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

[Vincent Carey]

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-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
> >
> > _______________________________________________
> > 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 the ...{{dropped:18}}
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

-- 
The information in this e-mail is intended only for the person to whom it 
is
addressed. If you believe this e-mail was sent to you in error and the 
e-mail
contains patient information, please contact the Partners Compliance 
HelpLine at
http://www.partners.org/complianceline 
<http://www.partners.org/complianceline> . If the e-mail was sent to you in 
error
but does not contain patient information, please contact the sender 
and properly
dispose of the e-mail.

	[[alternative HTML version deleted]]