[Bioc-devel] Fwd: failing package OUTRIDER

[Shepherd, Lori]

Thank you for bringing this to our attention.  If the package is building clear on the malbec2 and tokay2 platforms then you can ignore this ERROR for now.

We will look into the CAIRO installation on the MACOS.  Please note merida2 will be removed shortly and our main Mac builder is now celaya2.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Christian Mertes <mertes using in.tum.de>
Sent: Tuesday, March 5, 2019 10:24:40 AM
To: Felix Brechtmann; Shepherd, Lori
Cc: bioc-devel using r-project.org
Subject: Re: Fwd: failing package OUTRIDER


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><mailto:Lori.Shepherd using RoswellPark.org>
To:     brechtma using in.tum.de<mailto:brechtma using in.tum.de> <brechtma using in.tum.de><mailto: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<mailto: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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