[Bioc-devel] Shouldn't we distinguish between package-specific and dependency errors?

[Ludwig Geistlinger]

> Do you have any information on how often this kind of breakage occurs?

Having my package ~1 year in, I would say that happened roughly 5 times to
me.

I wonder whether other developers could comment on their experience with
that as well.


> On Thu, Sep 24, 2015 at 4:35 AM, Ludwig Geistlinger <
> Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:
>
>> Dear Bioc-Team,
>>
>> I would like to make this point brought up by Weijun more general.
>> He reported a considerable number of packages to be broken by
>> (recursively) depending on KEGGREST - which actually broke due to KEGG
>> itself (however, this seems to be resolved by the current build).
>>
>> Nevertheless, given that a dependency can break your package at any
>> time,
>> it is currently hard to device a robust and stable software product even
>> within the semi-annual release.
>>
>
> Do you have any information on how often this kind of breakage occurs?
>
>
>> Thus, I wonder whether Bioc packages in release (at least those having
>> other packages depending on them) shouldn't always be rolled back to the
>> last version that passed build and check without error, in order to
>> ensure
>> functioning of packages down the hierarchy.
>>
>> Based on these considerations, I also wonder whether the shield on the
>> package landing page indicating the result of the package building
>> (ok/warning/error) shouldn't distinguish between errors caused by
>> dependencies and errors caused by the package itself.
>>
>> Imagine the not too unrealistic case of a new Bioc package presented in
>> a
>> Software article under review.
>> Without doubt, a reviewer will be negatively influenced by the 'error'
>> shield indicating that the package has not been properly worked out.
>> This is fair enough if the package's own code produces these bugs, but
>> the
>> opposite it true if that is due to a broken dependency.
>>
>>
> Recent developments at the Volkswagen company should help raise general
> awareness that software development and maintenance is a fraught process.
> If
> software S depends on software T and T is unreliable then so is S.  The
> negative influence of events of the sort you describe has potential value.
>
> I believe there are ways of using containers so that software can be
> distributed
> in a verified working state, perhaps suitable for a fully predictable
> review,
> but I doubt this is a real solution to the actual problem.
>
>
>
>> In the worst case, the package will run fine the whole time the article
>> is
>> prepared, but breaks due to a broken dependency the day the reviewer
>> starts to evaluate the manuscript.
>>
>> I know that this does not resolves problems of dependencies outside of
>> BioC such as for KEGGREST with KEGG.
>> But at least for dependencies within BioC, I wonder whether this is a
>> point worth considering.
>>
>> Thanks & Best,
>> Ludwig
>>
>>
>> --
>> Dipl.-Bioinf. Ludwig Geistlinger
>>
>> Lehr- und Forschungseinheit für Bioinformatik
>> Institut für Informatik
>> Ludwig-Maximilians-Universität München
>> Amalienstrasse 17, 2. Stock, Büro A201
>> 80333 München
>>
>> Tel.: 089-2180-4067
>> eMail: Ludwig.Geistlinger at bio.ifi.lmu.de
>>
>>
>> > Hi Weijun,
>> >
>> > ----- Original Message -----
>> >> From: "Luo Weijun" <luo_weijun at yahoo.com>
>> >> To: maintainer at bioconductor.org, dtenenba at fredhutch.org
>> >> Cc: "Martin Morgan" <mtmorgan at fredhutch.org>,
>> Bioc-devel at r-project.org
>> >> Sent: Wednesday, September 23, 2015 9:44:13 AM
>> >> Subject: KEGG REST issue
>> >>
>> >> Dear BioC team,
>> >> I noticed some problem with keggLink() function of KEGGREST package,
>> >> and it can be traced back to KEGG REST API Linked entries. Some of
>> >> this API function is broken. For example, the following line used to
>> >> get all gene-pathway mapping for human, but retrieves nothing now.
>> >> path.hsa= KEGGREST::keggLink("pathway", "hsa")
>> >>
>> >> In fact, these two bulk queries with the rest api don’t work
>> anymore.
>> >> http://rest.kegg.jp/link/pathway/hsa
>> >> http://rest.kegg.jp/link/hsa/pathway
>> >> but smaller queries on Linked entries seem to be fine. not sure
>> >> whether other REST API functions are affected or not. As a
>> >> consequence, KEGGREST and many dependent packages had build error.
>> >>
>> http://bioconductor.org/checkResults/release/bioc-LATEST/KEGGREST/morelia-buildsrc.html
>> >>
>> >> anway, just want you know about this, see if you can do anything on
>> >> this.
>> >
>> > Yes, I am aware of this. It's an issue on the KEGG side and I have
>> > contacted the KEGG team. I have not heard back yet.
>> >
>> > Dan
>> >
>> >
>> >> Weijun
>> >>
>> >>
>> >
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>> _______________________________________________
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>>
>


-- 
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de