Re: [easybuild] Autoconf run in ./src rather than .
Hi,
Well, it's really quite straight forward to fix. I preferred dropping the
old, outdated easyblock, because it's no longer needed (fixing would mean
undo'ing literally everything it does, reverting it back to configuremake)
https://github.com/easybuilders/easybuild-easyconfigs/pull/
Personally, I prefer not having a blocks when there isn't any special logic
needed for the build.
Best regards, Mikael
On Fri, Dec 13, 2019 at 12:04 PM Christian Meesters
wrote:
> Hi,
>
> is there any update on this issue?
>
> Cheers,
>
> Christian
>
>
> On 8/27/19 2:06 PM, Loris Bennett wrote:
> > Hi Åke,
> >
> > Ah, thanks for the information. The change must have happened
> > post 3.2.6, as I have a working easyconfig for that version.
> >
> > I would in fact be happy to install an older version, but an apparently
> > bumpy transition from Sourceforge to Github seems to have broken all the
> > archived source packages :-(
> >
> > Cheers,
> >
> > Loris
> >
> > Åke Sandgren writes:
> >
> >> You're not doing anything wrong, but since MrBayes changed layout
> >> between some 3.2 version and 3.2.7 the easyblock need to be updated.
> >>
> >> (Don't have time to look at this myself)
> >>
> >> On 8/27/19 1:23 PM, Loris Bennett wrote:
> >>> Hi,
> >>>
> >>> With EasyBuild 3.9.4 and the following easyconfig:
> >>>
> >>>name = 'MrBayes'
> >>>version = '3.2.7'
> >>>
> >>>homepage = 'http://nbisweden.github.io'
> >>>description = "MrBayes is a program for the Bayesian estimation of
> phylogeny."
> >>>
> >>>toolchain = {'name': 'foss', 'version': '2018b'}
> >>>toolchainopts = {'usempi': True}
> >>>
> >>>source_urls = ['https://github.com/NBISweden/MrBayes/archive']
> >>>sources = ['v%(version)s.tar.gz']
> >>>
> >>>dependencies = [
> >>>('beagle-lib', '3.0.2'),
> >>>('libreadline', '7.0'),
> >>>]
> >>>
> >>>builddependencies = [
> >>>('Autotools', '20180311'),
> >>>]
> >>>
> >>>moduleclass = 'bio'
> >>>
> >>> I have the following error for a
> >>>
> >>>== 2019-08-27 13:12:36,748 run.py:173 DEBUG run_cmd: running cmd
> autoconf (in
> /trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/src)
> >>>== 2019-08-27 13:12:36,748 run.py:192 INFO running cmd: autoconf
> >>>== 2019-08-27 13:12:36,960 build_log.py:163 ERROR EasyBuild crashed
> with an
> >>> error (at
> >>>
> easybuild/software/EasyBuild/3.9.4/lib/python2.7/site-packages/vsc_base-2.8.4-py2.7.egg/vsc/utils/exceptions.py:124
> >>> in __init__): cmd "autoconf" exited with exit code 1 and output:
> >>>autoconf: error: no input file
> >>>
> >>> As the unpacked tarball has the structure
> >>>
> >>>
> /trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/
> >>>├── aclocal.m4
> >>>├── am-aux
> >>>├── am-macros
> >>>├── configure
> >>>├── configure.ac
> >>>├── COPYING
> >>>├── doc
> >>>├── examples
> >>>├── INSTALL
> >>>├── Makefile.am
> >>>├── Makefile.in
> >>>├── NEWS
> >>>├── README
> >>>├── src
> >>>└── TODO
> >>>
> >>> autoconf should be run in .../MrBayes-3.2.7, rather than
> >>> .../MrBayes-3.2.7/src
> >>>
> >>> What am I doing wrong?
> >>>
> >>> Cheers,
> >>>
> >>> Loris
> >>>
>
Re: [easybuild] Autoconf run in ./src rather than .
Hi,
is there any update on this issue?
Cheers,
Christian
On 8/27/19 2:06 PM, Loris Bennett wrote:
Hi Åke,
Ah, thanks for the information. The change must have happened
post 3.2.6, as I have a working easyconfig for that version.
I would in fact be happy to install an older version, but an apparently
bumpy transition from Sourceforge to Github seems to have broken all the
archived source packages :-(
Cheers,
Loris
Åke Sandgren writes:
You're not doing anything wrong, but since MrBayes changed layout
between some 3.2 version and 3.2.7 the easyblock need to be updated.
(Don't have time to look at this myself)
On 8/27/19 1:23 PM, Loris Bennett wrote:
Hi,
With EasyBuild 3.9.4 and the following easyconfig:
name = 'MrBayes'
version = '3.2.7'
homepage = 'http://nbisweden.github.io'
description = "MrBayes is a program for the Bayesian estimation of
phylogeny."
toolchain = {'name': 'foss', 'version': '2018b'}
toolchainopts = {'usempi': True}
source_urls = ['https://github.com/NBISweden/MrBayes/archive']
sources = ['v%(version)s.tar.gz']
dependencies = [
('beagle-lib', '3.0.2'),
('libreadline', '7.0'),
]
builddependencies = [
('Autotools', '20180311'),
]
moduleclass = 'bio'
I have the following error for a
== 2019-08-27 13:12:36,748 run.py:173 DEBUG run_cmd: running cmd autoconf
(in /trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/src)
== 2019-08-27 13:12:36,748 run.py:192 INFO running cmd: autoconf
== 2019-08-27 13:12:36,960 build_log.py:163 ERROR EasyBuild crashed with an
error (at
easybuild/software/EasyBuild/3.9.4/lib/python2.7/site-packages/vsc_base-2.8.4-py2.7.egg/vsc/utils/exceptions.py:124
in __init__): cmd "autoconf" exited with exit code 1 and output:
autoconf: error: no input file
As the unpacked tarball has the structure
/trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/
├── aclocal.m4
├── am-aux
├── am-macros
├── configure
├── configure.ac
├── COPYING
├── doc
├── examples
├── INSTALL
├── Makefile.am
├── Makefile.in
├── NEWS
├── README
├── src
└── TODO
autoconf should be run in .../MrBayes-3.2.7, rather than
.../MrBayes-3.2.7/src
What am I doing wrong?
Cheers,
Loris
Re: [easybuild] Autoconf run in ./src rather than .
Hi Åke,
Ah, thanks for the information. The change must have happened
post 3.2.6, as I have a working easyconfig for that version.
I would in fact be happy to install an older version, but an apparently
bumpy transition from Sourceforge to Github seems to have broken all the
archived source packages :-(
Cheers,
Loris
Åke Sandgren writes:
> You're not doing anything wrong, but since MrBayes changed layout
> between some 3.2 version and 3.2.7 the easyblock need to be updated.
>
> (Don't have time to look at this myself)
>
> On 8/27/19 1:23 PM, Loris Bennett wrote:
>> Hi,
>>
>> With EasyBuild 3.9.4 and the following easyconfig:
>>
>> name = 'MrBayes'
>> version = '3.2.7'
>>
>> homepage = 'http://nbisweden.github.io'
>> description = "MrBayes is a program for the Bayesian estimation of
>> phylogeny."
>>
>> toolchain = {'name': 'foss', 'version': '2018b'}
>> toolchainopts = {'usempi': True}
>>
>> source_urls = ['https://github.com/NBISweden/MrBayes/archive']
>> sources = ['v%(version)s.tar.gz']
>>
>> dependencies = [
>> ('beagle-lib', '3.0.2'),
>> ('libreadline', '7.0'),
>> ]
>>
>> builddependencies = [
>> ('Autotools', '20180311'),
>> ]
>>
>> moduleclass = 'bio'
>>
>> I have the following error for a
>>
>> == 2019-08-27 13:12:36,748 run.py:173 DEBUG run_cmd: running cmd autoconf
>> (in
>> /trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/src)
>> == 2019-08-27 13:12:36,748 run.py:192 INFO running cmd: autoconf
>> == 2019-08-27 13:12:36,960 build_log.py:163 ERROR EasyBuild crashed with an
>> error (at
>> easybuild/software/EasyBuild/3.9.4/lib/python2.7/site-packages/vsc_base-2.8.4-py2.7.egg/vsc/utils/exceptions.py:124
>> in __init__): cmd "autoconf" exited with exit code 1 and output:
>> autoconf: error: no input file
>>
>> As the unpacked tarball has the structure
>>
>> /trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/
>> ├── aclocal.m4
>> ├── am-aux
>> ├── am-macros
>> ├── configure
>> ├── configure.ac
>> ├── COPYING
>> ├── doc
>> ├── examples
>> ├── INSTALL
>> ├── Makefile.am
>> ├── Makefile.in
>> ├── NEWS
>> ├── README
>> ├── src
>> └── TODO
>>
>> autoconf should be run in .../MrBayes-3.2.7, rather than
>> .../MrBayes-3.2.7/src
>>
>> What am I doing wrong?
>>
>> Cheers,
>>
>> Loris
>>
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
[easybuild] Autoconf run in ./src rather than .
Hi,
With EasyBuild 3.9.4 and the following easyconfig:
name = 'MrBayes'
version = '3.2.7'
homepage = 'http://nbisweden.github.io'
description = "MrBayes is a program for the Bayesian estimation of phylogeny."
toolchain = {'name': 'foss', 'version': '2018b'}
toolchainopts = {'usempi': True}
source_urls = ['https://github.com/NBISweden/MrBayes/archive']
sources = ['v%(version)s.tar.gz']
dependencies = [
('beagle-lib', '3.0.2'),
('libreadline', '7.0'),
]
builddependencies = [
('Autotools', '20180311'),
]
moduleclass = 'bio'
I have the following error for a
== 2019-08-27 13:12:36,748 run.py:173 DEBUG run_cmd: running cmd autoconf (in
/trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/src)
== 2019-08-27 13:12:36,748 run.py:192 INFO running cmd: autoconf
== 2019-08-27 13:12:36,960 build_log.py:163 ERROR EasyBuild crashed with an
error (at
easybuild/software/EasyBuild/3.9.4/lib/python2.7/site-packages/vsc_base-2.8.4-py2.7.egg/vsc/utils/exceptions.py:124
in __init__): cmd "autoconf" exited with exit code 1 and output:
autoconf: error: no input file
As the unpacked tarball has the structure
/trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/
├── aclocal.m4
├── am-aux
├── am-macros
├── configure
├── configure.ac
├── COPYING
├── doc
├── examples
├── INSTALL
├── Makefile.am
├── Makefile.in
├── NEWS
├── README
├── src
└── TODO
autoconf should be run in .../MrBayes-3.2.7, rather than
.../MrBayes-3.2.7/src
What am I doing wrong?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
