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

[Ramon Diaz-Uriarte]

Hi Diego,


On Mon, 14-11-2016, at 12:25, Diego Diez <diego10ruiz at gmail.com> wrote:
> Hi Ramon,
>
> My experience with this issue is that it requires reinstalling the
> depending packages from source (but not ggplot2 itself).

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).


> 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

Thanks for the link.


Best,

R.

>
> Best,
> Diego
>
> On Mon, Nov 14, 2016 at 7:50 PM, Ramon Diaz-Uriarte <rdiaz02 at gmail.com> wrote:
>> 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).
>>
>>
>>
>>
>> --
>> Ramon Diaz-Uriarte
>> Department of Biochemistry, Lab B-25
>> Facultad de Medicina
>> Universidad Autónoma de Madrid
>> Arzobispo Morcillo, 4
>> 28029 Madrid
>> Spain
>>
>> Phone: +34-91-497-2412
>>
>> Email: rdiaz02 at gmail.com
>>        ramon.diaz at iib.uam.es
>>
>> http://ligarto.org/rdiaz
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es

http://ligarto.org/rdiaz