Hi Leonardo, I'm aware that the new ggplot2 is breaking ggbio. I haven't yet convinced myself to actually fix it, even though I know there's no way to avoid it. ggbio represents a big piece of technical debt, and I'm not sure how to pay it off.
Michael On Wed, Jun 6, 2018 at 1:03 PM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > 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. > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
