Re: [galaxy-dev] Conda problem

2018-05-25 Thread Peter Cock 
Good thinking, and that's useful advice if something like this comes up again.

I wonder if there is a bug here somewhere (remnants of the environment
remaining)?

Peter

On Thu, May 24, 2018 at 4:28 PM, David Lee <david@bristol.ac.uk> wrote:
> Hi Peter,
>
>
> Thanks for your reply which nudged me in the right direction and the problem
> seems to be solved. Although I uninstalled samtools and samba from Galaxy
> there were remnants of the packages remaining in
> galaxy/database/dependencies/_conda/envs and
> galaxy/database/dependencies/_conda/pkgs/. After I deleted these directories
> the error messages disappeared and tools are running again.
>
>
> Cheers, David
>
> 
> From: Peter Cock <p.j.a.c...@googlemail.com>
> Sent: 24 May 2018 14:22:40
> To: David Lee
> Cc: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Conda problem
>
> On Thu, May 24, 2018 at 2:14 PM, David Lee <david@bristol.ac.uk> wrote:
>> Hi,
>>
>>
>> I hope somebody can help me with this. I've been maintaining a Galaxy
>> installation for the past few months that has suddenly developed a problem
>> that I can't undo.
>
> Which version of Galaxy? Can you tell what version of conda it is using?
>
>> I think it occurred after installing samtools and sambamba packages
>> which I have subsequently uninstalled but which has made no
>> difference. Every tool I try to run fails with this error:
>>
>> "Conda dependency failed to build job environment. This is most likely
>> a limitation in conda. You can try to shorten the path to the
>> job_working_directory."
>>
>
> There are some very long path names used in Conda, perhaps
> something has pushed you over an OS limit (like the longest
> allowed command line)?
>
>>
>> Also, in the paster.log file I'm seeing this error that I've never seen
>> before:
>>
>>
>> "CondaError: RuntimeError('EnforceUnusedAdapter called with url
>>
>> https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2018.4.16-0.tar.bz2\nThis
>> command is using a remote connection in offline mode.\n',)"
>>
>>
>> Any suggestions?
>
> This could be a different issue with similar symptoms, but there
> is a known issue in conda 4.3.17, fixed in conda 4.4.0, which looks
> related: https://github.com/conda/conda/issues/5443
>
> Peter
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Re: [galaxy-dev] Conda problem

2018-05-24 Thread David Lee 
Hi Peter,


Thanks for your reply which nudged me in the right direction and the problem 
seems to be solved. Although I uninstalled samtools and samba from Galaxy there 
were remnants of the packages remaining in 
galaxy/database/dependencies/_conda/envs and 
galaxy/database/dependencies/_conda/pkgs/. After I deleted these directories 
the error messages disappeared and tools are running again.


Cheers, David


From: Peter Cock <p.j.a.c...@googlemail.com>
Sent: 24 May 2018 14:22:40
To: David Lee
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Conda problem

On Thu, May 24, 2018 at 2:14 PM, David Lee <david@bristol.ac.uk> wrote:
> Hi,
>
>
> I hope somebody can help me with this. I've been maintaining a Galaxy
> installation for the past few months that has suddenly developed a problem
> that I can't undo.

Which version of Galaxy? Can you tell what version of conda it is using?

> I think it occurred after installing samtools and sambamba packages
> which I have subsequently uninstalled but which has made no
> difference. Every tool I try to run fails with this error:
>
> "Conda dependency failed to build job environment. This is most likely
> a limitation in conda. You can try to shorten the path to the
> job_working_directory."
>

There are some very long path names used in Conda, perhaps
something has pushed you over an OS limit (like the longest
allowed command line)?

>
> Also, in the paster.log file I'm seeing this error that I've never seen
> before:
>
>
> "CondaError: RuntimeError('EnforceUnusedAdapter called with url
> https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2018.4.16-0.tar.bz2\nThis
> command is using a remote connection in offline mode.\n',)"
>
>
> Any suggestions?

This could be a different issue with similar symptoms, but there
is a known issue in conda 4.3.17, fixed in conda 4.4.0, which looks
related: https://github.com/conda/conda/issues/5443

Peter
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Re: [galaxy-dev] Conda problem

2018-05-24 Thread Peter Cock 
On Thu, May 24, 2018 at 2:14 PM, David Lee  wrote:
> Hi,
>
>
> I hope somebody can help me with this. I've been maintaining a Galaxy
> installation for the past few months that has suddenly developed a problem
> that I can't undo.

Which version of Galaxy? Can you tell what version of conda it is using?

> I think it occurred after installing samtools and sambamba packages
> which I have subsequently uninstalled but which has made no
> difference. Every tool I try to run fails with this error:
>
> "Conda dependency failed to build job environment. This is most likely
> a limitation in conda. You can try to shorten the path to the
> job_working_directory."
>

There are some very long path names used in Conda, perhaps
something has pushed you over an OS limit (like the longest
allowed command line)?

>
> Also, in the paster.log file I'm seeing this error that I've never seen
> before:
>
>
> "CondaError: RuntimeError('EnforceUnusedAdapter called with url
> https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2018.4.16-0.tar.bz2\nThis
> command is using a remote connection in offline mode.\n',)"
>
>
> Any suggestions?

This could be a different issue with similar symptoms, but there
is a known issue in conda 4.3.17, fixed in conda 4.4.0, which looks
related: https://github.com/conda/conda/issues/5443

Peter
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[galaxy-dev] Conda problem

2018-05-24 Thread David Lee 
Hi,


I hope somebody can help me with this. I've been maintaining a Galaxy 
installation for the past few months that has suddenly developed a problem that 
I can't undo. I think it occurred after installing samtools and sambamba 
packages which I have subsequently uninstalled but which has made no 
difference. Every tool I try to run fails with this error:


"Conda dependency failed to build job environment. This is most likely a 
limitation in conda. You can try to shorten the path to the 
job_working_directory."


Also, in the paster.log file I'm seeing this error that I've never seen before:


"CondaError: RuntimeError('EnforceUnusedAdapter called with url 
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2018.4.16-0.tar.bz2\nThis
 command is using a remote connection in offline mode.\n',)"


Any suggestions?


Regards, David
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Re: [galaxy-dev] conda problem

2017-09-01 Thread Matthias Bernt 

Hi Bjoern,

thanks for the information. Then I will check for a new version next 
week and check if the problem is gone.


Have a great weekend.

Cheers,
Matthias

On 31.08.2017 18:24, Björn Grüning wrote:

Hi Matthias,

conda-build only supported 80 chars limit for a long time. This has
fixed and all new packages don't have this problem.

So hopefully this PR will fix it:

https://github.com/bioconda/bioconda-recipes/pull/5912

Cheers,
bjeorn

On 31.08.2017 17:19, Matthias Bernt wrote:

Dear list,

When running rmarkdown_wgcna I get the following error in the logs:

PaddingError: Placeholder of length '80' too short in package
bioconda::r-wgcna-1.51-r3.3.1_0.
The package must be rebuilt with conda-build > 2.0.

The command that seems to lead to this is:

Executing command:
/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/bin/conda
create -y --name mulled-v1-3bfe8da4ed798836281cc963619917
317ae960c9a828f7ea05d1670c65b19619 pandoc=1.15.0.6-0 r-getopt=1.20.0
r-rmarkdown=1.2 r-plyr=1.8.4 r-highcharter=0.4.0 r-dt=0.2
r-htmltools=0.3.5 r-wgcna=1.51

Any ideas?

Best,
Matthias




--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
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Re: [galaxy-dev] conda problem

2017-08-31 Thread Björn Grüning 
Hi Matthias,

conda-build only supported 80 chars limit for a long time. This has
fixed and all new packages don't have this problem.

So hopefully this PR will fix it:

https://github.com/bioconda/bioconda-recipes/pull/5912

Cheers,
bjeorn

On 31.08.2017 17:19, Matthias Bernt wrote:
> Dear list,
> 
> When running rmarkdown_wgcna I get the following error in the logs:
> 
> PaddingError: Placeholder of length '80' too short in package
> bioconda::r-wgcna-1.51-r3.3.1_0.
> The package must be rebuilt with conda-build > 2.0.
> 
> The command that seems to lead to this is:
> 
> Executing command:
> /gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/bin/conda
> create -y --name mulled-v1-3bfe8da4ed798836281cc963619917
> 317ae960c9a828f7ea05d1670c65b19619 pandoc=1.15.0.6-0 r-getopt=1.20.0
> r-rmarkdown=1.2 r-plyr=1.8.4 r-highcharter=0.4.0 r-dt=0.2
> r-htmltools=0.3.5 r-wgcna=1.51
> 
> Any ideas?
> 
> Best,
> Matthias
> 
> 
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[galaxy-dev] conda problem

2017-08-31 Thread Matthias Bernt 

Dear list,

When running rmarkdown_wgcna I get the following error in the logs:

PaddingError: Placeholder of length '80' too short in package 
bioconda::r-wgcna-1.51-r3.3.1_0.

The package must be rebuilt with conda-build > 2.0.

The command that seems to lead to this is:

Executing command: 
/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/bin/conda 
create -y --name mulled-v1-3bfe8da4ed798836281cc963619917
317ae960c9a828f7ea05d1670c65b19619 pandoc=1.15.0.6-0 r-getopt=1.20.0 
r-rmarkdown=1.2 r-plyr=1.8.4 r-highcharter=0.4.0 r-dt=0.2 
r-htmltools=0.3.5 r-wgcna=1.51


Any ideas?

Best,
Matthias


--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
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[galaxy-dev] conda problem with R libraries

2017-07-04 Thread Jochen Bick 
Hi all,

I'm testing a tool with planemo and the conda dependencies are not running:


r-base
r-ggfortify
r-getoptlong



galaxy.jobs.handler INFO 2017-07-04 13:11:42,935 (2) Job dispatched
galaxy.util.object_wrapper WARNING 2017-07-04 13:11:43,062 Unable to
create dynamic subclass for , None: metaclass conflict:
the metaclass of a derived class must be a (non-strict) subclass of the
metaclasses of all its bases
...The following specifications were found to be in conflict:
  - cairo 1.14.6 4
  - r-assertthat (target=r-assertthat-0.1-r3.3.2_4.tar.bz2) -> r-base 3.3.2*
...
...

somehow the conflicts can not be resolved=?

Cheers Jochen


-- 
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
Office: Tannenstrasse 1 / TAN D 6.2
8092 Zurich, Switzerland

Phone +41 44 632 28 25
jochen.b...@usys.ethz.ch 
www.ap.ethz.ch
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