Undefined control sequence \bioctitle

[hpages]

We have a bunch of packages (30+, see list below) that are currently failing on all platforms in release and devel with the following error:

! Undefined control sequence.
l.53 \bioctitle
               []{PRAM: Pooling RNA-seq and Assembling Models} 

Not sure when the error appeared.

This error can actually be reproduced on the BiocStyle package itself by requesting PDF output for the AuthoringRmdVignettes.Rmd vignette which can be done by removing the 2 following lines

  BiocStyle::html_document:
    toc_float: true

from the vignette and running R CMD build BiocStyle:

hpages@spectre:~$ bdevbuild BiocStyle
* checking for file ‘BiocStyle/DESCRIPTION’ ... OK
* preparing ‘BiocStyle’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘AuthoringRmdVignettes.Rmd’ using rmarkdown
! Undefined control sequence.
l.53 \bioctitle
               []{Authoring R Markdown vignettes} 

Error: processing vignette 'AuthoringRmdVignettes.Rmd' failed with diagnostics:
Failed to compile AuthoringRmdVignettes.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See AuthoringRmdVignettes.log for more info.
--- failed re-building ‘AuthoringRmdVignettes.Rmd’

--- re-building ‘LatexStyle2.Rnw’ using Sweave
--- finished re-building ‘LatexStyle2.Rnw’

SUMMARY: processing the following file failed:
  ‘AuthoringRmdVignettes.Rmd’

Error: Vignette re-building failed.
Execution halted

Thanks!

sessionInfo:

> library(BiocStyle)
> sessionInfo()
R Under development (unstable) (2019-10-30 r77336)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS:   /home/hpages/R/R-4.0.r77336/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.0.r77336/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocStyle_2.15.2

loaded via a namespace (and not attached):
 [1] BiocManager_1.30.10 compiler_4.0.0      htmltools_0.4.0    
 [4] tools_4.0.0         yaml_2.2.0          Rcpp_1.0.3         
 [7] rmarkdown_2.0       knitr_1.26          digest_0.6.23      
[10] xfun_0.11           rlang_0.4.2         evaluate_0.14      

List of Bioconductor software packages currently affected:

abseqR
AllelicImbalance
AssessORF
BEARscc
CellBench
ChIPSeqSpike
CrispRVariants
DMRScan
epiNEM
FastqCleaner
FELLA
hipathia
Linnorm
MACPET
mdgsa
mnem
NormalyzerDE
nucleR
pram
profileScoreDist
projectR
pwrEWAS
restfulSE
RGMQL
rnaseqcomp
rScudo
SPLINTER
swfdr
transcriptR
TVTB (not supported on Windows)
universalmotif

[hpages]

FWIW this issue was also reported on the Bioc-devel mailing list a couple of days ago: https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015938.html

[hpages]

@aoles Do you think you can take a look at this?

[aoles]

Thanks, I can confirm the issue. It seems that the recent rmarkdown v2.0 release has broken BiocStyle yet again - at least I do not observe it with v1.18. I will give you an update once I know more.

[hpages]

Great! Thanks Andrzej

[mtmorgan]

It seems like the code here https://github.com/Bioconductor/BiocStyle/blob/0c3a2af3b603c53f1bb12fd996224e8eb98c0871/R/pdf_document.R#L254-L256 takes this template https://github.com/Bioconductor/BiocStyle/blob/master/inst/rmd/latex/default-1.17.0.2.tex and then modifies https://github.com/Bioconductor/BiocStyle/blob/0c3a2af3b603c53f1bb12fd996224e8eb98c0871/inst/rmd/latex/default-1.17.0.2.tex#L197-L212 after line 200 to inject Bioconductor.sty. But the line is in a conditional ($if(compact-title)$) so the injection is not always present. It seems really one would like to insert code at line 211.

[aoles]

Thanks @mtmorgan for sharing your findings! rmarkdown 2.0 does not support the option compact-title anymore so the referenced block is indeed not included causing Bioconductor.sty not being injected. I will look into fixing this.

Cheers, Andrzej

[stefangraw]

Hey bioc team,

My package (pwrEWAS) is one of the affected packages (vignette build is causing error). Is there anything I should do at this moment to fix the issue, or should I just wait?

Thanks, Stefan

[mtmorgan]

wait @aoles

[aoles]

Thank you for your patience! I have just committed a bugfix addressing the issue. The release and devel builds should clear up with the latest version of BiocStyle.

[hpages]

Thanks @aoles. We're going to keep a close eye on the daily reports for the release and devel builds in the next couple of days. Just want to make sure that the issue clears for all packages before closing the issue.

[vjcitn]

I used the latest git image of BiocStyle (2.15.4) and was able to build restfulSE, which is on the list above, and had a successful build and check. Is there a specific way of setting up the title in the yaml/latex that leads to this vulnerability for a minority of packages?

[hpages]

Heads-up: the devel builds picked up the latest BiocStyle (2.15.4) and are about to complete. The build report will be updated in the next hour or so with the new results. I can already confirm that the "Undefined control sequence \bioctitle" error is gone for all packages on all platforms. However, some other "Undefined control sequence" errors remain:

• SPLINTER:

  ! Undefined control sequence.
  l.59   \subtitle
                  {SPLice INTERpreter: Alternative splicing analysis toolkit}

  On all platforms.

• epiNEM, mCSEA, mnem, nucleR, transcriptR:

  ! Undefined control sequence.
  l.61 \definecolor
                   {fgcolor}{rgb}{0.251, 0.251, 0.251}

  On tokay2 and celaya2 only.

Note that except for mCSEA which is new, all these packages were in the original list above.

@aoles Let me know if you'd prefer me to open a new issue for this. Thanks!

[aoles]

I'm glad to hear that most of the errors cleared up. I've just committed a yet another fix addressing the \subtitle error.

Regarding the remaining issues, I'm not entirely sure what the root cause could be. At least I was unable to reproduce it locally, for me all of these package build just fine. It might be something specific to the LaTeX setup though. Maybe try checking whether these vignettes build with plain rmarkdown. You could do so by switching the output format from BiocStyle::pdf_document to rmarkdown::pdf_document and by loading BiocStyle right after the YAML header (in order to retain some of the BiocStyle macros) :

```{r}
library(BiocStyle)
```

Cheers, Andrzej

[hpages]

Thanks Andrzej.

Regarding the remaining issue (\definecolor error):

• Yes the epiNEM vignette builds with plain rmarkdown (only checked this on celaya2, the Mac builder).

• Note that we only see this issue on Windows (tokay2) and Mac (celaya2) where we have a fresh MiKTeX and MacTeX-2018, respectively. So TeX/LaTeX packages are current on tokay2 and reasonably recent on celaya2. OTOH the TeX/LaTeX packages on the Linux builder are the original packages shipped with Ubuntu 18.04 LTS. So of the 3 machines, the Linux builder has the oldest TeX/LaTeX packages. (BTW Is there an equivalent of sessionInfo() for TeX/LaTeX packages? Would be useful in this kind of situation.)

  Anyway, all this to say that it's not impossible that the error is related to a recent change in some TeX/LaTeX package. This would explain why we only see it on tokay2 and celaya2.

Thanks again, H.

[aoles]

Thanks! I have tested with the most recent MacTeX-2019 and haven't encountered any problems with building any of these packages.

[hpages]

The SPLINTER vignette now builds on all platforms even though the package has not been touched since October. Not clear what's causing the remaining "Undefined control sequence" errors on tokay2 (for mCSEA, mnem, nucleR, and transcriptR).

Anyway the original issue ("Undefined control sequence \bioctitle") is gone so I'm closing this. Thanks again!