[Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Sat Mar 7 20:33:28 CET 2020

I could be wrong but I think there is an open issue and PR already submitted that might be related.

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From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Vincent Carey <stvjc using channing.harvard.edu>
Sent: Saturday, March 7, 2020 12:58:57 PM
To: Ulrich Bodenhofer <bodenhofer using bioinf.jku.at>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>; Kurt Hornik <Kurt.Hornik using wu.ac.at>
Subject: Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

I have a feeling that the best way to get action here will be to file an
and perhaps a PR at https://github.com/Bioconductor/Biostrings

On Sat, Mar 7, 2020 at 7:12 AM Ulrich Bodenhofer <bodenhofer using bioinf.jku.at>

> Dear colleagues,
> As noted in my previous message, I have encountered problems with the
> new way of displaying sequences/sequence sets that now use a UTF-8
> ellipsis character (internally defined as R object 'compact_ellipsis' in
> the package) when the output is included in a LaTeX document (which
> happens when printing biological sequences via the 'Biostrings' package
> inside LaTeX-based Sweave or knitr documents). My question again: Is
> there any special measure that I can take to counteract this issue?
> (e.g. like loading \usepackage[xxx]{inputenc} in the vignette, setting
> an option, or manually refining 'compact_ellipsis') Is there a way that
> the users can revert to the old-style dots for such cases?
> As a sidenote: this causes the building of my package 'apcluster' to
> break on a non-UTF-8 locale
> (
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/apcluster-00check.html),
> but leads to warnings also in a UTF-8 locale.
> Any help is gratefully appreciated, thanks so much in advance!
> Best regards,
> Ulrich
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