[package - 122arm64-quarterly][science/libghemical] Failed for libghemical-3.0.0_16 in configure

From: <pkg-fallout_at_FreeBSD.org>
Date: Tue, 08 Jun 2021 06:31:12 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:     yuri@FreeBSD.org
Log URL:        http://ampere1.nyi.freebsd.org/data/122arm64-quarterly/ef55dcb4849d/logs/libghemical-3.0.0_16.log
Build URL:      http://ampere1.nyi.freebsd.org/build.html?mastername=122arm64-quarterly&build=ef55dcb4849d
Log:

=>> Building science/libghemical
build started at Tue Jun  8 06:30:14 UTC 2021
port directory: /usr/ports/science/libghemical
package name: libghemical-3.0.0_16
building for: FreeBSD 122arm64-quarterly-job-11 12.2-RELEASE FreeBSD 12.2-RELEASE arm64
maintained by: yuri@FreeBSD.org
Makefile ident: 
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--PLIST_SUB--
LIBGHEMICAL_VERSION="3.0.0" OSREL=12.2 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/libghemical"  EXAMPLESDIR="share/examples/libghemical"  DATADIR="share/libghemical"  WWWDIR="www/libghemical"  ETCDIR="etc/libghemical"
--End PLIST_SUB--

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PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/libghemical DOCSDIR=/usr/local/share/doc/libghemical EXAMPLESDIR=/usr/local/share/examples/libghemical  WWWDIR=/usr/local/www/libghemical ETCDIR=/usr/local/etc/libghemical
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=======================<phase: check-sanity   >============================
===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   libghemical-3.0.0_16 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.16.3.txz
[122arm64-quarterly-job-11] Installing pkg-1.16.3...
[122arm64-quarterly-job-11] Extracting pkg-1.16.3: .......... done
===>   libghemical-3.0.0_16 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of libghemical-3.0.0_16
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by libghemical-3.0.0_16 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by libghemical-3.0.0_16 for building
=> SHA256 Checksum OK for libghemical-3.0.0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by libghemical-3.0.0_16 for building
===>  Extracting for libghemical-3.0.0_16
=> SHA256 Checksum OK for libghemical-3.0.0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for libghemical-3.0.0_16
===========================================================================
=======================<phase: build-depends  >============================
===>   libghemical-3.0.0_16 depends on executable: obabel - not found
===>   Installing existing package /packages/All/openbabel-3.1.1.txz
[122arm64-quarterly-job-11] Installing openbabel-3.1.1...
[122arm64-quarterly-job-11] `-- Installing boost-libs-1.72.0_4...
[122arm64-quarterly-job-11] |   `-- Installing icu-68.2,1...
[122arm64-quarterly-job-11] |   `-- Extracting icu-68.2,1: .......... done
[122arm64-quarterly-job-11] `-- Extracting boost-libs-1.72.0_4: .......... done
[122arm64-quarterly-job-11] `-- Installing cairo-1.16.0_1,3...
[122arm64-quarterly-job-11] |   `-- Installing fontconfig-2.13.93,1...
[122arm64-quarterly-job-11] |   | `-- Installing expat-2.2.10...
[122arm64-quarterly-job-11] |   | `-- Extracting expat-2.2.10: .......... done
[122arm64-quarterly-job-11] |   | `-- Installing freetype2-2.10.4...
[122arm64-quarterly-job-11] |   |   `-- Installing png-1.6.37_1...
[122arm64-quarterly-job-11] |   |   `-- Extracting png-1.6.37_1: .......... done
[122arm64-quarterly-job-11] |   | `-- Extracting freetype2-2.10.4: .......... done
[122arm64-quarterly-job-11] |   `-- Extracting fontconfig-2.13.93,1: .......... done
[122arm64-quarterly-job-11] |   `-- Installing gettext-runtime-0.21...
[122arm64-quarterly-job-11] |   | `-- Installing indexinfo-0.3.1...
[122arm64-quarterly-job-11] |   | `-- Extracting indexinfo-0.3.1: .... done
[122arm64-quarterly-job-11] |   `-- Extracting gettext-runtime-0.21: .......... done
[122arm64-quarterly-job-11] |   `-- Installing glib-2.66.7_1,1...
[122arm64-quarterly-job-11] |   | `-- Installing libffi-3.3_1...
<snip>
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
=====
Message from trousers-0.3.14_3:

--
To run tcsd automatically, add the following line to /etc/rc.conf:

tcsd_enable="YES"

You might want to edit /usr/local/etc/tcsd.conf to reflect your setup.

If you want to use tcsd with software TPM emulator, use the following
configuration in /etc/rc.conf:

tcsd_enable="YES"
tcsd_mode="emulator"
tpmd_enable="YES"

To use TPM, add your_account to '_tss' group like following:

# pw groupmod _tss -m your_account
===>   libghemical-3.0.0_16 depends on executable: obabel - found
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on executable: intltool-update - not found
===>   Installing existing package /packages/All/intltool-0.51.0_1.txz
[122arm64-quarterly-job-11] Installing intltool-0.51.0_1...
[122arm64-quarterly-job-11] `-- Installing p5-XML-Parser-2.44...
[122arm64-quarterly-job-11] `-- Extracting p5-XML-Parser-2.44: .......... done
[122arm64-quarterly-job-11] Extracting intltool-0.51.0_1: .......... done
===>   libghemical-3.0.0_16 depends on executable: intltool-update - found
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on executable: ld - found
===>   libghemical-3.0.0_16 depends on executable: gfortran10 - not found
===>   Installing existing package /packages/All/gcc10-10.2.0_1.txz
[122arm64-quarterly-job-11] Installing gcc10-10.2.0_1...
[122arm64-quarterly-job-11] `-- Installing binutils-2.33.1_4,1...
[122arm64-quarterly-job-11] `-- Extracting binutils-2.33.1_4,1: .......... done
[122arm64-quarterly-job-11] `-- Installing mpc-1.2.0...
[122arm64-quarterly-job-11] |   `-- Installing mpfr-4.1.0...
[122arm64-quarterly-job-11] |   `-- Extracting mpfr-4.1.0: .......... done
[122arm64-quarterly-job-11] `-- Extracting mpc-1.2.0: ......... done
[122arm64-quarterly-job-11] Extracting gcc10-10.2.0_1: .......... done
=====
Message from gcc10-10.2.0_1:

--
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.
===>   libghemical-3.0.0_16 depends on executable: gfortran10 - found
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on executable: msgfmt - not found
===>   Installing existing package /packages/All/gettext-tools-0.21.txz
[122arm64-quarterly-job-11] Installing gettext-tools-0.21...
[122arm64-quarterly-job-11] `-- Installing libtextstyle-0.21...
[122arm64-quarterly-job-11] `-- Extracting libtextstyle-0.21: .......... done
[122arm64-quarterly-job-11] Extracting gettext-tools-0.21: .......... done
===>   libghemical-3.0.0_16 depends on executable: msgfmt - found
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on package: gmake>=4.3 - not found
===>   Installing existing package /packages/All/gmake-4.3_2.txz
[122arm64-quarterly-job-11] Installing gmake-4.3_2...
[122arm64-quarterly-job-11] Extracting gmake-4.3_2: .......... done
===>   libghemical-3.0.0_16 depends on package: gmake>=4.3 - found
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on package: pkgconf>=1.3.0_1 - not found
===>   Installing existing package /packages/All/pkgconf-1.7.4,1.txz
[122arm64-quarterly-job-11] Installing pkgconf-1.7.4,1...
[122arm64-quarterly-job-11] Extracting pkgconf-1.7.4,1: .......... done
===>   libghemical-3.0.0_16 depends on package: pkgconf>=1.3.0_1 - found
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on file: /usr/local/bin/as - found
===>   libghemical-3.0.0_16 depends on package: xorgproto>=0 - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   libghemical-3.0.0_16 depends on shared library: libblas.so - not found
===>   Installing existing package /packages/All/blas-3.5.0_6.txz
[122arm64-quarterly-job-11] Installing blas-3.5.0_6...
[122arm64-quarterly-job-11] Extracting blas-3.5.0_6: ....... done
===>   libghemical-3.0.0_16 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so)
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on shared library: libint.so - not found
===>   Installing existing package /packages/All/libint-1.2.1.15.txz
[122arm64-quarterly-job-11] Installing libint-1.2.1.15...
[122arm64-quarterly-job-11] Extracting libint-1.2.1.15: .......... done
===>   libghemical-3.0.0_16 depends on shared library: libint.so - found (/usr/local/lib/libint.so)
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on shared library: libf2c.so - not found
===>   Installing existing package /packages/All/f2c-20200916.txz
[122arm64-quarterly-job-11] Installing f2c-20200916...
[122arm64-quarterly-job-11] Extracting f2c-20200916: .......... done
===>   libghemical-3.0.0_16 depends on shared library: libf2c.so - found (/usr/local/lib/libf2c.so)
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on shared library: liblapack.so - not found
===>   Installing existing package /packages/All/lapack-3.5.0_8.txz
[122arm64-quarterly-job-11] Installing lapack-3.5.0_8...
[122arm64-quarterly-job-11] Extracting lapack-3.5.0_8: .......... done
===>   libghemical-3.0.0_16 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so)
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on shared library: libmpqc.so - not found
===>   Installing existing package /packages/All/mpqc-2.3.1_46.txz
[122arm64-quarterly-job-11] Installing mpqc-2.3.1_46...
[122arm64-quarterly-job-11] `-- Installing graphviz-2.44.1_8...
[122arm64-quarterly-job-11] |   `-- Installing libXaw-1.0.13_3,2...
[122arm64-quarterly-job-11] |   | `-- Installing libXmu-1.1.3,1...
[122arm64-quarterly-job-11] |   | `-- Extracting libXmu-1.1.3,1: .......... done
[122arm64-quarterly-job-11] |   | `-- Installing libXpm-3.5.13...
[122arm64-quarterly-job-11] |   | `-- Extracting libXpm-3.5.13: .......... done
[122arm64-quarterly-job-11] |   `-- Extracting libXaw-1.0.13_3,2: .......... done
[122arm64-quarterly-job-11] |   `-- Installing libgd-2.3.1,1...
[122arm64-quarterly-job-11] |   `-- Extracting libgd-2.3.1,1: .......... done
[122arm64-quarterly-job-11] |   `-- Installing libltdl-2.4.6...
[122arm64-quarterly-job-11] |   `-- Extracting libltdl-2.4.6: .......... done
[122arm64-quarterly-job-11] `-- Extracting graphviz-2.44.1_8: .......... done
[122arm64-quarterly-job-11] `-- Installing mpich-3.4.1...
[122arm64-quarterly-job-11] |   `-- Installing bash-5.1.4_1...
[122arm64-quarterly-job-11] |   `-- Extracting bash-5.1.4_1: .......... done
[122arm64-quarterly-job-11] |   `-- Installing hwloc2-2.4.1...
[122arm64-quarterly-job-11] |   `-- Extracting hwloc2-2.4.1: .......... done
[122arm64-quarterly-job-11] |   `-- Installing json-c-0.15_1...
[122arm64-quarterly-job-11] |   `-- Extracting json-c-0.15_1: .......... done
[122arm64-quarterly-job-11] |   `-- Installing libfabric-1.11.2...
[122arm64-quarterly-job-11] |   `-- Extracting libfabric-1.11.2: .......... done
[122arm64-quarterly-job-11] |   `-- Installing slurm-wlm-20.02.1_6...
[122arm64-quarterly-job-11] |   | `-- Installing hdf-szip-2.1.1...
[122arm64-quarterly-job-11] |   | `-- Extracting hdf-szip-2.1.1: .......... done
[122arm64-quarterly-job-11] |   | `-- Installing hdf5-1.10.6,1...
[122arm64-quarterly-job-11] |   | `-- Extracting hdf5-1.10.6,1: .......... done
[122arm64-quarterly-job-11] |   | `-- Installing libsysinfo-0.0.3_2...
[122arm64-quarterly-job-11] |   | `-- Extracting libsysinfo-0.0.3_2: ......... done
[122arm64-quarterly-job-11] |   | `-- Installing lua52-5.2.4...
[122arm64-quarterly-job-11] |   | `-- Extracting lua52-5.2.4: ......... done
[122arm64-quarterly-job-11] |   | `-- Installing munge-0.5.14_1...
[122arm64-quarterly-job-11] |   | `-- Extracting munge-0.5.14_1: ......... done
===> Creating groups.
Creating group 'slurm' with gid '468'.
===> Creating users
Creating user 'slurm' with uid '468'.
[122arm64-quarterly-job-11] |   `-- Extracting slurm-wlm-20.02.1_6: .......... done
[122arm64-quarterly-job-11] `-- Extracting mpich-3.4.1: .......... done
[122arm64-quarterly-job-11] `-- Installing tk-wrapper-1.1_3...
[122arm64-quarterly-job-11] |   `-- Installing tk86-8.6.11_2...
[122arm64-quarterly-job-11] |   | `-- Installing tcl86-8.6.11_1...
[122arm64-quarterly-job-11] |   | `-- Extracting tcl86-8.6.11_1: .......... done
[122arm64-quarterly-job-11] |   `-- Extracting tk86-8.6.11_2: .......... done
[122arm64-quarterly-job-11] `-- Extracting tk-wrapper-1.1_3: ..... done
[122arm64-quarterly-job-11] Extracting mpqc-2.3.1_46: .......... done
=====
Message from mpich-3.4.1:

--
===>   NOTICE:

The mpich 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
=====
Message from tk-wrapper-1.1_3:

--
You may wish to modify (or create) the configuration file:
/usr/local/etc/wish.conf

Sample configuration file is located at:
/usr/local/etc/wish.conf.sample
===>   libghemical-3.0.0_16 depends on shared library: libmpqc.so - found (/usr/local/lib/libmpqc.so)
===>   Returning to build of libghemical-3.0.0_16
===>   libghemical-3.0.0_16 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===>   libghemical-3.0.0_16 depends on shared library: libGL.so - found (/usr/local/lib/libGL.so)
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for libghemical-3.0.0_16
===>   FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/libghemical/work/libghemical-3.0.0/aclocal.m4
===>   FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/libghemical/work/libghemical-3.0.0/configure
ld-elf.so.1: /usr/local/lib/gcc10/libgcc_s.so: invalid file format
===>  Script "configure" failed unexpectedly.
Please report the problem to yuri@FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/science/libghemical/work/libghemical-3.0.0/config.log"
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/science/libghemical