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[Bioc-devel] recent changes in ggplot2 break some packages

4 messages · Diego Diez, Ramon Diaz-Uriarte, Hervé Pagès

Original
Ramon Diaz-Uriarte
# 
Dear All,

At least some packages (partial list in links below) are failing checks in
both release and devel; the error logs for Linux, Windows, and Mac all show


"Error: processing vignette 'OncoSimulR.Rmd' failed with diagnostics:
[GeomTextRepel/PositionQuasirandom/etc] was built with an incompatible
version of ggproto.  Please reinstall the package that provides this
extension."


A partial list for devel:
http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/malbec2-buildsrc.html
http://bioconductor.org/checkResults/devel/bioc-LATEST/cytofkit/malbec2-buildsrc.html
http://bioconductor.org/checkResults/devel/bioc-LATEST/maftools/malbec2-buildsrc.html
http://bioconductor.org/checkResults/devel/bioc-LATEST/MoonlightR/malbec2-buildsrc.html
http://bioconductor.org/checkResults/devel/bioc-LATEST/pcaExplorer/malbec2-buildsrc.html
http://bioconductor.org/checkResults/devel/bioc-LATEST/scater/malbec2-buildsrc.html



For release:
http://bioconductor.org/checkResults/release/bioc-LATEST/OncoSimulR/malbec1-buildsrc.html
http://bioconductor.org/checkResults/release/bioc-LATEST/cytofkit/malbec1-buildsrc.html
etc


This seems related to very recent changes in ggplot2 (and other people have
reported similar problems in oter forums). It is fixed reinstalling ggplot2
and the other package that depends on it (e.g., ggrepel)[1]. 

Should we just wait for ggplot2 and ggrepel to be reinstalled in the build
machines? How often do these happen?


Best,


R.


[1] And, at least for the package I maintain, OncoSimulR, there are no
issues with R-devel in my local machines or with Travis
(https://travis-ci.org/rdiaz02/OncoSimul), or Appveyor
(https://ci.appveyor.com/project/rdiaz02/OncoSimul).
Diego Diez
# 
Hi Ramon,

My experience with this issue is that it requires reinstalling the
depending packages from source (but not ggplot2 itself).
Alternatively, this should be fixed (I think) once all dependent
packages are rebuilt with the newest ggplot2 installed. See this
related post in the ggtree package issue tracker:

https://github.com/GuangchuangYu/ggtree/issues/91

Best,
Diego
On Mon, Nov 14, 2016 at 7:50 PM, Ramon Diaz-Uriarte <rdiaz02 at gmail.com> wrote:
Ramon Diaz-Uriarte
# 
Hi Diego,
On Mon, 14-11-2016, at 12:25, Diego Diez <diego10ruiz at gmail.com> wrote:
Makes sense (in my machines, I just reinstalled both, for the sake of
expediency :-) so I should have said that was sufficient but wasn't sure
what was necessary).
Thanks for the link.


Best,

R.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
      #
    

  


  

      
Hi Ramon, Diego,

Thanks for bringing this to our attention. This week we'll update R
to 3.3.2 on the machines building release and that will trigger
re-installation of all the packages on these machines. For the devel
builds, the issue will also go away when we update R, which we'll do
in 4 or 5 weeks from now. We'll try to manually re-install some of
the packages that depend on ggplot2 in the mean time.

Cheers,
H.

        
On 11/14/2016 10:35 AM, Ramon Diaz-Uriarte wrote: