[package - 120powerpc64-quarterly][biology/cufflinks] Failed for cufflinks-2.2.1.83_2 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Wed Jan 29 14:13:28 UTC 2020
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 at FreeBSD.org
Last committer: jbeich at FreeBSD.org
Ident: $FreeBSD: branches/2020Q1/biology/cufflinks/Makefile 519824 2019-12-11 17:53:48Z jbeich $
Log URL: http://pylon.nyi.freebsd.org/data/120powerpc64-quarterly/524449/logs/cufflinks-2.2.1.83_2.log
Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=120powerpc64-quarterly&build=524449
Log:
=>> Building biology/cufflinks
build started at Wed Jan 29 14:11:34 UTC 2020
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.83_2
building for: FreeBSD 120powerpc64-quarterly-job-09 12.0-RELEASE-p12 FreeBSD 12.0-RELEASE-p12 1200086 powerpc
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2020Q1/biology/cufflinks/Makefile 519824 2019-12-11 17:53:48Z jbeich $
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CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11"
CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14"
CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17"
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=======================<phase: check-sanity >============================
===> License BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> cufflinks-2.2.1.83_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.12.0.txz
[120powerpc64-quarterly-job-09] Installing pkg-1.12.0...
[120powerpc64-quarterly-job-09] Extracting pkg-1.12.0: .......... done
===> cufflinks-2.2.1.83_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of cufflinks-2.2.1.83_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.83_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.83_2 for building
=> SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.83_2 for building
===> Extracting for cufflinks-2.2.1.83_2
=> SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for cufflinks-2.2.1.83_2
===> Applying FreeBSD patches for cufflinks-2.2.1.83_2
===========================================================================
=======================<phase: build-depends >============================
===> cufflinks-2.2.1.83_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found
===> Installing existing package /packages/All/eigen-3.3.7.txz
[120powerpc64-quarterly-job-09] Installing eigen-3.3.7...
[120powerpc64-quarterly-job-09] Extracting eigen-3.3.7: .......... done
===> cufflinks-2.2.1.83_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found
===> Returning to build of cufflinks-2.2.1.83_2
===> cufflinks-2.2.1.83_2 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.2.1_3.txz
[120powerpc64-quarterly-job-09] Installing gmake-4.2.1_3...
[120powerpc64-quarterly-job-09] `-- Installing gettext-runtime-0.20.1...
[120powerpc64-quarterly-job-09] | `-- Installing indexinfo-0.3.1...
[120powerpc64-quarterly-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[120powerpc64-quarterly-job-09] `-- Extracting gettext-runtime-0.20.1: .......... done
[120powerpc64-quarterly-job-09] Extracting gmake-4.2.1_3: .......... done
===> cufflinks-2.2.1.83_2 depends on executable: gmake - found
===> Returning to build of cufflinks-2.2.1.83_2
===> cufflinks-2.2.1.83_2 depends on file: /usr/local/bin/python3.7 - not found
===> Installing existing package /packages/All/python37-3.7.6.txz
[120powerpc64-quarterly-job-09] Installing python37-3.7.6...
<snip>
./../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
./../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
./../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from...
configure.ac:40: the top level
configure.ac:42: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
./../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
./../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
./../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
./../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
./../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
./../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:42: the top level
configure.ac:35: installing 'build-aux/ar-lib'
configure.ac:31: installing 'build-aux/compile'
configure.ac:39: installing 'build-aux/config.guess'
configure.ac:39: installing 'build-aux/config.sub'
configure.ac:16: installing 'build-aux/install-sh'
configure.ac:16: 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 a 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,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
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 build environment is sane... yes
checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether gmake sets $(MAKE)... yes
checking whether gmake supports nested variables... yes
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 we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking whether gmake supports the include directive... yes (GNU style)
checking dependency style of c++... gcc3
checking for gcc... cc
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking whether cc understands -c and -o together... yes
checking dependency style of cc... gcc3
checking whether gmake sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for ar... ar
checking the archiver (ar) interface... ar
checking whether /usr/local/bin/python3.7 version is >= 2.4... yes
checking for /usr/local/bin/python3.7 version... 3.7
checking for /usr/local/bin/python3.7 platform... freebsd12
checking for /usr/local/bin/python3.7 script directory... ${prefix}/lib/python3.7/site-packages
checking for /usr/local/bin/python3.7 extension module directory... ${exec_prefix}/lib/python3.7/site-packages
checking for boostlib >= 1.47.0... yes
checking for htslib or bamlib... yes
checking build system type... powerpc64-portbld-freebsd12.0
checking whether the Boost::System library is available... yes
checking for exit in -lboost_system... yes
checking for exit in -lboost_system... (cached) yes
checking whether the Boost::Serialization library is available... yes
checking for exit in -lboost_serialization... no
checking for exit in -lboost_serialization... (cached) no
checking for exit in -lboost_serialization... (cached) no
checking for exit in -lboost_serialization... (cached) no
checking for exit in -lboost_serialization... (cached) no
checking for exit in -llibboost_serialization.a... no
checking for exit in -lboost_serialization... (cached) no
checking for exit in -lboost_serialization... (cached) no
checking for exit in -lboost_serialization... (cached) no
checking for exit in -lboost_serialization... (cached) no
checking for exit in -lboost_serialization... (cached) no
checking for exit in -llibboost_serialization.a... (cached) no
checking whether the Boost::Filesystem library is available... yes
checking for exit in -lboost_filesystem... no
checking for exit in -lboost_filesystem... (cached) no
checking for exit in -lboost_filesystem... (cached) no
checking for exit in -lboost_filesystem... (cached) no
checking for exit in -lboost_filesystem... (cached) no
configure: error: Could not link against boost_filesystem !
===> Script "configure" failed unexpectedly.
Please report the problem to yuri at FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050/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 in /usr/ports/biology/cufflinks
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