[R] valid package repositories

[Federico Calboli]

Hi All,

I noticed that it is quite common to find in papers mentions to ‘R libraries’ developed for the algorithms/models/code/whatever that is being described by the paper, so that third parties will be able to use said method for themselves.  On further enquiries these libraries are not actually available on CRAN, but need to be requested from the devs.  

That is in itself does not seem a big issue, were it not for the fact most of the time I am in such situation the code is very specific for the environment of the developer, and does not actually work on any machine I try to run it on (something that is painfully true for code calling C/C++/Fortran).  A second pattern I seem to have noticed is that, despite said libraries being advertised for general use in a *published* paper, when I raise the issue the library is not actually formally published and it does not actually work like a CRAN published library would, I get a vague ‘the person who actually did the work left and nobody can maintain the code/fix stuff/finish the job’.

As a referee I am trying to weed out what I see as malpractice: the promise that third parties outside the developers might actually use the code because it has been packaged as a R library, a claim that seems to boost publishing chances.

Thus my question: when can I consider a library to be properly published and really publicly available?  CRAN and BioConductor are clearly gold standards.  What about Github?  I am currently using the rule ‘not on CRAN == outright rejection’.  If Github is as good as CRAN I will include it on my list of ‘the code is available in a functional state as claimed’.

Finally, please note the scope of my query:  I am not looking at those cases where a colleague gives me half finished code that might be useful but I need to sort out.  I am looking at formal claims ‘we have developed a method to do X and said method is available to the public as a R library’.  If that is the claim I expect it to be true.

Best

F




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Federico Calboli
LBEG - Laboratory of Biodiversity and Evolutionary Genomics
Charles Deberiotstraat 32 box 2439
3000 Leuven
+32 16 32 87 67