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

[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:
> 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
>
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