[Bioc-devel] ggplot2 update coming on June 25 and how it affects ggbio + other packages

[Leonardo Collado Torres]

Hi,

Two of my Bioconductor packages (regionReport and derfinderPlot) use
ggplot2 via ggbio. Since other packages import/suggest ggbio
http://bioconductor.org/packages/release/bioc/html/ggbio.html I'm
curious if you've taken a look at the email from Hadley Wickham and
the upcoming update to ggplot2 on June 25.

That email includes:

1. Read about the changes to ggplot2 at
   https://github.com/tidyverse/ggplot2/blob/master/NEWS.md#ggplot2-2219000.
   This page includes a list of breaking changes, the reasoning behind
   them, and to how to update your code.


2. Carefully inspect the failing checks listed at the bottom of this email.


I'm not sure if some of these issues are actually from ggbio or maybe
from my own code. If you think that they are on my end, please let me
know (like if you know that ggbio runs well with the new ggplot2).

Since it might be helpful for ggbio maintainers, I'm including my
check results from Hadley at the end of this email.

Best,
Leo


## regionReport https://github.com/leekgroup/regionReport

== CHECK RESULTS ========================================

*   checking examples ... ERROR
    ```
    ...
    label: MAstyle (with options)
    List of 2
     $ fig.width : num 10
     $ fig.height: num 10

       inline R code fragments

    label: genomeOverview1 (with options)
    List of 6
     $ message   : logi FALSE
     $ fig.width : num 7
     $ fig.height: num 9
     $ dpi       : num 300
     $ eval      : symbol nullExist
     $ echo      : symbol nullExist

    Scale for 'x' is already present. Adding another scale for 'x', which will
    replace the existing scale.
    Quitting from lines 365-366 (basicExploration.Rmd)
    Error: subscript contains invalid names
    Execution halted
    ```

*   checking re-building of vignette outputs ... WARNING
    ```
    ...
      ...
    [WARNING] This document format requires a nonempty <title> element.
      Please specify either 'title' or 'pagetitle' in the metadata.
      Falling back to 'bumphunterExampleOutput.utf8'
    [WARNING] This document format requires a nonempty <title> element.
      Please specify either 'title' or 'pagetitle' in the metadata.
      Falling back to 'bumphunterExampleOutput.utf8'
    Warning in citation("BiocStyle") :
      no date field in DESCRIPTION file of package 'BiocStyle'
    Warning in citation("biovizBase") :
      no date field in DESCRIPTION file of package 'biovizBase'
    Warning in citation("TxDb.Hsapiens.UCSC.hg19.knownGene") :
      no date field in DESCRIPTION file of package
'TxDb.Hsapiens.UCSC.hg19.knownGene'
    Warning in citation("DEFormats") :
      no date field in DESCRIPTION file of package 'DEFormats'
    Writing 34 Bibtex entries ... OK
    Results written to file 'regionReportRef.bib'
    Quitting from lines 230-235 (basicExploration.Rmd)
    Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
    subscript contains invalid names
    Execution halted
    ```

## Notes by Leo: derfinderPlot::plotOverview() seems to be the culprit
here https://github.com/leekgroup/derfinderPlot/blob/master/R/plotOverview.R.
That function ends up using autoplot() and layout_karyogram() from
ggbio. Or maybe the issue is on my end with the use of
scale_colour_manual() and scale_fill_manual().





## derfinderPlot https://github.com/leekgroup/derfinderPlot


== CHECK RESULTS ========================================

*   checking examples ... ERROR
    ```
    ...

    > genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
    +     annotationPackage = 'org.Hs.eg.db')
    Getting TSS and TSE.
    Getting CSS and CSE.
    Getting exons.
    Annotating genes.
    > annotation <- matchGenes(x = genomeRegions$regions, subject = genes)
    >
    > ## Make the plot
    > plotCluster(idx=1, regions=genomeRegions$regions, annotation=annotation,
    +     coverageInfo=genomeDataRaw$coverage, groupInfo=genomeInfo$pop,
    +     txdb=TxDb.Hsapiens.UCSC.hg19.knownGene)
    Warning in getIdeoGR(data) :
      geom(ideogram) need valid seqlengths information for accurate mapping,
                     now use reduced information as ideogram...
    Warning: `panel.margin` is deprecated. Please use `panel.spacing`
property instead
    Error in rep(startY, each = length(yy)) :
      attempt to replicate an object of type 'language'
    Calls: plotCluster ... layout_karyogram -> layout_karyogram ->
.local -> geom_arch_flip2
    Execution halted
    ```

*   checking tests ...
    ```
     ERROR
    Running the tests in ‘tests/test-all.R’ failed.
    Last 13 lines of output:
      5: print(e1)
      6: print(e1)
      7: .local(x, ...)
      8: layout_karyogram(obj, cytobands = cytoband, geom = NULL)
      9: layout_karyogram(obj, cytobands = cytoband, geom = NULL)
      10: .local(data, ...)
      11: geom_arch_flip2(df.tri.p2, aes(x = x, y = y, xend = xend,
yend = yend, height = height),
             color = "black", size = 0.5)

      ══ testthat results
═══════════════════════════════════════════════════════════
      OK: 7 SKIPPED: 0 FAILED: 1
      1. Error: (unknown) (@test_adv-plotCluster.R#38)

      Error: testthat unit tests failed
      Execution halted
    ```

*   checking re-building of vignette outputs ... WARNING
    ```
    Error in re-building vignettes:
      ...
    Warning in citation("BiocStyle") :
      no date field in DESCRIPTION file of package 'BiocStyle'
    Warning in citation("biovizBase") :
      no date field in DESCRIPTION file of package 'biovizBase'
    Warning in citation("TxDb.Hsapiens.UCSC.hg19.knownGene") :
      no date field in DESCRIPTION file of package
'TxDb.Hsapiens.UCSC.hg19.knownGene'
    Writing 24 Bibtex entries ... OK
    Results written to file 'derfinderPlotRef.bib'
    Quitting from lines 233-235 (derfinderPlot.Rmd)
    Error: processing vignette 'derfinderPlot.Rmd' failed with diagnostics:
    subscript contains invalid names
    Execution halted
    ```

## Notes from Leo: looks like the issue here is layout_karyogram()
from ggbio that is used by plotCluster()
https://github.com/leekgroup/derfinderPlot/blob/master/R/plotCluster.R.