[Bioc-devel] Fwd: failing package OUTRIDER

[Christian Mertes]

Dear Lori,


I checked our package OUTRIDER on the devel branch and I guess that the 
error arises from a misconfiguration on the OSX platform. It looks like 
a problem with the cairo library/package on the OSX system.

── 1. Error: plotting (@test_plotting.R#9)  ────────────────────────────────────
.onLoad failed in loadNamespace() for 'Cairo', details:
   call: dyn.load(file, DLLpath = DLLpath, ...)
   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Cairo/libs/Cairo.so':
   dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Cairo/libs/Cairo.so, 6): Symbol not found: _FcConfigGetCurrent
   Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Cairo/libs/Cairo.so
   Expected in: flat namespace
  in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Cairo/libs/Cairo.so


A detailed error message can be found here: 
http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/merida2-checksrc.html



This same error was already reported in 2015 and fixed pretty fix but 
without stating the bugfix: 
https://stat.ethz.ch/pipermail/bioc-devel/2015-June/007644.html


And we are also not the only package having the problem:


https://bioc.ism.ac.jp/checkResults/devel/bioc-LATEST/CATALYST/merida2-checksrc.html
https://bioc.ism.ac.jp/checkResults/devel/bioc-LATEST/scde/merida2-checksrc.html
https://bioc.ism.ac.jp/checkResults/devel/bioc-LATEST/singscore/merida2-checksrc.html
...


Let me know if you need any more information on this and if I can help 
solving this.


Best,

Chriss


PS: I also updated the package to remove the warning.


Am 2/23/2019 um 2:49 AM schrieb Felix Brechtmann:
>
> Hi,
>
>
> Can you please check this.
>
>
> Felix
>
>
>
> -------- Forwarded Message --------
> Subject: 	failing package OUTRIDER
> Date: 	Fri, 22 Feb 2019 13:32:52 +0000
> From: 	Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> To: 	brechtma using in.tum.de <brechtma using in.tum.de>
>
>
>
> Dear OUTRIDER maintainer,
>
> I'd like to bring to your attention that the OUTRIDER package is 
> failing to pass 'R CMD check' on all platforms in the devel version of 
> Bioconductor (3.9)
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/
>
> Would you mind taking a look at this? Don't hesitate to ask on the 
> bioc-devel using r-project.org mailing list if you have any question or need 
> help.
>
>
> While devel is a place to experiment with new features, we expect 
> packages to build and check cleanly in a reasonable time period and 
> not stay broken for any extended period of time.   The package has 
> been failing since 01/25/19
>
> If no action is taken over the next few weeks we will begin the 
> deprecation process for your package.
>
> Thank you for your time and effort, and your continued contribution to 
> Bioconductor.
>
> Pleae be advised that Bioconductor has switched from svn to Git. Some 
> helpful links can be found here:
> https://bioconductor.org/developers/how-to/git/
> http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
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-- 
*Christian Mertes* | PhD Student / Lab Administrator

*Gagneur Lab* - Computational Genomics
I12 - Department of Informatics
Technical University of Munich
Boltzmannstr. 3, 85748 Garching, Germany

mertes using in.tum.de <mailto:mertes using in.tum.de> | http://gagneurlab.in.tum.de

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