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

Vincent Carey stvjc at channing.harvard.edu
Thu Sep 24 13:20:35 CEST 2015


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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