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

Mon Mar 9 11:29:16 CET 2020

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-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://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.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://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-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://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
>>> <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://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
>>>>
>>>> _______________________________________________
>>>> Bioc-devel using r-project.org mailing list
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iEfGQDmbJr0Dp78RIYxXPcyoSMXMo31SAqDdWvOcdxI&s=q-0nEguTQCQNv04U4nju5HMBn6l8GmC_yCd7KSemIU8&e= 
>>>>
>>> -- 
>>> The information in this e-mail is intended only for t...{{dropped:24}}
> 
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-- 
Hervé Pagès

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