beefy4/build.html?mastername=124i386-quarterly&build=56368df6bdde
Log:
=>> Building biology/cufflinks
build started at Thu May 25 15:22:43 UTC 2023
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.89_4
building for: FreeBSD 124i386-quarterly-job-07 12.4-RELEASE-p2 FreeBSD 12.4-RELEASE-p2 i386
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400078
Jail OSVERSION: 1204000
Job Id: 07
---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1204000
UNAME_v=FreeBSD 12.4-RELEASE-p2
UNAME_r=12.4-RELEASE-p2
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-23-ga7f8d188
MASTERMNT=/usr/local/poudriere/data/.m/124i386-quarterly/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/124i386-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=124i386-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/124i386-quarterly/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake PYTHON="/usr/local/bin/python3.9" 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=2.71 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=2.71 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=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/eigen3 " MANPREFIX="/usr/local" BSD_INSTALL_PR
OGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=12.4 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/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 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---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/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 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd12.4 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd12.4 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_53255a77=yes
CC_OUTPUT_921dbbb2_911cfe02=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
CC_OUTPUT_921dbbb2_af59ad06=yes
CC_OUTPUT_921dbbb2_a15f3fcf=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd12.4 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=12.4-RELEASE-p2
OSREL=12.4
OSVERSION=1204000
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
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) 524288
stack size (kbytes, -s) 65536
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) 1024
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
--End resource limits--
=======================<phase: check-sanity >============================
===> License BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> cufflinks-2.2.1.89_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[124i386-quarterly-job-07] Installing pkg-1.19.1_1...
[124i386-quarterly-job-07] Extracting pkg-1.19.1_1: .......... done
===> cufflinks-2.2.1.89_4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of cufflinks-2.2.1.89_4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_4 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_4 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>============================
===========================================================================
=======================<phase: extract >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_4 for building
===> Extracting for cufflinks-2.2.1.89_4
=> 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 >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for cufflinks-2.2.1.89_4
===> Applying distribution patches for cufflinks-2.2.1.89_4
===> Applying FreeBSD patches for cufflinks-2.2.1.89_4 from /usr/ports/biology/cufflinks/files
===========================================================================
=======================<phase: build-depends >============================
===> cufflinks-2.2.1.89_4 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found
===> Installing existing package /packages/All/eigen-3.4.0_1.pkg
[124i386-quarterly-job-07] Installing eigen-3.4.0_1...
[124i386-quarterly-job-07] `-- Installing blas-3.11.0...
[124i386-quarterly-job-07] | `-- Installing gcc12-12.2.0_5...
[124i386-quarterly-job-07] | | `-- Installing binutils-2.40_4,1...
[124i386-quarterly-job-07] | | `-- Installing gettext-runtime-0.21.1...
[124i386-quarterly-job-07] | | | `-- Installing indexinfo-0.3.1...
[124i386-quarterly-job-07] | | | `-- Extracting indexinfo-0.3.1: .... done
[124i386-quarterly-job-07] | | `-- Extracting gettext-runtime-0.21.1: .......... done
[124i386-quarterly-job-07] | | `-- Installing zstd-1.5.4...
[124i386-quarterly-job-07] | | | `-- Installing liblz4-1.9.4,1...
[124i386-quarterly-job-07] | | | `-- Extracting liblz4-1.9.4,1: .......... done
[124i386-quarterly-job-07] | | `-- Extracting zstd-1.5.4: .......... done
[124i386-quarterly-job-07] | | `-- Extracting binutils-2.40_4,1: .......... done
[124i386-quarterly-job-07] | | `-- Installing gmp-6.2.1...
[124i386-quarterly-job-07] | | `-- Extracting gmp-6.2.1: .......... done
[124i386-quarterly-job-07] | | `-- Installing mpc-1.2.1...
[124i386-quarterly-job-07] | | `-- Installing mpfr-4.2.0,1...
[124i386-quarterly-job-07] | | `-- Extracting mpfr-4.2.0,1: .......... done
[124i386-quarterly-job-07] | | `-- Extracting mpc-1.2.1: ......... done
[124i386-quarterly-job-07] | `-- Extracting gcc12-12.2.0_5: .......... done
[124i386-quarterly-job-07] `-- Extracting blas-3.11.0: ........ done
[124i386-quarterly-job-07] `-- Installing lapack-3.11.0...
[124i386-quarterly-job-07] `-- Extracting lapack-3.11.0: .......... done
[124i386-quarterly-job-07] Extracting eigen-3.4.0_1: .......... done
=====
Message from gcc12-12.2.0_5:
--
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc12
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> cufflinks-2.2.1.89_4 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found
===> Returning to build of cufflinks-2.2.1.89_4
===> cufflinks-2.2.1.89_4 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[124i386-quarterly-job-07] Installing gmake-4.3_2...
[124i386-quarterly-job-07] Extracting gmake-4.3_2: .......... done
===> cufflinks-2.2.1.89_4 depends on package: gmake>=4.3 - found
===> Returning to build of cufflinks-2.2.1.89_4
===> cufflinks-2.2.1.89_4 depends on file: /usr/local/bin/python3.9 - not found
===> Installing existing package /packages/All/python39-3.9.16_2.pkg
[124i386-quarterly-job-07] Installing python39-3.9.16_2...
[124i386-quarterly-job-07] `-- Installing libffi-3.4.4...
[124i386-quarterly-job-07] `-- Extracting libffi-3.4.4: .......... done
[124i386-quarterly-job-07] `-- Installing mpdecimal-2.5.1...
[124i386-quarterly-job-07] `-- Extracting mpdecimal-2.5.1: .......... done
[124i386-quarterly-job-07] `-- Installing readline-8.2.1...
[124i386-quarterly-job-07] `-- Extracting readline-8.2.1: .......... done
[124i386-quarterly-job-07] Extracting python39-3.9.16_2: .......... done
=====
Message from python39-3.9.16_2:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> cufflinks-2.2.1.89_4 depends on file: /usr/local/bin/python3.9 - found
===> Returning to build of cufflinks-2.2.1.89_4
===> cufflinks-2.2.1.89_4 depends on package: autoconf>=2.71 - not found
===> Installing existing package /packages/All/autoconf-2.71.pkg
[124i386-quarterly-job-07] Installing autoconf-2.71...
[124i386-quarterly-job-07] `-- Installing autoconf-switch-20220527...
[124i386-quarterly-job-07] `-- Extracting autoconf-switch-20220527: .......... done
[124i386-quarterly-job-07] `-- Installing m4-1.4.19,1...
[124i386-quarterly-job-07] `-- Extracting m4-1.4.19,1: .......... done
[124i386-quarterly-job-07] `-- Installing perl5-5.32.1_3...
[124i386-quarterly-job-07] `-- Extracting perl5-5.32.1_3: .......... done
[124i386-quarterly-job-07] Extracting autoconf-2.71: .......... done
===> cufflinks-2.2.1.89_4 depends on package: autoconf>=2.71 - found
===> Returning to build of cufflinks-2.2.1.89_4
===> cufflinks-2.2.1.89_4 depends on package: automake>=1.16.5 - not found
===> Installing existing package /packages/All/automake-1.16.5.pkg
[124i386-quarterly-job-07] Installing automake-1.16.5...
[124i386-quarterly-job-07] Extracting automake-1.16.5: .......... done
===> cufflinks-2.2.1.89_4 depends on package: automake>=1.16.5 - found
===> Returning to build of cufflinks-2.2.1.89_4
===========================================================================
=======================<phase: lib-depends >============================
===> cufflinks-2.2.1.89_4 depends on shared library: libboost_system.so - not found
===> Installing existing package /packages/All/boost-libs-1.81.0.pkg
[124i386-quarterly-job-07] Installing boost-libs-1.81.0...
[124i386-quarterly-job-07] `-- Installing icu-72.1,1...
[124i386-quarterly-job-07] `-- Extracting icu-72.1,1: .......... done
[124i386-quarterly-job-07] Extracting boost-libs-1.81.0: .......... done
=====
Message from boost-libs-1.81.0:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> cufflinks-2.2.1.89_4 depends on shared library: libboost_system.soSegmentation fault
- not found
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/cufflinks