From htl10 at users.sourceforge.net  Thu Aug  4 02:38:39 2011
From: htl10 at users.sourceforge.net (Hin-Tak Leung)
Date: Thu, 4 Aug 2011 01:38:39 +0100 (BST)
Subject: [Rd] R check mis-identifying Illumina data file format as
	executable and other thoughts.
Message-ID: <1312418319.73495.YahooMailClassic@web29514.mail.ird.yahoo.com>

This is somewhat a summary/continuation of an R bug report:
(https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14645)

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 1.17.0.7 onwards 
(http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/)
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?




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