Hi Geert,
Thanks for letting us know - I've added the folllowing Trello card for this and
we'll get it fixed asap.
https://trello.com/c/65DOL7PL/160-repository-package-libpng-owned-by-devteam-on-main-tool-shed-bug
Greg Von Kuster
On Feb 20, 2014, at 5:10 PM, Geert Vandeweyer
wrote:
> Hi Bjoern & devteam members,
>
> I tried to install R_3_0_2 iuc version from the main toolshed, but got an
> error from the package_libpng from the devteam. I checked between the working
> tool_dependency from the testtoolshed and the failing one from the main.
>
> working:
>type="download_by_url">http://downloads.sourceforge.net/project/libpng/libpng16/older-releases/1.6.7/libpng-1.6.7.tar.gz
>
> failing :
>type="download_by_url">http://downloads.sourceforge.net/project/libpng/libpng16/1.6.7/libpng-1.6.7.tar.gz
>
> The package_libpng from the devteam is downloading a different version on
> test and main.
>
> Best,
>
> Geert
>
>
>
>
> On 02/20/2014 12:56 PM, Björn Grüning wrote:
>> Hello,
>>
>>> Hi,
>>>
>>> Compilation/installing works now. Using this R from the commandline no
>>> longer complains about missing X. With regards to cairo, I don't think I
>>> explicitly need it, but as I understood it, it was used in case there was
>>> no X11 server on the system?
>>
>> Not sure, I will add it if anyone complains :)
>>
>>> would you add it to the main toolshed? Then I can put is as a dependency on
>>> my tools that create plots from R (coverage_report), which has now the
>>> system version hardcoded.
>>
>> Done!
>> Thanks for testing!
>> Bjoern
>>
>>> Best,
>>>
>>> Geert
>>>
>>> On 02/20/2014 01:45 AM, Björn Grüning wrote:
Hi Geert,
can you retest please, I had a typo. Unfortunately, I can't test it by
myself since my internet connection is to bad here in Slovenia to download
that R-tarball.
Sorry,
Bjoern
> hi,
>
> The dependencies installed fine, but R itself gave this error:
>
> configure: error: unrecognized option:
> `-I/galaxy/galaxy_tool_binaries/libpng/1.6.7/devteam/package_libpng_1_6_7/a0b0e0281cc4/include'
> Try `./configure --help' for more information
>
>
> Any idea what might be wrong?
>
> Best,
>
> Geert
>
>
> On 02/19/2014 12:55 PM, Björn Grüning wrote:
>> Hi Geert,
>>
>> I tried to update the R package to include the libpng dependency, if you
>> like to test it ...
>>
>> http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_2
>>
>> Do you know if cairo is really needed? If I can I would omit to have a
>> dependency on cairo :)
>>
>> Cheers,
>> Bjoern
>>
>>> Hi all,
>>>
>>> I installed to package_r_2.11 and r_3x from the devteam to use as tool
>>> dependency. All installation goes fine, but when I run my tool I get
>>> the following error:
>>>
>>> Error in png(file = "../Plots/outname.png", bg = "white", width = 480,
>>> :
>>> X11 is not available
>>>
>>> The tool uses the installed R :
>>> /galaxy/galaxy_tool_binaries/R/2.11.0/devteam/package_r_2_11_0/8d0a55bf7aaf/lib/R/bin/R
>>>
>>> If I force the tool to use the system installed version of R, it works
>>> fine. Are there packages available in the toolsheds that allow the
>>> 'png' function to work? I already tried the R-packages from boris, but
>>> they gave compilation errors... I also tried to install the R-png
>>> package from cran as a galaxy dependency, but that didn't help either.
>>>
>>>
>>> Thanks for the help,
>>>
>>> Geert
>>>
>>
>
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: geert.vandewe...@ua.ac.be
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/in/geertvandeweyer
>>>
>>>
>>> --
>>>
>>> Geert Vandeweyer, Ph.D.
>>> Department of Medical Genetics
>>> University of Antwerp
>>> Prins Boudewijnlaan 43
>>> 2650 Edegem
>>> Belgium
>>> Tel: +32 (0)3 275 97 56
>>> E-mail: geert.vandewe...@ua.ac.be
>>> http://ua.ac.be/cognitivegenetics
>>> http://www.linkedin.com/in/geertvandeweyer
>>
>
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: geert.vandewe...@ua.ac.be
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/in/geertvandeweyer
> ___
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