[package - main-i386-default][science/afni] Failed for afni-21.3.16 in build
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Date: Thu, 30 Dec 2021 01:32:01 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: fernape@FreeBSD.org
Log URL: http://beefy17.nyi.freebsd.org/data/main-i386-default/pb62f24f32e66_sc3a688ef4d/logs/afni-21.3.16.log
Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=main-i386-default&build=pb62f24f32e66_sc3a688ef4d
Log:
=>> Building science/afni
build started at Thu Dec 30 01:31:07 UTC 2021
port directory: /usr/ports/science/afni
package name: afni-21.3.16
building for: FreeBSD main-i386-default-job-08 14.0-CURRENT FreeBSD 14.0-CURRENT 1400045 i386
maintained by: fernape@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400042
Jail OSVERSION: 1400045
Job Id: 08
!!! Jail is newer than host. (Jail: 1400045, Host: 1400042) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for afni-21.3.16:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
fernape@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.8" XDG_DATA_HOME=/wrkdirs/usr/ports/science/afni/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/afni/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/afni/work/.cache HOME=/wrkdirs/usr/ports/science/afni/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/afni/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8
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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"
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--PLIST_SUB--
PORTDOCS="" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" PYTHON_INCLUDEDIR=include/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/afni" EXAMPLESDIR="share/examples/afni" DATADIR="share/afni" WWWDIR="www/afni" ETCDIR="etc/afni"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/afni DOCSDIR=/usr/local/share/doc/afni EXAMPLESDIR=/usr/local/share/examples/afni WWWDIR=/usr/local/www/afni ETCDIR=/usr/local/etc/afni
--End SUB_LIST--
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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
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# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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CC_OUTPUT_921dbbb2_fb62803b=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc"
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swap limit (kbytes, -w) unlimited
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kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> afni-21.3.16 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5.pkg
[main-i386-default-job-08] Installing pkg-1.17.5...
[main-i386-default-job-08] Extracting pkg-1.17.5: .......... done
===> afni-21.3.16 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of afni-21.3.16
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2 accepted by the user
=> afni-afni-AFNI_21.3.16_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/afni/afni/tar.gz/AFNI_21.3.16?dummy=/afni-afni-AFNI_21.3.16_GH0.tar.gz
fetch: https://codeload.github.com/afni/afni/tar.gz/AFNI_21.3.16?dummy=/afni-afni-AFNI_21.3.16_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/afni/afni/tar.gz/AFNI_21.3.16?dummy=/afni-afni-AFNI_21.3.16_GH0.tar.gz: size of remote file is not known
afni-afni-AFNI_21.3.16_GH0.tar.gz 41 MB 9637 kBps 05s
===> Fetching all distfiles required by afni-21.3.16 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by afni-21.3.16 for building
=> SHA256 Checksum OK for afni-afni-AFNI_21.3.16_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by afni-21.3.16 for building
===> Extracting for afni-21.3.16
=> SHA256 Checksum OK for afni-afni-AFNI_21.3.16_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for afni-21.3.16
===> Applying FreeBSD patches for afni-21.3.16 from /usr/ports/science/afni/files
===========================================================================
=======================<phase: build-depends >============================
<snip>
[main-i386-default-job-08] | | `-- Installing suitesparse-umfpack-5.7.9...
[main-i386-default-job-08] | | | `-- Installing metis-5.1.0_9...
[main-i386-default-job-08] | | | `-- Extracting metis-5.1.0_9: .......... done
[main-i386-default-job-08] | | | `-- Installing suitesparse-amd-2.4.6...
[main-i386-default-job-08] | | | `-- Installing suitesparse-config-5.10.1...
[main-i386-default-job-08] | | | `-- Extracting suitesparse-config-5.10.1: ......... done
[main-i386-default-job-08] | | | `-- Extracting suitesparse-amd-2.4.6: .......... done
[main-i386-default-job-08] | | | `-- Installing suitesparse-camd-2.4.6...
[main-i386-default-job-08] | | | `-- Extracting suitesparse-camd-2.4.6: ......... done
[main-i386-default-job-08] | | | `-- Installing suitesparse-ccolamd-2.9.6...
[main-i386-default-job-08] | | | `-- Extracting suitesparse-ccolamd-2.9.6: ........ done
[main-i386-default-job-08] | | | `-- Installing suitesparse-cholmod-3.0.14...
[main-i386-default-job-08] | | | `-- Installing suitesparse-colamd-2.9.6...
[main-i386-default-job-08] | | | `-- Extracting suitesparse-colamd-2.9.6: ........ done
[main-i386-default-job-08] | | | `-- Extracting suitesparse-cholmod-3.0.14: .......... done
[main-i386-default-job-08] | | `-- Extracting suitesparse-umfpack-5.7.9: .......... done
[main-i386-default-job-08] | | `-- Extracting py38-numpy-1.20.3,1: .......... done
[main-i386-default-job-08] | `-- Extracting nlopt-2.7.1: .......... done
[main-i386-default-job-08] `-- Extracting R-cran-nloptr-1.2.2.3: .......... done
[main-i386-default-job-08] Extracting R-cran-lme4-1.1.27.1: .......... done
=====
Message from metis-5.1.0_9:
--
===> NOTICE:
The metis port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> afni-21.3.16 depends on package: R-cran-lme4>0 - found
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on package: R-cran-snow>0 - not found
===> Installing existing package /packages/All/R-cran-snow-0.4.4.pkg
[main-i386-default-job-08] Installing R-cran-snow-0.4.4...
[main-i386-default-job-08] Extracting R-cran-snow-0.4.4: .......... done
===> afni-21.3.16 depends on package: R-cran-snow>0 - found
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on package: R-cran-psych>0 - not found
===> Installing existing package /packages/All/R-cran-psych-1.2.1_12.pkg
[main-i386-default-job-08] Installing R-cran-psych-1.2.1_12...
[main-i386-default-job-08] Extracting R-cran-psych-1.2.1_12: .......... done
===> afni-21.3.16 depends on package: R-cran-psych>0 - found
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on executable: msgfmt - not found
===> Installing existing package /packages/All/gettext-tools-0.21.pkg
[main-i386-default-job-08] Installing gettext-tools-0.21...
[main-i386-default-job-08] `-- Installing libtextstyle-0.21...
[main-i386-default-job-08] `-- Extracting libtextstyle-0.21: .......... done
[main-i386-default-job-08] Extracting gettext-tools-0.21: .......... done
===> afni-21.3.16 depends on executable: msgfmt - found
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on package: gmake>=4.3 - found
===> afni-21.3.16 depends on file: /usr/local/bin/python3.8 - found
===> afni-21.3.16 depends on package: xorgproto>=0 - found
===> afni-21.3.16 depends on package: xorgproto>=0 - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xau.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xcb.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xdmcp.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xft.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xi.pc - not found
===> Installing existing package /packages/All/libXi-1.8,1.pkg
[main-i386-default-job-08] Installing libXi-1.8,1...
[main-i386-default-job-08] `-- Installing libXfixes-6.0.0...
[main-i386-default-job-08] `-- Extracting libXfixes-6.0.0: .......... done
[main-i386-default-job-08] Extracting libXi-1.8,1: .......... done
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xrender.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - not found
===> Installing existing package /packages/All/libXpm-3.5.13.pkg
[main-i386-default-job-08] Installing libXpm-3.5.13...
[main-i386-default-job-08] Extracting libXpm-3.5.13: .......... done
===> afni-21.3.16 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - found
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on package: perl5>=5.32.r0<5.33 - not found
===> Installing existing package /packages/All/perl5-5.32.1_1.pkg
[main-i386-default-job-08] Installing perl5-5.32.1_1...
[main-i386-default-job-08] Extracting perl5-5.32.1_1: .......... done
===> afni-21.3.16 depends on package: perl5>=5.32.r0<5.33 - found
===> Returning to build of afni-21.3.16
===========================================================================
=======================<phase: lib-depends >============================
===> afni-21.3.16 depends on shared library: libexpat.so - found (/usr/local/lib/libexpat.so)
===> afni-21.3.16 depends on shared library: libXm.so - not found
===> Installing existing package /packages/All/open-motif-2.3.8_2.pkg
[main-i386-default-job-08] Installing open-motif-2.3.8_2...
[main-i386-default-job-08] `-- Installing libXaw-1.0.14,2...
[main-i386-default-job-08] `-- Extracting libXaw-1.0.14,2: .......... done
[main-i386-default-job-08] `-- Installing xbitmaps-1.1.2...
[main-i386-default-job-08] `-- Extracting xbitmaps-1.1.2: .......... done
[main-i386-default-job-08] Extracting open-motif-2.3.8_2: .......... done
===> afni-21.3.16 depends on shared library: libXm.so - found (/usr/local/lib/libXm.so)
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on shared library: libf2c.so - not found
===> Installing existing package /packages/All/f2c-20200916.pkg
[main-i386-default-job-08] Installing f2c-20200916...
[main-i386-default-job-08] Extracting f2c-20200916: .......... done
===> afni-21.3.16 depends on shared library: libf2c.so - found (/usr/local/lib/libf2c.so)
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on shared library: libfontconfig.so - found (/usr/local/lib/libfontconfig.so)
===> afni-21.3.16 depends on shared library: libfreetype.so - found (/usr/local/lib/libfreetype.so)
===> afni-21.3.16 depends on shared library: libgsl.so - not found
===> Installing existing package /packages/All/gsl-2.7.pkg
[main-i386-default-job-08] Installing gsl-2.7...
[main-i386-default-job-08] Extracting gsl-2.7: .......... done
===> afni-21.3.16 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so)
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on shared library: libicudata.so - found (/usr/local/lib/libicudata.so)
===> afni-21.3.16 depends on shared library: libnetcdff.so - not found
===> Installing existing package /packages/All/netcdf-fortran-4.5.3.pkg
[main-i386-default-job-08] Installing netcdf-fortran-4.5.3...
[main-i386-default-job-08] `-- Installing netcdf-4.7.4...
[main-i386-default-job-08] | `-- Installing hdf-szip-2.1.1...
[main-i386-default-job-08] | `-- Extracting hdf-szip-2.1.1: .......... done
[main-i386-default-job-08] | `-- Installing hdf5-1.10.6,1...
[main-i386-default-job-08] | `-- Extracting hdf5-1.10.6,1: .......... done
[main-i386-default-job-08] | `-- Installing pkgconf-1.8.0,1...
[main-i386-default-job-08] | `-- Extracting pkgconf-1.8.0,1: .......... done
[main-i386-default-job-08] `-- Extracting netcdf-4.7.4: .......... done
[main-i386-default-job-08] Extracting netcdf-fortran-4.5.3: .......... done
===> afni-21.3.16 depends on shared library: libnetcdff.so - found (/usr/local/lib/libnetcdff.so)
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on shared library: libnetpbm.so - not found
===> Installing existing package /packages/All/netpbm-10.91.01.pkg
[main-i386-default-job-08] Installing netpbm-10.91.01...
[main-i386-default-job-08] `-- Installing jasper-2.0.33...
[main-i386-default-job-08] | `-- Installing freeglut-3.2.1...
[main-i386-default-job-08] | | `-- Installing libGLU-9.0.2_1...
[main-i386-default-job-08] | | `-- Extracting libGLU-9.0.2_1: ..... done
[main-i386-default-job-08] | | `-- Installing libXrandr-1.5.2...
[main-i386-default-job-08] | | `-- Extracting libXrandr-1.5.2: .......... done
[main-i386-default-job-08] | | `-- Installing libXxf86vm-1.1.4_3...
[main-i386-default-job-08] | | `-- Extracting libXxf86vm-1.1.4_3: .......... done
[main-i386-default-job-08] | `-- Extracting freeglut-3.2.1: .......... done
[main-i386-default-job-08] `-- Extracting jasper-2.0.33: .......... done
[main-i386-default-job-08] Extracting netpbm-10.91.01: .......... done
=====
Message from freeglut-3.2.1:
--
Joystick support is untested and it is unknown if it works.
Do not hesitate to contact x11@FreeBSD.org if this causes issues.
===> afni-21.3.16 depends on shared library: libnetpbm.so - found (/usr/local/lib/libnetpbm.so)
===> Returning to build of afni-21.3.16
===> afni-21.3.16 depends on shared library: libpcre2-8.so - found (/usr/local/lib/libpcre2-8.so)
===> afni-21.3.16 depends on shared library: libpng16.so - found (/usr/local/lib/libpng16.so)
===> afni-21.3.16 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so)
===> afni-21.3.16 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===> afni-21.3.16 depends on shared library: libGL.so - found (/usr/local/lib/libGL.so)
===> afni-21.3.16 depends on shared library: libGLU.so - found (/usr/local/lib/libGLU.so)
===> afni-21.3.16 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so)
===> afni-21.3.16 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===> afni-21.3.16 depends on shared library: libXm.so.4 - found (/usr/local/lib/libXm.so.4)
===> afni-21.3.16 depends on shared library: libreadline.so.8 - found (/usr/local/lib/libreadline.so.8)
===========================================================================
=======================<phase: configure >============================
===> Configuring for afni-21.3.16
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/afni/work/afni-AFNI_21.3.16/src/mpegtoppm_dir/aclocal.m4
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/afni/work/afni-AFNI_21.3.16/src/mpegtoppm_dir/configure
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/afni/work/afni-AFNI_21.3.16/src/SUMA/gts/aclocal.m4
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/afni/work/afni-AFNI_21.3.16/src/SUMA/gts/configure
===========================================================================
=======================<phase: build >============================
===> Building for afni-21.3.16
gmake[1]: Entering directory '/wrkdirs/usr/ports/science/afni/work/afni-AFNI_21.3.16/src'
Makefile.INCLUDE:2915: warning: ignoring prerequisites on suffix rule definition
Makefile.INCLUDE:2986: warning: ignoring prerequisites on suffix rule definition
/bin/cp -f niml/niml.h .
echo "#undef AFNI_VERSION_LABEL" > AFNI_version.h ; \
echo '#define AFNI_VERSION_LABEL "'`cat AFNI_version_base.txt`'"' \
>> AFNI_version.h ; \
echo "#undef AFNI_VERSION_PLATFORM" >> AFNI_version.h ; \
echo '#define AFNI_VERSION_PLATFORM "''"' \
>> AFNI_version.h ;
( cd niml/ ; gmake all 'CC=cc -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DPIC -fPIC ' ; /bin/mv -f *.o .. ; )
gmake[2]: Entering directory '/wrkdirs/usr/ports/science/afni/work/afni-AFNI_21.3.16/src/niml'
cc -O2 -pipe -fcommon -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DPIC -fPIC -I../f2c -c niml_b64.c
ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc"
gmake[2]: *** [Makefile:4: niml_b64.o] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/afni/work/afni-AFNI_21.3.16/src/niml'
mv: rename *.o to ../*.o: No such file or directory
gmake[1]: *** [Makefile.INCLUDE:3263: niml_b64.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/afni/work/afni-AFNI_21.3.16/src'
*** Error code 1
Stop.
make: stopped in /usr/ports/science/afni