[package - 120armv6-quarterly][biology/prodigy-lig] Failed for prodigy-lig-1.0.0.3 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Fri Apr 26 12:38:09 UTC 2019
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 at FreeBSD.org
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: branches/2019Q2/biology/prodigy-lig/Makefile 492059 2019-02-03 18:49:23Z yuri $
Log URL: http://beefy15.nyi.freebsd.org/data/120armv6-quarterly/499925/logs/prodigy-lig-1.0.0.3.log
Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=120armv6-quarterly&build=499925
Log:
=>> Building biology/prodigy-lig
build started at Fri Apr 26 12:37:24 UTC 2019
port directory: /usr/ports/biology/prodigy-lig
package name: prodigy-lig-1.0.0.3
building for: FreeBSD 120armv6-quarterly-job-06 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 arm
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2019Q2/biology/prodigy-lig/Makefile 492059 2019-02-03 18:49:23Z yuri $
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=======================<phase: check-sanity >============================
===> License APACHE20 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> prodigy-lig-1.0.0.3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.5_5.txz
[120armv6-quarterly-job-06] Installing pkg-1.10.5_5...
[120armv6-quarterly-job-06] Extracting pkg-1.10.5_5: .......... done
===> prodigy-lig-1.0.0.3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of prodigy-lig-1.0.0.3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License APACHE20 accepted by the user
=> haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/haddocking/prodigy-lig/tar.gz/v1.0.0-3-g152ac59?dummy=/haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz
fetch: https://codeload.github.com/haddocking/prodigy-lig/tar.gz/v1.0.0-3-g152ac59?dummy=/haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/haddocking/prodigy-lig/tar.gz/v1.0.0-3-g152ac59?dummy=/haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz: size of remote file is not known
haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz 151 kB 3821 kBps 00s
===> Fetching all distfiles required by prodigy-lig-1.0.0.3 for building
===========================================================================
=======================<phase: checksum >============================
===> License APACHE20 accepted by the user
===> Fetching all distfiles required by prodigy-lig-1.0.0.3 for building
<snip>
[120armv6-quarterly-job-06] | | `-- Installing binutils-2.32,1...
[120armv6-quarterly-job-06] | | `-- Installing gettext-runtime-0.19.8.1_2...
[120armv6-quarterly-job-06] | | | `-- Installing indexinfo-0.3.1...
[120armv6-quarterly-job-06] | | | `-- Extracting indexinfo-0.3.1: .... done
[120armv6-quarterly-job-06] | | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[120armv6-quarterly-job-06] | | `-- Extracting binutils-2.32,1: .......... done
[120armv6-quarterly-job-06] | | `-- Installing gmp-6.1.2_1...
[120armv6-quarterly-job-06] | | `-- Extracting gmp-6.1.2_1: .......... done
[120armv6-quarterly-job-06] | | `-- Installing mpc-1.1.0_2...
[120armv6-quarterly-job-06] | | `-- Installing mpfr-4.0.2...
[120armv6-quarterly-job-06] | | `-- Extracting mpfr-4.0.2: .......... done
[120armv6-quarterly-job-06] | | `-- Extracting mpc-1.1.0_2: ......... done
[120armv6-quarterly-job-06] | `-- Extracting gcc8-8.3.0_1: .......... done
[120armv6-quarterly-job-06] `-- Extracting blas-3.5.0_5: ....... done
[120armv6-quarterly-job-06] `-- Installing cblas-1.0_10...
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[120armv6-quarterly-job-06] `-- Installing lapack-3.5.0_6...
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[120armv6-quarterly-job-06] `-- Installing py36-setuptools-40.8.0...
[120armv6-quarterly-job-06] | `-- Installing python36-3.6.8_1...
[120armv6-quarterly-job-06] | | `-- Installing libffi-3.2.1_3...
[120armv6-quarterly-job-06] | | `-- Extracting libffi-3.2.1_3: .......... done
[120armv6-quarterly-job-06] | | `-- Installing readline-7.0.5...
[120armv6-quarterly-job-06] | | `-- Extracting readline-7.0.5: .......... done
[120armv6-quarterly-job-06] | `-- Extracting python36-3.6.8_1: .......... done
[120armv6-quarterly-job-06] `-- Extracting py36-setuptools-40.8.0: .......... done
[120armv6-quarterly-job-06] `-- Installing suitesparse-5.2.0_2...
[120armv6-quarterly-job-06] | `-- Installing metis-5.1.0_7...
[120armv6-quarterly-job-06] | `-- Extracting metis-5.1.0_7: .......... done
[120armv6-quarterly-job-06] | `-- Installing openblas-0.2.20_7,1...
[120armv6-quarterly-job-06] | `-- Extracting openblas-0.2.20_7,1: ......... done
[120armv6-quarterly-job-06] `-- Extracting suitesparse-5.2.0_2: .......... done
[120armv6-quarterly-job-06] Extracting py36-numpy-1.16.1,1: .......... done
Message from gcc8-8.3.0_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/gcc8
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
Message from cblas-1.0_10:
===> NOTICE:
The cblas 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 python36-3.6.8_1:
===========================================================================
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py36-gdbm databases/py-gdbm at py36
py36-sqlite3 databases/py-sqlite3 at py36
py36-tkinter x11-toolkits/py-tkinter at py36
===========================================================================
Message from py36-setuptools-40.8.0:
*******************************************************************
Only /usr/local/bin/easy_install-3.6 script has been installed
since Python 3.6 is not the default Python version.
*******************************************************************
Message from metis-5.1.0_7:
===> 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
===> prodigy-lig-1.0.0.3 depends on package: py36-numpy>0 - found
===> Returning to build of prodigy-lig-1.0.0.3
===> prodigy-lig-1.0.0.3 depends on package: py36-biopython>0 - not found
===> Installing existing package /packages/All/py36-biopython-1.73.txz
[120armv6-quarterly-job-06] Installing py36-biopython-1.73...
[120armv6-quarterly-job-06] `-- Installing py36-reportlab-3.5.13...
[120armv6-quarterly-job-06] | `-- Installing adobe-cmaps-20051217_4...
[120armv6-quarterly-job-06] | | `-- Installing fontconfig-2.12.6,1...
[120armv6-quarterly-job-06] | | `-- Installing expat-2.2.6_1...
[120armv6-quarterly-job-06] | | `-- Extracting expat-2.2.6_1: .......... done
[120armv6-quarterly-job-06] | | `-- Installing freetype2-2.9.1...
[120armv6-quarterly-job-06] | | `-- Extracting freetype2-2.9.1: .......... done
[120armv6-quarterly-job-06] | | `-- Extracting fontconfig-2.12.6,1: .......... done
Running fc-cache to build fontconfig cache...
/usr/local/share/fonts: skipping, no such directory
/usr/local/lib/X11/fonts: skipping, no such directory
/var/db/fontconfig: cleaning cache directory
fc-cache: succeeded
[120armv6-quarterly-job-06] | | `-- Installing mkfontscale-1.2.1...
[120armv6-quarterly-job-06] | | `-- Installing libfontenc-1.1.4...
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[120armv6-quarterly-job-06] | `-- Installing py36-pillow-5.3.0...
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[120armv6-quarterly-job-06] | | `-- Installing openjpeg-2.3.0_4...
[120armv6-quarterly-job-06] | | `-- Installing lcms2-2.9...
[120armv6-quarterly-job-06] | | | `-- Installing tiff-4.0.10...
[120armv6-quarterly-job-06] | | | `-- Installing jbigkit-2.1_1...
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[120armv6-quarterly-job-06] | | `-- Installing png-1.6.36...
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[120armv6-quarterly-job-06] | | `-- Extracting openjpeg-2.3.0_4: .......... done
[120armv6-quarterly-job-06] | | `-- Installing py36-tkinter-3.6.8_6...
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[120armv6-quarterly-job-06] | | | `-- Installing libXdmcp-1.1.3...
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[120armv6-quarterly-job-06] | | | `-- Installing libxcb-1.13.1...
[120armv6-quarterly-job-06] | | | | `-- Installing libpthread-stubs-0.4...
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[120armv6-quarterly-job-06] | | | | `-- Installing libxml2-2.9.8...
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[120armv6-quarterly-job-06] | | | `-- Installing libXft-2.3.2_3...
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[120armv6-quarterly-job-06] | | `-- Installing webp-1.0.2...
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[120armv6-quarterly-job-06] | `-- Extracting py36-pillow-5.3.0: .......... done
[120armv6-quarterly-job-06] `-- Extracting py36-reportlab-3.5.13: .......... done
[120armv6-quarterly-job-06] Extracting py36-biopython-1.73: .......... done
Message from freetype2-2.9.1:
The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as
the default, emulating a modern version of ClearType. This change inevitably
leads to different rendering results, and you might change port's options to
adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment
variable).
The environment variable "FREETYPE_PROPERTIES" can be used to control the
driver properties. Example:
FREETYPE_PROPERTIES=truetype:interpreter-version=35 \
cff:no-stem-darkening=1 \
autofitter:warping=1
This allows to select, say, the subpixel hinting mode at runtime for a given
application.
The controllable properties are listed in the section "Controlling FreeType
Modules" in the reference's table of contents
(/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed).
===> prodigy-lig-1.0.0.3 depends on package: py36-biopython>0 - found
===> Returning to build of prodigy-lig-1.0.0.3
===> prodigy-lig-1.0.0.3 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.2.1_3.txz
[120armv6-quarterly-job-06] Installing gmake-4.2.1_3...
[120armv6-quarterly-job-06] Extracting gmake-4.2.1_3: .......... done
===> prodigy-lig-1.0.0.3 depends on executable: gmake - found
===> Returning to build of prodigy-lig-1.0.0.3
===> prodigy-lig-1.0.0.3 depends on package: py36-setuptools>0 - found
===> prodigy-lig-1.0.0.3 depends on file: /usr/local/bin/python3.6 - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for prodigy-lig-1.0.0.3
prodigy_lig depends on Biopython. Please install Biopython along with its dependencies and restart.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/prodigy-lig
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