[BioC] pckg Resourcerer : can't read "affy_HG-U133_Plus_2.zip" with getResourcerer()

[Wong, Chao-Jen]

Hi, Guillaume,

It seems likely a bug in the package. If you just need the annotation of affy HGU133 plus 2, you can simply install the hug133plus2.db package. See more detail, visit 
  http://bioconductor.org/packages/release/data/annotation/html/hgu133plus2.db.html

Chao-Jen


-- 
Chao-Jen Wong 
Program in Computational Biology 
Division of Public Health Sciences 
Fred Hutchinson Cancer Research Center 
1100 Fairview Avenue N., M1-B514 
PO Box 19024 
Seattle, WA 98109 
206.667.4485 
cwon2 at fhcrc.org 

----- Original Message -----
From: "Johannes Freudenberg (NIH/NIEHS) [E]" <johannes.freudenberg at nih.gov>
To: "Guillaume Tiberi" <guillaume.tiberi at gmail.com>, bioconductor at r-project.org
Sent: Tuesday, August 2, 2011 9:49:27 AM
Subject: Re: [BioC] pckg Resourcerer : can't read "affy_HG-U133_Plus_2.zip" with	getResourcerer()

It seems that the function getResourcerer() expects to find a file named "affy_HG-U133_Plus_2" in the destDir after unzipping the file "affy_HG-U133_Plus_2.zip"
However, it finds a file named "affy_U133Plus2" instead.  I would probably just rename the file accordingly and run the same function call again, e.g.

> annot <- getResourcerer("affy_HG-U133_Plus_2.zip", organism = "Human")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file '... /Resourcerer/temp/affy_HG-U133_Plus_2': No such file or directory
> file.rename(paste(file.path(.path.package("Resourcerer"), "temp"), "affy_U133Plus2", sep="/"), paste(file.path(.path.package("Resourcerer"), "temp"), "affy_HG-U133_Plus_2", sep="/"))
[1] TRUE
> annot <- getResourcerer("affy_HG-U133_Plus_2.zip", organism = "Human")


--Johannes



/home/freudenbergjm/R/x86_64-redhat-linux-gnu-library/2.13/Resourcerer/temp/
Browse[1]> fileName <- "/home/freudenbergjm/R/x86_64-redhat-linux-gnu-library/2.13/Resourcerer/temp/affy_U133Plus2"

-----Original Message-----
From: Guillaume Tiberi [mailto:guillaume.tiberi at gmail.com] 
Sent: Tuesday, August 02, 2011 11:40 AM
To: bioconductor at r-project.org
Subject: [BioC] pckg Resourcerer : can't read "affy_HG-U133_Plus_2.zip" with getResourcerer()

Hi all

I want to load annotation file "affy_HG-U133_Plus_2.zip" with "Resourcerer"
and its function getResourcerer(). Sorry for french error_message ;)

library("Resourcerer")
list.files(file.path(.path.package("Resourcerer"), "temp")) *# > [1] "README"*

annot <- getResourcerer(
"affy_HG-U133_Plus_2.zip",
organism = "human",
destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer",
clean = TRUE,
exten = "zip"
)

# *Erreur dans file(file, "rt") : impossible d'ouvrir la connexion* *# De plus : Message d'avis :* *# In file(file, "rt") :* *#  impossible d'ouvrir le fichier '/home/tiberi/R/i486-pc-linux-gnu-library/2.10/Resourcerer/temp/affy_HG-U133_Plus_2'
: Aucun fichier ou dossier de ce type*

ls()
*# character(0)*

# Files are created
list.files(file.path(.path.package("Resourcerer"), "temp")) *# > [1] "affy_U133Plus2"
 "file643c9869affy_HG-U133_Plus_2.zip"                   "README"*
*
*
# You can see the problem is uncorrectly named : temp file was named "affy_U133Plus2" instead of "affy_HG-U133Plus2". "HG-" is missing # Strangely, exemple shown in ?getResourcerer() is functionnal, and resourcerer object is correctly created

resourcerer <- getResourcerer(
"Agilent_Human1_cDNA.zip",
 organism = "human",
destDir = file.path(.path.package("Resourcerer"), "temp"),  baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer",
 clean = TRUE,
exten = "zip"
)

> ls()
# [1] "resourcerer"


Have you got an idear ?

thanks

Guillaume

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