[package - 130releng-riscv64-quarterly][biology/mmseqs2] Failed for MMseqs2-13.45111_2 in configure
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Date: Thu, 09 Sep 2021 05:00:51 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://beefy7.nyi.freebsd.org/data/130releng-riscv64-quarterly/2963f756953b/logs/MMseqs2-13.45111_2.log
Build URL: http://beefy7.nyi.freebsd.org/build.html?mastername=130releng-riscv64-quarterly&build=2963f756953b
Log:
=>> Building biology/mmseqs2
build started at Thu Sep 9 05:00:10 UTC 2021
port directory: /usr/ports/biology/mmseqs2
package name: MMseqs2-13.45111_2
building for: FreeBSD 130releng-riscv64-quarterly-job-01 13.0-RELEASE-p4 FreeBSD 13.0-RELEASE-p4 1300139 riscv
maintained by: jwb@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> MMseqs2-13.45111_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.16.3.txz
[130releng-riscv64-quarterly-job-01] Installing pkg-1.16.3...
[130releng-riscv64-quarterly-job-01] Extracting pkg-1.16.3: .......... done
===> MMseqs2-13.45111_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of MMseqs2-13.45111_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by MMseqs2-13.45111_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by MMseqs2-13.45111_2 for building
=> SHA256 Checksum OK for soedinglab-MMseqs2-13-45111_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by MMseqs2-13.45111_2 for building
===> Extracting for MMseqs2-13.45111_2
=> SHA256 Checksum OK for soedinglab-MMseqs2-13-45111_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for MMseqs2-13.45111_2
===> Applying FreeBSD patches for MMseqs2-13.45111_2 from /usr/ports/biology/mmseqs2/files
===========================================================================
=======================<phase: build-depends >============================
===> MMseqs2-13.45111_2 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-3.20.4.txz
[130releng-riscv64-quarterly-job-01] Installing cmake-3.20.4...
[130releng-riscv64-quarterly-job-01] `-- Installing curl-7.78.0...
[130releng-riscv64-quarterly-job-01] | `-- Installing ca_root_nss-3.63...
[130releng-riscv64-quarterly-job-01] | `-- Extracting ca_root_nss-3.63: ........ done
[130releng-riscv64-quarterly-job-01] | `-- Installing libnghttp2-1.43.0...
[130releng-riscv64-quarterly-job-01] | `-- Extracting libnghttp2-1.43.0: .......... done
[130releng-riscv64-quarterly-job-01] `-- Extracting curl-7.78.0: .......... done
[130releng-riscv64-quarterly-job-01] `-- Installing expat-2.4.1...
[130releng-riscv64-quarterly-job-01] `-- Extracting expat-2.4.1: .......... done
[130releng-riscv64-quarterly-job-01] `-- Installing jsoncpp-1.9.4...
[130releng-riscv64-quarterly-job-01] `-- Extracting jsoncpp-1.9.4: .......... done
[130releng-riscv64-quarterly-job-01] `-- Installing libarchive-3.5.1,1...
[130releng-riscv64-quarterly-job-01] | `-- Installing liblz4-1.9.3,1...
[130releng-riscv64-quarterly-job-01] | `-- Extracting liblz4-1.9.3,1: .......... done
[130releng-riscv64-quarterly-job-01] `-- Extracting libarchive-3.5.1,1: .......... done
[130releng-riscv64-quarterly-job-01] `-- Installing libuv-1.41.0...
[130releng-riscv64-quarterly-job-01] `-- Extracting libuv-1.41.0: .......... done
[130releng-riscv64-quarterly-job-01] `-- Installing rhash-1.4.1...
[130releng-riscv64-quarterly-job-01] | `-- Installing gettext-runtime-0.21...
[130releng-riscv64-quarterly-job-01] | | `-- Installing indexinfo-0.3.1...
[130releng-riscv64-quarterly-job-01] | | `-- Extracting indexinfo-0.3.1: .... done
[130releng-riscv64-quarterly-job-01] | `-- Extracting gettext-runtime-0.21: .......... done
[130releng-riscv64-quarterly-job-01] `-- Extracting rhash-1.4.1: .......... done
[130releng-riscv64-quarterly-job-01] Extracting cmake-3.20.4: .......... done
=====
Message from ca_root_nss-3.63:
--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.
Assessment and verification of trust is the complete responsibility of the
system administrator.
This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.
This enables SSL Certificate Verification by client software without manual
intervention.
If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.
* /etc/ssl/cert.pem
* /usr/local/etc/ssl/cert.pem
* /usr/local/openssl/cert.pem
===> MMseqs2-13.45111_2 depends on file: /usr/local/bin/cmake - found
===> Returning to build of MMseqs2-13.45111_2
===> MMseqs2-13.45111_2 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.10.2,2.txz
[130releng-riscv64-quarterly-job-01] Installing ninja-1.10.2,2...
[130releng-riscv64-quarterly-job-01] `-- Installing python38-3.8.10...
[130releng-riscv64-quarterly-job-01] | `-- Installing libffi-3.3_1...
[130releng-riscv64-quarterly-job-01] | `-- Extracting libffi-3.3_1: .......... done
[130releng-riscv64-quarterly-job-01] | `-- Installing mpdecimal-2.5.1...
[130releng-riscv64-quarterly-job-01] | `-- Extracting mpdecimal-2.5.1: .......... done
[130releng-riscv64-quarterly-job-01] | `-- Installing readline-8.1.1...
[130releng-riscv64-quarterly-job-01] | `-- Extracting readline-8.1.1: .......... done
[130releng-riscv64-quarterly-job-01] `-- Extracting python38-3.8.10: .......... done
[130releng-riscv64-quarterly-job-01] Extracting ninja-1.10.2,2: ........ done
=====
Message from python38-3.8.10:
--
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
===> MMseqs2-13.45111_2 depends on executable: ninja - found
===> Returning to build of MMseqs2-13.45111_2
===> MMseqs2-13.45111_2 depends on package: perl5>=5.32.r0<5.33 - not found
===> Installing existing package /packages/All/perl5-5.32.1_1.txz
[130releng-riscv64-quarterly-job-01] Installing perl5-5.32.1_1...
[130releng-riscv64-quarterly-job-01] Extracting perl5-5.32.1_1: .......... done
===> MMseqs2-13.45111_2 depends on package: perl5>=5.32.r0<5.33 - found
===> Returning to build of MMseqs2-13.45111_2
===========================================================================
=======================<phase: lib-depends >============================
===> MMseqs2-13.45111_2 depends on shared library: libzstd.so - not found
===> Installing existing package /packages/All/zstd-1.5.0.txz
[130releng-riscv64-quarterly-job-01] Installing zstd-1.5.0...
[130releng-riscv64-quarterly-job-01] Extracting zstd-1.5.0: .......... done
===> MMseqs2-13.45111_2 depends on shared library: libzstd.so - found (/usr/local/lib/libzstd.so)
===> Returning to build of MMseqs2-13.45111_2
===========================================================================
=======================<phase: configure >============================
===> Configuring for MMseqs2-13.45111_2
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build
-- The CXX compiler identification is Clang 11.0.1
-- The C compiler identification is Clang 11.0.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /nxb-bin/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /nxb-bin/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Source Directory: /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111
-- Project Directory: /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111
-- Compiler is clang(++)
CMake Warning at CMakeLists.txt:83 (message):
CPU without native SIMD instructions. Performance will be bad.
-- Found ZSTD: /usr/local/lib/libzstd.a
-- xxd not found, using xxdi.pl instead
-- ShellCheck disabled
-- Performing Test HAVE_POSIX_FADVISE
-- Performing Test HAVE_POSIX_FADVISE - Success
-- Performing Test HAVE_POSIX_MADVISE
-- Performing Test HAVE_POSIX_MADVISE - Success
-- OMPTL sorting fallback
-- Found ZLIB
-- Performing Test HAVE_ZLIB_CHECK
-- Performing Test HAVE_ZLIB_CHECK - Success
-- ZLIB works
-- Found BZLIB
-- Performing Test HAVE_BZLIB_CHECK
-- Performing Test HAVE_BZLIB_CHECK - Success
-- BZLIB works
CMake Error at src/CMakeLists.txt:228 (message):
-- Could not find OpenMP. Skip check with -DREQUIRE_OPENMP=0.
-- Configuring incomplete, errors occurred!
See also "/wrkdirs/usr/ports/biology/mmseqs2/work/.build/CMakeFiles/CMakeOutput.log".
See also "/wrkdirs/usr/ports/biology/mmseqs2/work/.build/CMakeFiles/CMakeError.log".
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/mmseqs2