[Bioc-devel] how can I contribute to the success of great packages?

[Martin Morgan]

On 10/20/2017 09:00 PM, Dario Strbenac wrote:
> Good day,
> 
> Thanks for the clarification. I appreciate your regular insights on the support forum over the years. It seems that Gviz will be stable enough to use, although the same maintainer's domainsignatures package has strikethrough across its name in the 3.6 build report, indicating its deprecation from Bioconductor. domainsignatures has no NEWS file explaining why it is being deprecated, so the deprecation seems unplanned and unintentional, so end-users of it would have no advance notice if it later became defunct until they were faced with failed biocLite installation command. I simply wish to avoid that situation with genomic plotting. Indeed, I wouldn't be as cautious if I was considering csaw, for example, and noticed build system warnings close to the deadline.

domainsignatures is a pretty reasonable example of the deprecation 
process. The core team noted that it had intermittent build failures, 
the code was quite old, it was no longer used extensively, it relied on 
flaky web services not under the maintainer's control -- it was an old 
horse that had provided many years of service, but was now clearly on 
it's last legs.

I initiated an email exchange with the maintainer about the status of 
the package, and I suggested it should be deprecated. The maintainer 
responded promptly (within 24 hours) and agreed with my suggestion. The 
package was marked as deprecated in the 'devel' branch a few days later 
by one of the core team members. There was a public announcement once 
the candidates for deprecation were identified

   https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011522.html

and the build report was marked appropriately. Developers were now 
equipped with the information to act if they wished to further maintain 
the package; no one has stepped forward.

NEWS files are optional, so it's absence is not relevant or surprising, 
especially in older packages.

Loading deprecated packages results in a message

 > suppressPackageStartupMessages(library(domainsignatures))
Warning message:
Package 'domainsignatures' is deprecated and will be removed from
   Bioconductor version 3.7

so users and developers are informed of the problem in a fairly forceful 
way.

Actually, though, a deprecated package has to build and check to 
propagate for downloading via biocLite(), and from the build report

 
http://bioconductor.org/checkResults/3.6/bioc-LATEST/domainsignatures/malbec1-buildsrc.html

we see that it is failing to build -- because the addition of the 
deprecation message by the core team broke it!

We all make mistakes, and this one is on us. Oops.

This has been fixed, the package will perhaps now propagate (though the 
intermittent failures are likely to persist, and my attempts to build 
the  package just now were unsuccessful because of failed web service 
calls) and the message will be seen by users.

Sometimes there are more significant problems with deprecated packages, 
and they don't build and check at all. We're then stuck without a 
package to release, and of course users and developers are taken by 
surprise. This can occur abruptly and due to reasons outside the control 
of the maintainer.

I personally would choose Gviz rather than csaw to build genomic 
visualizations around ;) And csaw has an ERROR on Windows in today's 
builds (though through no fault of it's own...)

Martin

> 
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
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