[Bioc-devel] BiocStyle2: issue with wide figure command

[Ludwig Geistlinger]

Dear Andrzej,

BiocStyle2 is a great piece of work and the new vignettes look really nice!
Thank you!

However, I am having a problem with the widefigure (figure*) environment,
which apparently only holds for my local installation, as the same
vignette builds fine here:

http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/



However, on my machine (- do I need to update any external dependencies?):

Rdev CMD build EnrichmentBrowser
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* preparing ‘EnrichmentBrowser’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
  Execution of 'texi2dvi' for 'EnrichmentBrowser.tex' failed.
LaTeX errors:
! Undefined control sequence.
\\figure* [#1]->\blockmargin
                             \@biocfloat at wide {figure}{#1}
l.761 \centering

! Undefined control sequence.
\endfigure* ->\endfigure \unblockmargin
                                        [1em]
l.768 \end{figure*}

! Undefined control sequence.
\\figure* [#1]->\blockmargin
                             \@biocfloat at wide {figure}{#1}
l.1002 \begin{figure*}[!h]

! Undefined control sequence.
\endfigure* ->\endfigure \unblockmargin
                                        [1em]
l.1008 \end{figure*}

Call: <Anonymous> -> texi2pdf -> texi2dvi
Exectuion halted.



Here is some information on the build environment, please let me know if I
should provide additional information:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] C/UTF-8/C/C/C/C

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

other attached packages:
[1] BiocStyle_2.5.37

loaded via a namespace (and not attached):
 [1] compiler_3.4.1  backports_1.1.0 magrittr_1.5    rprojroot_1.2
 [5] htmltools_0.3.6 tools_3.4.1     yaml_2.1.14     Rcpp_0.12.12
 [9] stringi_1.1.5   rmarkdown_1.6   knitr_1.16      stringr_1.2.0
[13] digest_0.6.12   evaluate_0.10.1


Thanks,
Ludwig


> Dear Bioconductor Developers,
>
> overall the transition to the updated formatting went smooth considering
> the number of packages using BiocStyle, and the different possible input
> (.Rnw/.Rmd) and output formats (PDF/HTML).
>
> However, we have identified some common issues with specifying author
> information in Sweave/knitr (.Rnw) vignettes which lead to package build
> errors or timeouts. The updated style loads the 'authblk' LaTeX package to
> standardize the way of specifying author affiliations, but unfortunately
> this approach is also more fragile than the default LaTeX macros. In
> particular, the usual author separator ' \and' is not compatible with the
> authblk's footnote mode used by BiocStyle.
>
> The maintainers of the following packages are encouraged to review their
> vignettes and ensure that '\author{}' does not contain any custom
> formatting and meets the guidelines outlined in Section 2.1.2 "Authors and
> affiliations" of the "Bioconductor LaTeX Style 2.0" vignette [1].
>
> DiffBind
> GMRP
> groHMM
> MBttest
> MutationalPatterns
> OncoScore
> OperaMate
> quantro
> rCGH
> RiboProfiling
> sampleClassifier
> TRONCO
>
>
> Additionally, the following packages fail to build because their vignettes
> contain some LaTeX customizations incompatible with the current version of
> BiocStyle.
>
> funtooNorm
> Linnorm
> NanoStringQCPro
>
>
> Thank you for your understanding and cooperation.
>
> Kind regards,
> Andrzej OleÅ›
>
> [1]
> http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle2.pdf
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Dr. Ludwig Geistlinger
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de