[R] vcf, plink and other files in the /demo of a package

[Federico Calboli]

Hi All,

together with colleagues we are planning to submit a 2.0 version of a package we have on CRAN.  Because the package deals with high throughput genomic data we though it would be nice to have some sort of guidance for the users.  This should ideally mean a 'vignette', but as the time of writing nobody had time to set one up.  What we have is three scripts that are heavily commented and a bunch of files (plink binary files and vcd files) that provide the 'example' data for these scripts.  I was wondering whether the /demo directory would be an appropriate place where to put these scripts and the relative data.  

I ask because I am checking the package build and I get:

checking index information ... WARNING
Demo index entries without corresponding demo:
[1] "/plink/MultiPhen_plink" "/simul/MultiPhen_simul" "/vcf/MultiPhen_vcf"
See the information on INDEX files and package subdirectories in the
chapter ‘Creating R packages’ of the ‘Writing R Extensions’ manual.

despite the fact I did create a 00Index file in /demo:

/demo$ cat 00Index
/plink/MultiPhen_plink     MultiPhen demo of how to use PLINK BED files
/simul/MultiPhen_simul     MultiPhen demo of how to run a simulation with MultiPhen
/vcf/MultiPhen_vcf     MultiPhen demo of how to use data in vcf format

What am I missing?  Given the state of the documentation (i.e. no vignette and demo scripts that rely on data that is not in .rda format) would we be better off removing this stuff altogether?


BW

F



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