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

[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:
> 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
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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