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

Ulrich Bodenhofer bodenho|er @end|ng |rom b|o|n|@jku@@t
Mon Mar 9 09:00:52 CET 2020

Dear colleagues,

Thanks for your replies to my message! A few more comments:

  * The issue I was reporting appeared on a Linux system
  * I agree that this is mainly a problem related to how LaTeX deals
    with unicode characters. However, to be frank, I still consider
    LaTeX-based Rnw documents (regardless of whether Sweave or knitr is
    used) an important (and still really cool) way of working with R.
    Not to be able to show/print 'XString' / 'XStringSet' objects would
    be quite a shortcoming in my humble opinion. Therefore, I would
    consider it important to be able to - optionally - switch back to a
    LaTeX-safe way of showing the ellipsis character(s).

Thanks and best regards,

Am 3/7/2020 um 21:52 schrieb Felix Ernst:
> Hi,
> If you can replicate the latex/knitr/sweave issue locally, try installing Biostrings from my GitHub fork used in the PR. This should solve the issue, if it is about the ellipsis character causing problems on windows only.
> If it doesn't, it probably has more to do with the way unicode characters are handeled in latex. I had a lot of problems, when trying to develop the Modstrings package vignette and I couldn't get it to work with a pdf output. The number of special characters I had to deal with were from many different alphabets and resisted my attempts (without any detailed knowledge about latex to pdf conversion) to get to the bottom of it.
> Maybe someone else has more experience regarding unicode characters in latex and can take a look at this (if it persists).
> Felix
> -----Ursprüngliche Nachricht-----
> Von: Bioc-devel <bioc-devel-bounces using r-project.org> Im Auftrag von Vincent Carey
> Gesendet: Samstag, 7. März 2020 20:50
> An: Shepherd, Lori <Lori.Shepherd using roswellpark.org>
> Cc: bioc-devel using r-project.org; Ulrich Bodenhofer <bodenhofer using bioinf.jku.at>; Kurt Hornik <Kurt.Hornik using wu.ac.at>
> Betreff: Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)
> you are not wrong ... thanks for pointing this out
> https://github.com/Bioconductor/Biostrings/pull/33
> On Sat, Mar 7, 2020 at 2:33 PM Shepherd, Lori <Lori.Shepherd using roswellpark.org>
> wrote:
>> I could be wrong but I think there is an open issue and PR already
>> submitted that might be related.
>> Get Outlook for Android <https://aka.ms/ghei36>
>> ------------------------------
>> *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 issue 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
>> wrote:
>>> 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-cl
>> ang/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
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> --
>> The information in this e-mail is intended only for t...{{dropped:24}}

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