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

[Ludwig Geistlinger]

Yes, I was indeed sitting on an old Tex version.
Upgrading to Tex Live 2017 fixed that.

Thanks,
Ludwig


> Hi Ludwig,
>
> thank you! This sounds like an issue with your LaTeX distribution, in
> particular the package 'marginfix'. Please make sure that all the packages
> listed in the BiocStyle vignette under Appendix B "Attached LATEX
> packages"
> are installed, and possibly the up-to-date.
>
> Best,
> Andrzej
>
> On Tue, Sep 12, 2017 at 11:03 PM, Ludwig Geistlinger <
> Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:
>
>> 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 OleÃ
›
>> >
>> > [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
>>
>>
>


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