[package - 113arm64-quarterly][biology/bolt-lmm] Failed for bolt-lmm-2.3.4_2 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Wed Jan 29 11:19:43 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: jwb at FreeBSD.org
Last committer: jbeich at FreeBSD.org
Ident: $FreeBSD: branches/2020Q1/biology/bolt-lmm/Makefile 519824 2019-12-11 17:53:48Z jbeich $
Log URL: http://thunderx1.nyi.freebsd.org/data/113arm64-quarterly/524449/logs/bolt-lmm-2.3.4_2.log
Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=113arm64-quarterly&build=524449
Log:
=>> Building biology/bolt-lmm
build started at Wed Jan 29 11:18:10 UTC 2020
port directory: /usr/ports/biology/bolt-lmm
package name: bolt-lmm-2.3.4_2
building for: FreeBSD 113arm64-quarterly-job-16 11.3-RELEASE-p5 FreeBSD 11.3-RELEASE-p5 1103000 arm64
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: branches/2020Q1/biology/bolt-lmm/Makefile 519824 2019-12-11 17:53:48Z jbeich $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300002
Jail OSVERSION: 1103000
Job Id: 16
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===> The following configuration options are available for bolt-lmm-2.3.4_2:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bolt-lmm-2.3.4_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.12.0.txz
[113arm64-quarterly-job-16] Installing pkg-1.12.0...
[113arm64-quarterly-job-16] Extracting pkg-1.12.0: .......... done
===> bolt-lmm-2.3.4_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bolt-lmm-2.3.4_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bolt-lmm-2.3.4_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bolt-lmm-2.3.4_2 for building
=> SHA256 Checksum OK for BOLT-LMM_v2.3.4.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bolt-lmm-2.3.4_2 for building
===> Extracting for bolt-lmm-2.3.4_2
=> SHA256 Checksum OK for BOLT-LMM_v2.3.4.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bolt-lmm-2.3.4_2
===> Applying FreeBSD patches for bolt-lmm-2.3.4_2
===========================================================================
=======================<phase: build-depends >============================
===> bolt-lmm-2.3.4_2 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.2.1_3.txz
[113arm64-quarterly-job-16] Installing gmake-4.2.1_3...
[113arm64-quarterly-job-16] `-- Installing gettext-runtime-0.20.1...
[113arm64-quarterly-job-16] | `-- Installing indexinfo-0.3.1...
[113arm64-quarterly-job-16] | `-- Extracting indexinfo-0.3.1: .... done
[113arm64-quarterly-job-16] `-- Extracting gettext-runtime-0.20.1: .......... done
[113arm64-quarterly-job-16] Extracting gmake-4.2.1_3: .......... done
===> bolt-lmm-2.3.4_2 depends on executable: gmake - found
===> Returning to build of bolt-lmm-2.3.4_2
===> bolt-lmm-2.3.4_2 depends on executable: gcc9 - not found
===> Installing existing package /packages/All/gcc9-9.2.0.txz
[113arm64-quarterly-job-16] Installing gcc9-9.2.0...
[113arm64-quarterly-job-16] `-- Installing binutils-2.33.1,1...
[113arm64-quarterly-job-16] `-- Extracting binutils-2.33.1,1: .......... done
[113arm64-quarterly-job-16] `-- Installing gmp-6.1.2_1...
[113arm64-quarterly-job-16] `-- Extracting gmp-6.1.2_1: .......... done
[113arm64-quarterly-job-16] `-- Installing mpc-1.1.0_2...
[113arm64-quarterly-job-16] | `-- Installing mpfr-4.0.2...
[113arm64-quarterly-job-16] | `-- Extracting mpfr-4.0.2: .......... done
[113arm64-quarterly-job-16] `-- Extracting mpc-1.1.0_2: ......... done
[113arm64-quarterly-job-16] Extracting gcc9-9.2.0: .......... done
=====
Message from gcc9-9.2.0:
--
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/gcc9
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> bolt-lmm-2.3.4_2 depends on executable: gcc9 - found
===> Returning to build of bolt-lmm-2.3.4_2
===> bolt-lmm-2.3.4_2 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===> bolt-lmm-2.3.4_2 depends on shared library: libnlopt.so - not found
===> Installing existing package /packages/All/nlopt-2.6.1_2.txz
[113arm64-quarterly-job-16] Installing nlopt-2.6.1_2...
[113arm64-quarterly-job-16] `-- Installing guile2-2.2.6_1...
[113arm64-quarterly-job-16] | `-- Installing boehm-gc-threaded-8.0.4_1...
[113arm64-quarterly-job-16] | | `-- Installing boehm-gc-8.0.4_1...
[113arm64-quarterly-job-16] | | `-- Extracting boehm-gc-8.0.4_1: .......... done
[113arm64-quarterly-job-16] | `-- Extracting boehm-gc-threaded-8.0.4_1: .......... done
[113arm64-quarterly-job-16] | `-- Installing libffi-3.2.1_3...
[113arm64-quarterly-job-16] | `-- Extracting libffi-3.2.1_3: .......... done
[113arm64-quarterly-job-16] | `-- Installing libltdl-2.4.6...
[113arm64-quarterly-job-16] | `-- Extracting libltdl-2.4.6: .......... done
[113arm64-quarterly-job-16] | `-- Installing libunistring-0.9.10_1...
[113arm64-quarterly-job-16] | `-- Extracting libunistring-0.9.10_1: .......... done
[113arm64-quarterly-job-16] | `-- Installing readline-8.0.1...
[113arm64-quarterly-job-16] | `-- Extracting readline-8.0.1: .......... done
[113arm64-quarterly-job-16] `-- Extracting guile2-2.2.6_1: .......... done
[113arm64-quarterly-job-16] `-- Installing py37-numpy-1.16.5_2,1...
[113arm64-quarterly-job-16] | `-- Installing openblas-0.2.20_11,1...
[113arm64-quarterly-job-16] | `-- Extracting openblas-0.2.20_11,1: .......... done
[113arm64-quarterly-job-16] | `-- Installing py37-setuptools-41.4.0_1...
[113arm64-quarterly-job-16] | | `-- Installing python37-3.7.6...
[113arm64-quarterly-job-16] | | `-- Extracting python37-3.7.6: .......... done
[113arm64-quarterly-job-16] | `-- Extracting py37-setuptools-41.4.0_1: .......... done
[113arm64-quarterly-job-16] | `-- Installing suitesparse-5.4.0_4...
[113arm64-quarterly-job-16] | | `-- Installing metis-5.1.0_8...
[113arm64-quarterly-job-16] | | `-- Extracting metis-5.1.0_8: .......... done
[113arm64-quarterly-job-16] | | `-- Installing tbb-2020.0...
[113arm64-quarterly-job-16] | | `-- Extracting tbb-2020.0: .......... done
[113arm64-quarterly-job-16] | `-- Extracting suitesparse-5.4.0_4: .......... done
[113arm64-quarterly-job-16] `-- Extracting py37-numpy-1.16.5_2,1: .......... done
[113arm64-quarterly-job-16] Extracting nlopt-2.6.1_2: .......... done
=====
Message from python37-3.7.6:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py37-gdbm databases/py-gdbm at py37
py37-sqlite3 databases/py-sqlite3 at py37
py37-tkinter x11-toolkits/py-tkinter at py37
=====
Message from metis-5.1.0_8:
--
===> 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port
===> bolt-lmm-2.3.4_2 depends on shared library: libnlopt.so - found (/usr/local/lib/libnlopt.so)
===> Returning to build of bolt-lmm-2.3.4_2
===> bolt-lmm-2.3.4_2 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so)
===> bolt-lmm-2.3.4_2 depends on shared library: libboost_program_options.so - not found
===> Installing existing package /packages/All/boost-libs-1.72.0.txz
[113arm64-quarterly-job-16] Installing boost-libs-1.72.0...
[113arm64-quarterly-job-16] `-- Installing icu-65.1,1...
[113arm64-quarterly-job-16] `-- Extracting icu-65.1,1: .......... done
[113arm64-quarterly-job-16] Extracting boost-libs-1.72.0: .......... done
=====
Message from boost-libs-1.72.0:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> bolt-lmm-2.3.4_2 depends on shared library: libboost_program_options.so - found (/usr/local/lib/libboost_program_options.so)
===> Returning to build of bolt-lmm-2.3.4_2
===========================================================================
=======================<phase: configure >============================
===> Configuring for bolt-lmm-2.3.4_2
===========================================================================
=======================<phase: build >============================
===> Building for bolt-lmm-2.3.4_2
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bolt-lmm/work/BOLT-LMM_v2.3.4/src'
g++9 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -nostdinc++ -isystem /usr/include/c++/v1 -Wl,-rpath=/usr/local/lib/gcc9 -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o BoltMain.o -c BoltMain.cpp
In file included from BoltMain.cpp:38:
MemoryUtils.hpp:34:10: fatal error: xmmintrin.h: No such file or directory
34 | #include <xmmintrin.h>
| ^~~~~~~~~~~~~
compilation terminated.
gmake[1]: *** [Makefile:134: BoltMain.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bolt-lmm/work/BOLT-LMM_v2.3.4/src'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/bolt-lmm
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