Sorry for the inconvenience. I reverted this in Biostrings 2.55.5:
https://github.com/Bioconductor/Biostrings/commit/567d8c30609783f87d7c641a98be1711ea47fb38
Using the compact ellipsis was an experiment in Bioc devel. Didn't
really like it anyway (was hard to see).
H.
On 3/9/20 01:00, Ulrich Bodenhofer wrote:
Dear colleagues,
Thanks for your replies to my message! A few more comments:
* The issue I was reporting appeared on a Linux system
(https://urldefense.proofpoint.com/v2/url?u=https-3A__-3Bwww.r-2Dproject.org_nosvn_R.check_r-2Ddevel-2Dlinux-2Dx86-5F64-2Ddebian-2Dclang_apcluster-2D00check.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iEfGQDmbJr0Dp78RIYxXPcyoSMXMo31SAqDdWvOcdxI&s=c7f8tWuZzGjURMMtAEVCkNNMuGLBDlCuujaoB91Eo1g&e=
).
* 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,
Ulrich
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-boun...@r-project.org> Im Auftrag von
Vincent Carey
Gesendet: Samstag, 7. März 2020 20:50
An: Shepherd, Lori <lori.sheph...@roswellpark.org>
Cc: bioc-devel@r-project.org; Ulrich Bodenhofer
<bodenho...@bioinf.jku.at>; Kurt Hornik <kurt.hor...@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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Biostrings_pull_33&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iEfGQDmbJr0Dp78RIYxXPcyoSMXMo31SAqDdWvOcdxI&s=s45mMwMyzSrBouUhst04cjjMqk6CIJzPBQ1VspefIjg&e=
On Sat, Mar 7, 2020 at 2:33 PM Shepherd, Lori
<lori.sheph...@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://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_ghei36&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iEfGQDmbJr0Dp78RIYxXPcyoSMXMo31SAqDdWvOcdxI&s=0iDgxpRdwa6D4m4i5lnSSpQqBobKPIesZuBKYsO3e3M&e=
>
------------------------------
*From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of
Vincent Carey <st...@channing.harvard.edu>
*Sent:* Saturday, March 7, 2020 12:58:57 PM
*To:* Ulrich Bodenhofer <bodenho...@bioinf.jku.at>
*Cc:* bioc-devel@r-project.org <bioc-devel@r-project.org>; Kurt Hornik
< kurt.hor...@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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Biostrings&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iEfGQDmbJr0Dp78RIYxXPcyoSMXMo31SAqDdWvOcdxI&s=CIPKRp4LkAjMLFyKmqFWUt2kygq_WhLi1zU4th96C_Y&e=
On Sat, Mar 7, 2020 at 7:12 AM Ulrich Bodenhofer
<bodenho...@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://urldefense.proofpoint.com/v2/url?u=https-3A__www.r-2Dproject.org_nosvn_R.check_r-2Ddevel-2Dlinux-2Dx86-5F64-2Ddebian-2Dcl&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iEfGQDmbJr0Dp78RIYxXPcyoSMXMo31SAqDdWvOcdxI&s=YtTzYBdTB81bDnav9WcphW_315e5Urmzz03mziPFAOc&e=
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
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