R help - Dec 2013 - vcf, plink and other files in the /demo of a package

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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On 02/12/2013 11:59 AM, Federico Calboli wrote:
> 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?
Those index entries should be filenames of the demo files. The leading 
slash likely means R will interpret them as absolute paths, not relative 
paths, and that won't work.

A more usual way to do it would be to give them simple names, e.g. 
MultiPhen_plink (corresponding to MultiPhen_plink.R).

Since your demos refer to data files that are not embedded in the R 
code, you need to put those data files somewhere. They should go into 
the data directory if they are data a user can read (and then you need 
to follow the restrictions on things in that directory), or into your 
own directory below inst, to just be installed and available for use. In 
the latter case use system.file() to refer to them from within your demo 
code.

Duncan Murdoch