[BioC] bug in resourcerer2BioC in Resourcerer package

[Francois Pepin]

Hi everyone,

There's a bug in resourcerer2BioC in the Resourcerer package version
1.0.4 (I'm using R 2.0.0 and all packages were current ).

The parameter organism has to be either "human", "mouse" or "rat" and
it's changed to the full name ("Homo sapiens" in this case). All of the
other functions afterwards expect to have "human", "mouse" or "rat" as
the organism.

Using debug(resourcerer2BioC) and setting organism back to "human" in
the browser solves the problem.

The first 2 lines of resourcerer2BioC:
{
    organism <- match.arg(organism)
    switch(toupper(organism), HUMAN = organism <- "Homo sapiens",
        MOUSE = organism <- "Mus musculus", RAT = organism <- "Rattus
norvegicus")

The command (from the vignette) along with the traceback(): 
> resourcerer2BioC("Agilent_Human1_cDNA.zip", organism = "human",
destDir = file.path(.path.package("Resourcerer"), "temp"), pkgName =
"AgilentHsa1", srcUrls = getSrcUrl("all", "Homo sapiens"), pkgPath =
file.path(.path.package("Resourcerer"), "temp"), otherSrc = NULL,
baseMapType = "gb", version = "1.1.0",  makeXML = TRUE, fromWeb = TRUE,
baseUrl = "ftp://ftp.tigr.org/pub/data/tgi/Resourcerer",  check =
TRUE,author = list(author = "Anonymous", maintainer =
"anonymous at email.com"))
Error in match.arg(organism) : ARG should be one of human, mouse, rat

>traceback()
4: stop(paste("ARG should be one of", paste(choices, collapse = ", "),
       sep = " "))
3: match.arg(organism)
2: loadResourcerer(which, organism, destDir, baseUrl, exten)
1: resourcerer2BioC("Agilent_Human1_cDNA.zip", organism = "human",
       destDir = file.path(.path.package("Resourcerer"), "temp"),
       pkgName = "AgilentHsa1", srcUrls = getSrcUrl("all", "Homo
sapiens"),
       pkgPath = file.path(.path.package("Resourcerer"), "temp"),
       otherSrc = NULL, baseMapType = "gb", version = "1.1.0", makeXML =
TRUE,
       fromWeb = TRUE, baseUrl =
"ftp://ftp.tigr.org/pub/data/tgi/Resourcerer",                                                                               
       check = TRUE, author = list(author = "Anonymous", maintainer =
"anonymous at email.com"))

Francois Pepin