Re: [Bioc-devel] ggplot2 update coming on June 25 and how it affects ggbio + other packages
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
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 element.
> Please specify either 'title' or 'pagetitle' in the metadata.
> Falling back to 'bumphunterExampleOutput.utf8'
> [WARNING] This document format requires a nonempty 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
>
[Bioc-devel] ggplot2 update coming on June 25 and how it affects ggbio + other packages
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 element.
Please specify either 'title' or 'pagetitle' in the metadata.
Falling back to 'bumphunterExampleOutput.utf8'
[WARNING] This document format requires a nonempty 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
