[Bioc-devel] Encoding issues with citations (Windows only)

[Leonardo Collado Torres]

Hi,

Explicitly specifying the citation worked, just like in
https://github.com/leekgroup/derfinderHelper/commit/b63f8c4119686630a5b3cf71c36b16e3e719cf89.
Here are the citations I ended up using:

S4Vectors = RefManageR::BibEntry(bibtype = 'manual', key = 'S4Vectors',
    author = 'Hervé Pagès and Michael Lawrence and Patrick Aboyoun',
    title = "S4Vectors: S4 implementation of vector-like and list-like objects",
    year = 2017, doi = '10.18129/B9.bioc.S4Vectors')


GenomeInfoDb = RefManageR::BibEntry(bibtype = 'manual',
    key = 'GenomeInfoDb',
    author = 'Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès',
    title = "GenomeInfoDb: Utilities for manipulating chromosome and
other 'seqname' identifiers",
    year = 2017, doi = '10.18129/B9.bioc.GenomeInfoDb')

AnnotationDbi = RefManageR::BibEntry(bibtype = 'manual',
    key = 'AnnotationDbi',
    author = 'Hervé Pagès and Marc Carlson and Seth Falcon and Nianhua Li',
    title = 'AnnotationDbi: Annotation Database Interface',
    year = 2017, doi = '10.18129/B9.bioc.AnnotationDbi')

SummarizedExperiment = RefManageR::BibEntry(bibtype = 'manual',
    key = 'SummarizedExperiment',
    author = 'Martin Morgan and Valerie Obenchain and Jim Hester and
Hervé Pagès',
    title = 'SummarizedExperiment: SummarizedExperiment container',
    year = 2017, doi = '10.18129/B9.bioc.SummarizedExperiment')

You can view the code nicely formatted at
https://github.com/cboettig/knitcitations/issues/103#issuecomment-337248710

Best,
Leo

On Mon, Oct 2, 2017 at 7:43 PM, Leonardo Collado Torres
<lcollado at jhu.edu> wrote:
> Hi,
>
> I've been using knitcitations for a while to handle citations in HTML
> vignettes. I had been using knitcitations::read.bibtex() until I
> realized that it no longer reads the entries in the order that were
> given in the bib file**. So I made a change and it all works... except
> on Windows. I finally updated my R installation in a Windows laptop
> and saw that the problem is with encoding.
>
>
> This short code reproduces the issue:
>
> ## Load package
> library('knitcitations')
>
> ## Tries to cite, prints package name and error when it fails
> check_bib <- function() {
> xx <- sapply(bib, function(x) {
> tryCatch(citep(x), error = function(e) {
> message(paste('found an error attempting to cite', names(x)))
> print(e)
> })
> })
> }
>
>
> ## list of citations
> bib <- c(knitcitations = citation('knitcitations'),
>     IRanges = citation('IRanges'),
>     S4Vectors = citation('S4Vectors'))
> check_bib()
> citep(bib[['S4Vectors']])
>
> ## Error message:
> Error in nchar(aut) : invalid multibyte string, element 1
>
> ## Entry that fails
>> bib[['S4Vectors']]
> Pag<U+653C><U+3E38>s H, Lawrence M and Aboyoun P (2017). _S4Vectors:
> S4 implementation of vector-like and list-like objects_. R package
> version 0.15.10.
>
>
> I see that knitcitations::write.bibtex() uses a "?" in authors in
> situations like this which is why I didn't notice this issue before.
> From https://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file
> I see that 'Encoding' in the DESCRIPTION file is used for the citation
> and I do see "Encoding: UTF-8" in the S4Vectors DESCRIPTION file.
>
> I get this error with GenomeInfoDb, AnnotationDbi, S4Vectors and
> SummarizedExperiment (details and reproducibility info at
> https://gist.github.com/anonymous/a8c6374b381dc9c27f55487756cb4e1b)
> across the different vignettes I maintain. But I don't get it with
> IRanges, GenomicRanges and other packages where Hervé Pagès is an
> author (those packages cite the 2013 PLoS paper). For example, the
> IRanges package has a inst/CITATION file that uses citEntry(    ,
> textVersion = "Pag\\es"). So, specifying an inst/CITATION file works.
>
>> citep(bib[['IRanges']])
> [1] "(Lawrence, Huber, Pagès, et al., 2013)"
>
> I imagine that there is a way to deal with the encoding problem
> properly but I haven't been able to find it. If you have ideas on how
> I can fix this please let me know.
>
>
> Thanks!
> Leo
>
> PS I posted this information at
> https://github.com/cboettig/knitcitations/issues/103 as well.
>
>
>
>
>
>
>
> ** As you can see below read.bibtex() changes the order of the
> citations, so I can't cite them later using citep().
>
>> write.bibtex(bib, file = 'test.bib')
> Writing 3 Bibtex entries ... OK
> Results written to file 'test.bib'
>
>
> ## test.bib contents
> @Manual{boettiger2017knitcitations,
>   title = {knitcitations: Citations for 'Knitr' Markdown Files},
>   author = {Carl Boettiger},
>   year = {2017},
>   note = {R package version 1.0.8},
>   url = {https://CRAN.R-project.org/package=knitcitations},
> }
>
> @Article{lawrence2013software,
>   title = {Software for Computing and Annotating Genomic Ranges},
>   author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es
> and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin
> Morgan and Vincent Carey},
>   year = {2013},
>   journal = {{PLoS} Computational Biology},
>   volume = {9},
>   issue = {8},
>   doi = {10.1371/journal.pcbi.1003118},
>   url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
> }
>
> @Manual{pags2017s4vectors,
>   title = {S4Vectors: S4 implementation of vector-like and list-like objects},
>   author = {?},
>   year = {2017},
>   note = {R package version 0.15.10},
> }
>
>
> ## read.bibtex() changes the order
>
>> read.bibtex('test.bib')
> [1] ? _S4Vectors: S4 implementation of vector-like and list-like
> objects_. R package version 0.15.10. 2017.
>
> [2] C. Boettiger. _knitcitations: Citations for 'Knitr' Markdown
> Files_. R package version 1.0.8. 2017. <URL:
> https://CRAN.R-project.org/package=knitcitations>.
>
> [3] M. Lawrence, W. Huber, H. Pagès, et al. “Software for Computing
> and Annotating Genomic Ranges”. In: _PLoS Computational Biology_ 9 (8
> 2013). DOI:
> 10.1371/journal.pcbi.1003118. <URL:
> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118}.>