> 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 < > [email protected]> 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: [email protected] >> >> >> > Hi Weijun, >> > >> > ----- Original Message ----- >> >> From: "Luo Weijun" <[email protected]> >> >> To: [email protected], [email protected] >> >> Cc: "Martin Morgan" <[email protected]>, >> [email protected] >> >> 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 donââ¬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 >> >> >> >> >> > >> > _______________________________________________ >> > [email protected] mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >> >> _______________________________________________ >> [email protected] 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: [email protected] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
