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

Thu Sep 24 14:56:20 CEST 2015

Hi,

we need to distinguish here between build/install and check errors. The
first ones hold the package update (instead, the last working version is
used). On the other hand, check errors do not hold the package from
propagating into the repository causing collateral damage (at least that's
what I observe in the devel branch).

A good example is EBImage which is currently broken for all architectures
but Linux (see:
http://bioconductor.org/checkResults/devel/bioc-LATEST/EBImage/). It
doesn't affect it's downstream dependencies because the error occurs at
build stage, see for example imageHTS (
http://bioconductor.org/packages/3.2/bioc/html/imageHTS.html). Fair enough,
EBImage has a red badge, whereas imageHTS has a green one.

So the issue raised by Ludwig occurs only with packages which fail during
check. Maybe changing the publication policy in such cases, i.e. hold the
updated package from going into the repository when it fails 'R CMD check'
would help to address the problem, at least for BioC packages?

Best,
Andrzej

On Thu, Sep 24, 2015 at 2:22 PM, Wolfgang Huber <whuber at embl.de> wrote:

> It seems that the “build” shield on the package landing page conflates
> things that happen in the package, and in its dependencies.
> Do we have a clear spec of what the purpose of that shield is?
>
> Something to avoid IMHO is creating incentives for package developers to
> reduce dependencies to make their package “look" more robust, at the cost
> of duplication or functionality.
>
> Wolfgang
>
>
> > On 24 Sep 2015, at 14:13, Ludwig Geistlinger <
> Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:
> >
> >> 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 fÃ¼r Bioinformatik
> >>> Institut fÃ¼r Informatik
> >>> Ludwig-Maximilians-UniversitÃ¤t MÃ¼nchen
> >>> Amalienstrasse 17, 2. Stock, BÃ¼ro A201
> >>> 80333 MÃ¼nchen
> >>>
> >>> 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 donÃ¢â‚¬â„¢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
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >
> >
> > --
> > 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
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]