[package - 124i386-quarterly][biology/freebayes] Failed for freebayes-1.3.6_2 in configure
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Date: Tue, 11 Jul 2023 23:00:43 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: https://pkg-status.freebsd.org/beefy4/data/124i386-quarterly/6777c48daefc/logs/freebayes-1.3.6_2.log
Build URL: https://pkg-status.freebsd.org/beefy4/build.html?mastername=124i386-quarterly&build=6777c48daefc
Log:
=>> Building biology/freebayes
build started at Tue Jul 11 23:00:30 UTC 2023
port directory: /usr/ports/biology/freebayes
package name: freebayes-1.3.6_2
building for: FreeBSD 124i386-quarterly-job-09 12.4-RELEASE-p3 FreeBSD 12.4-RELEASE-p3 i386
maintained by: jwb@FreeBSD.org
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ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/freebayes/work/.cache HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/freebayes/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8
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CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" 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"
--End MAKE_ENV--
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--End PLIST_SUB--
--SUB_LIST--
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> freebayes-1.3.6_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.2.pkg
[124i386-quarterly-job-09] Installing pkg-1.19.2...
[124i386-quarterly-job-09] Extracting pkg-1.19.2: .......... done
===> freebayes-1.3.6_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of freebayes-1.3.6_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by freebayes-1.3.6_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by freebayes-1.3.6_2 for building
=> SHA256 Checksum OK for ekg-freebayes-v1.3.6_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-intervaltree-17ddd57_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-vcflib-d4073c3_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz.
=> SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz.
=> SHA256 Checksum OK for edawson-libVCFH-615a06b_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-multichoose-68733cd_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-smithwaterman-2610e25_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-tabixpp-b255df1_GH0.tar.gz.
=> SHA256 Checksum OK for simd-everywhere-simde-no-tests-2931676_GH0.tar.gz.
=> SHA256 Checksum OK for ingydotnet-test-simple-bash-124673f_GH0.tar.gz.
=> SHA256 Checksum OK for illusori-bash-tap-c38fbfa_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by freebayes-1.3.6_2 for building
===> Extracting for freebayes-1.3.6_2
=> SHA256 Checksum OK for ekg-freebayes-v1.3.6_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-intervaltree-17ddd57_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-vcflib-d4073c3_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz.
=> SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz.
=> SHA256 Checksum OK for edawson-libVCFH-615a06b_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-multichoose-68733cd_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-smithwaterman-2610e25_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-tabixpp-b255df1_GH0.tar.gz.
=> SHA256 Checksum OK for simd-everywhere-simde-no-tests-2931676_GH0.tar.gz.
=> SHA256 Checksum OK for ingydotnet-test-simple-bash-124673f_GH0.tar.gz.
=> SHA256 Checksum OK for illusori-bash-tap-c38fbfa_GH0.tar.gz.
cp -f -r /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6/vcflib-temp/* /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6/vcflib
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for freebayes-1.3.6_2
===> Applying FreeBSD patches for freebayes-1.3.6_2 from /usr/ports/biology/freebayes/files
===========================================================================
=======================<phase: build-depends >============================
===> freebayes-1.3.6_2 depends on executable: meson - not found
===> Installing existing package /packages/All/meson-1.1.1.pkg
[124i386-quarterly-job-09] Installing meson-1.1.1...
[124i386-quarterly-job-09] `-- Installing ninja-1.11.1,2...
[124i386-quarterly-job-09] | `-- Installing python39-3.9.17...
[124i386-quarterly-job-09] | | `-- Installing gettext-runtime-0.21.1...
[124i386-quarterly-job-09] | | `-- Installing indexinfo-0.3.1...
[124i386-quarterly-job-09] | | `-- Extracting indexinfo-0.3.1: .... done
[124i386-quarterly-job-09] | | `-- Extracting gettext-runtime-0.21.1: .......... done
[124i386-quarterly-job-09] | | `-- Installing libffi-3.4.4...
[124i386-quarterly-job-09] | | `-- Extracting libffi-3.4.4: .......... done
[124i386-quarterly-job-09] | | `-- Installing mpdecimal-2.5.1...
[124i386-quarterly-job-09] | | `-- Extracting mpdecimal-2.5.1: .......... done
[124i386-quarterly-job-09] | | `-- Installing readline-8.2.1...
[124i386-quarterly-job-09] | | `-- Extracting readline-8.2.1: .......... done
[124i386-quarterly-job-09] | `-- Extracting python39-3.9.17: .......... done
[124i386-quarterly-job-09] `-- Extracting ninja-1.11.1,2: ........ done
[124i386-quarterly-job-09] Extracting meson-1.1.1: .......... done
=====
Message from python39-3.9.17:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> freebayes-1.3.6_2 depends on executable: meson - found
===> Returning to build of freebayes-1.3.6_2
===> freebayes-1.3.6_2 depends on executable: ninja - found
===> freebayes-1.3.6_2 depends on package: pkgconf>=1.3.0_1 - not found
===> Installing existing package /packages/All/pkgconf-1.8.1,1.pkg
[124i386-quarterly-job-09] Installing pkgconf-1.8.1,1...
[124i386-quarterly-job-09] Extracting pkgconf-1.8.1,1: .......... done
===> freebayes-1.3.6_2 depends on package: pkgconf>=1.3.0_1 - found
===> Returning to build of freebayes-1.3.6_2
===> freebayes-1.3.6_2 depends on package: perl5>=5.32.r0<5.33 - not found
===> Installing existing package /packages/All/perl5-5.32.1_3.pkg
[124i386-quarterly-job-09] Installing perl5-5.32.1_3...
[124i386-quarterly-job-09] Extracting perl5-5.32.1_3: .......... done
===> freebayes-1.3.6_2 depends on package: perl5>=5.32.r0<5.33 - found
===> Returning to build of freebayes-1.3.6_2
===========================================================================
=======================<phase: lib-depends >============================
===> freebayes-1.3.6_2 depends on shared library: libhts.so - not found
===> Installing existing package /packages/All/htslib-1.17.pkg
[124i386-quarterly-job-09] Installing htslib-1.17...
[124i386-quarterly-job-09] `-- Installing curl-8.1.2...
[124i386-quarterly-job-09] | `-- Installing ca_root_nss-3.89.1...
[124i386-quarterly-job-09] | `-- Extracting ca_root_nss-3.89.1: .......... done
[124i386-quarterly-job-09] | `-- Installing libnghttp2-1.53.0...
[124i386-quarterly-job-09] | `-- Extracting libnghttp2-1.53.0: .......... done
[124i386-quarterly-job-09] | `-- Installing libpsl-0.21.2_3...
[124i386-quarterly-job-09] | | `-- Installing libidn2-2.3.4...
[124i386-quarterly-job-09] | | `-- Installing libunistring-1.1...
[124i386-quarterly-job-09] | | `-- Extracting libunistring-1.1: .......... done
[124i386-quarterly-job-09] | | `-- Extracting libidn2-2.3.4: .......... done
[124i386-quarterly-job-09] | `-- Extracting libpsl-0.21.2_3: .......... done
[124i386-quarterly-job-09] | `-- Installing libssh2-1.11.0,3...
[124i386-quarterly-job-09] | `-- Extracting libssh2-1.11.0,3: .......... done
[124i386-quarterly-job-09] `-- Extracting curl-8.1.2: .......... done
[124i386-quarterly-job-09] `-- Installing libdeflate-1.18...
[124i386-quarterly-job-09] `-- Extracting libdeflate-1.18: .......... done
[124i386-quarterly-job-09] Extracting htslib-1.17: .......... done
=====
Message from ca_root_nss-3.89.1:
--
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
===> freebayes-1.3.6_2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===> Returning to build of freebayes-1.3.6_2
===========================================================================
=======================<phase: configure >============================
===> Configuring for freebayes-1.3.6_2
The Meson build system
Version: 1.1.1
Source dir: /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6
Build dir: /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6/_build
Build type: native build
Project name: freebayes
Project version: 1.3.6
meson.build:17:0: ERROR: Unknown compiler(s): [['cc']]
A full log can be found at /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6/_build/meson-logs/meson-log.txt
WARNING: Running the setup command as `meson [options]` instead of `meson setup [options]` is ambiguous and deprecated.
===> Script "configure" failed unexpectedly.
Please report the problem to jwb@FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.3.6/_build/meson-logs/meson-log.txt"
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/freebayes