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 f??r Bioinformatik
Institut f??r Informatik
Ludwig-Maximilians-Universit??t M??nchen
Amalienstrasse 17, 2. Stock, B??ro A201
80333 M??nchen
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
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