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
