[BioC] bug in resourcerer2BioC in Resourcerer package

[John Zhang]

Thank you for reporting!

>From: Francois Pepin <fpepin at cs.mcgill.ca>
>To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
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>Subject: [BioC] bug in resourcerer2BioC in Resourcerer package
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>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
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084