[Rd] R check mis-identifying Illumina data file format as executable and other thoughts.

Hin-Tak Leung htl10 at users.sourceforge.net
Thu Aug 4 02:38:39 CEST 2011

This is somewhat a summary/continuation of an R bug report:

Illumina's cluster definition files (*.egt) are one of the proprietary and
undocumented file formats used by their GenomeStudio line of products for
genomic studies.

snpMatrix onwards 
contains codes for reading that file format, as well as two example files of such type generated from public data, and also a vignette demonstrating their usefulness and relevance to genomic studies.

R svn check (the upcoming 2.14) mis-identifies those bundled files as undeclared binary executable files and aborts with that as error.
(1) the files are not executables, they just happened to be mis-identified as such
(2) even if they are genuine binary executables, there might be legitimate
reasons to bundle them with a package? (e.g. I have R code to look at their
content, and just treat them as arbitrary proprietary undocumented formats).

I can think of some rather interesting possible enhancement to R core's bytecode-compiler for parsing and morphing genuine binary executables - that might be useful for just-in-time compilation for R on the android platform. So surely there are genuine/legitimate needs for shipping binary executables in an R package?

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