[package - main-arm64-default][biology/bolt-lmm] Failed for bolt-lmm-2.3.4_4 in build
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Date: Fri, 24 Sep 2021 19:04:13 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: jwb@FreeBSD.org
Log URL: http://ampere2.nyi.freebsd.org/data/main-arm64-default/p5f5c0fe00a09_s3fcbde5e88/logs/bolt-lmm-2.3.4_4.log
Build URL: http://ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p5f5c0fe00a09_s3fcbde5e88
Log:
=>> Building biology/bolt-lmm
build started at Fri Sep 24 19:03:44 UTC 2021
port directory: /usr/ports/biology/bolt-lmm
package name: bolt-lmm-2.3.4_4
building for: FreeBSD main-arm64-default-job-14 14.0-CURRENT FreeBSD 14.0-CURRENT 1400033 arm64
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400008
Jail OSVERSION: 1400033
Job Id: 14
!!! Jail is newer than host. (Jail: 1400033, Host: 1400008) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for bolt-lmm-2.3.4_4:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bolt-lmm-2.3.4_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.2.pkg
[main-arm64-default-job-14] Installing pkg-1.17.2...
[main-arm64-default-job-14] Extracting pkg-1.17.2: .......... done
===> bolt-lmm-2.3.4_4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bolt-lmm-2.3.4_4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bolt-lmm-2.3.4_4 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bolt-lmm-2.3.4_4 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_4 for building
===> Extracting for bolt-lmm-2.3.4_4
=> SHA256 Checksum OK for BOLT-LMM_v2.3.4.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bolt-lmm-2.3.4_4
===> Applying FreeBSD patches for bolt-lmm-2.3.4_4 from /usr/ports/biology/bolt-lmm/files
===========================================================================
=======================<phase: build-depends >============================
===> bolt-lmm-2.3.4_4 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[main-arm64-default-job-14] Installing gmake-4.3_2...
[main-arm64-default-job-14] `-- Installing gettext-runtime-0.21...
[main-arm64-default-job-14] | `-- Installing indexinfo-0.3.1...
[main-arm64-default-job-14] | `-- Extracting indexinfo-0.3.1: .... done
[main-arm64-default-job-14] `-- Extracting gettext-runtime-0.21: .......... done
[main-arm64-default-job-14] Extracting gmake-4.3_2: .......... done
===> bolt-lmm-2.3.4_4 depends on package: gmake>=4.3 - found
===> Returning to build of bolt-lmm-2.3.4_4
===> bolt-lmm-2.3.4_4 depends on executable: gcc10 - not found
===> Installing existing package /packages/All/gcc10-10.3.0.pkg
[main-arm64-default-job-14] Installing gcc10-10.3.0...
[main-arm64-default-job-14] `-- Installing binutils-2.37_1,1...
[main-arm64-default-job-14] `-- Extracting binutils-2.37_1,1: .......... done
[main-arm64-default-job-14] `-- Installing gmp-6.2.1...
[main-arm64-default-job-14] `-- Extracting gmp-6.2.1: .......... done
[main-arm64-default-job-14] `-- Installing mpc-1.2.1...
[main-arm64-default-job-14] | `-- Installing mpfr-4.1.0_1...
[main-arm64-default-job-14] | `-- Extracting mpfr-4.1.0_1: .......... done
[main-arm64-default-job-14] `-- Extracting mpc-1.2.1: ......... done
[main-arm64-default-job-14] Extracting gcc10-10.3.0: .......... done
=====
Message from gcc10-10.3.0:
--
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/gcc10
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> bolt-lmm-2.3.4_4 depends on executable: gcc10 - found
===> Returning to build of bolt-lmm-2.3.4_4
===> bolt-lmm-2.3.4_4 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===> bolt-lmm-2.3.4_4 depends on shared library: libnlopt.so - not found
===> Installing existing package /packages/All/nlopt-2.7.0.pkg
[main-arm64-default-job-14] Installing nlopt-2.7.0...
[main-arm64-default-job-14] `-- Installing guile2-2.2.7_1...
[main-arm64-default-job-14] | `-- Installing boehm-gc-threaded-8.0.4_1...
[main-arm64-default-job-14] | | `-- Installing boehm-gc-8.0.4_1...
[main-arm64-default-job-14] | | `-- Extracting boehm-gc-8.0.4_1: .......... done
[main-arm64-default-job-14] | `-- Extracting boehm-gc-threaded-8.0.4_1: .......... done
[main-arm64-default-job-14] | `-- Installing libffi-3.3_1...
[main-arm64-default-job-14] | `-- Extracting libffi-3.3_1: .......... done
[main-arm64-default-job-14] | `-- Installing libltdl-2.4.6...
[main-arm64-default-job-14] | `-- Extracting libltdl-2.4.6: .......... done
[main-arm64-default-job-14] | `-- Installing libunistring-0.9.10_1...
[main-arm64-default-job-14] | `-- Extracting libunistring-0.9.10_1: .......... done
[main-arm64-default-job-14] | `-- Installing readline-8.1.1...
[main-arm64-default-job-14] | `-- Extracting readline-8.1.1: .......... done
[main-arm64-default-job-14] `-- Extracting guile2-2.2.7_1: .......... done
[main-arm64-default-job-14] `-- Installing py38-numpy-1.16.6_2,1...
[main-arm64-default-job-14] | `-- Installing openblas-0.3.16,1...
[main-arm64-default-job-14] | `-- Extracting openblas-0.3.16,1: .......... done
[main-arm64-default-job-14] | `-- Installing py38-setuptools-57.0.0...
[main-arm64-default-job-14] | | `-- Installing python38-3.8.12...
[main-arm64-default-job-14] | | `-- Installing mpdecimal-2.5.1...
[main-arm64-default-job-14] | | `-- Extracting mpdecimal-2.5.1: .......... done
[main-arm64-default-job-14] | | `-- Extracting python38-3.8.12: .......... done
[main-arm64-default-job-14] | `-- Extracting py38-setuptools-57.0.0: .......... done
[main-arm64-default-job-14] | `-- Installing suitesparse-umfpack-5.7.9...
[main-arm64-default-job-14] | | `-- Installing metis-5.1.0_8...
[main-arm64-default-job-14] | | `-- Extracting metis-5.1.0_8: .......... done
[main-arm64-default-job-14] | | `-- Installing suitesparse-amd-2.4.6...
[main-arm64-default-job-14] | | `-- Installing suitesparse-config-5.10.1...
[main-arm64-default-job-14] | | `-- Extracting suitesparse-config-5.10.1: ......... done
[main-arm64-default-job-14] | | `-- Extracting suitesparse-amd-2.4.6: .......... done
[main-arm64-default-job-14] | | `-- Installing suitesparse-camd-2.4.6...
[main-arm64-default-job-14] | | `-- Extracting suitesparse-camd-2.4.6: ......... done
[main-arm64-default-job-14] | | `-- Installing suitesparse-ccolamd-2.9.6...
[main-arm64-default-job-14] | | `-- Extracting suitesparse-ccolamd-2.9.6: ........ done
[main-arm64-default-job-14] | | `-- Installing suitesparse-cholmod-3.0.14...
[main-arm64-default-job-14] | | `-- Installing suitesparse-colamd-2.9.6...
[main-arm64-default-job-14] | | `-- Extracting suitesparse-colamd-2.9.6: ........ done
[main-arm64-default-job-14] | | `-- Extracting suitesparse-cholmod-3.0.14: .......... done
[main-arm64-default-job-14] | `-- Extracting suitesparse-umfpack-5.7.9: .......... done
[main-arm64-default-job-14] `-- Extracting py38-numpy-1.16.6_2,1: .......... done
[main-arm64-default-job-14] Extracting nlopt-2.7.0: .......... done
=====
Message from python38-3.8.12:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py38-gdbm databases/py-gdbm@py38
py38-sqlite3 databases/py-sqlite3@py38
py38-tkinter x11-toolkits/py-tkinter@py38
=====
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://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> bolt-lmm-2.3.4_4 depends on shared library: libnlopt.so - found (/usr/local/lib/libnlopt.so)
===> Returning to build of bolt-lmm-2.3.4_4
===> bolt-lmm-2.3.4_4 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so)
===> bolt-lmm-2.3.4_4 depends on shared library: libboost_program_options.so - not found
===> Installing existing package /packages/All/boost-libs-1.72.0_5.pkg
[main-arm64-default-job-14] Installing boost-libs-1.72.0_5...
[main-arm64-default-job-14] `-- Installing icu-69.1,1...
[main-arm64-default-job-14] `-- Extracting icu-69.1,1: .......... done
[main-arm64-default-job-14] Extracting boost-libs-1.72.0_5: .......... done
=====
Message from boost-libs-1.72.0_5:
--
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_4 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_4
===========================================================================
=======================<phase: configure >============================
===> Configuring for bolt-lmm-2.3.4_4
===========================================================================
=======================<phase: build >============================
===> Building for bolt-lmm-2.3.4_4
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bolt-lmm/work/BOLT-LMM_v2.3.4/src'
g++10 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -nostdinc++ -isystem /usr/include/c++/v1 -Wl,-rpath=/usr/local/lib/gcc10 -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o BoltMain.o -c BoltMain.cpp
g++10 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -nostdinc++ -isystem /usr/include/c++/v1 -Wl,-rpath=/usr/local/lib/gcc10 -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o Bolt.o -c Bolt.cpp
In file included from Bolt.cpp:49:
MemoryUtils.hpp:34:10: fatal error: xmmintrin.h: No such file or directory
34 | #include <xmmintrin.h>
| ^~~~~~~~~~~~~
compilation terminated.
gmake[1]: *** [Makefile:134: Bolt.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
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'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/bolt-lmm