[BioC] lumiHumanIDMapping package does not exist for windows?

[Ekta Jain]

Dear Dan,
Only the tar.gz file is available, the windows binary is not there. Please find below the error messages and sessionInfo. Thanks for your help.

Error Message:
> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.4, ?biocLite for help
> biocLite("lumiHumanIDMapping", type="source")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.4.
Installing package(s) 'lumiHumanIDMapping'
trying URL 'http://www.bioconductor.org/packages/2.10/data/annotation/src/contrib/lumiHumanIDMapping_1.10.0.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://www.bioconductor.org/packages/2.10/data/annotation/src/contrib/lumiHumanIDMapping_1.10.0.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '0 (nil)'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'lumiHumanIDMapping' failed
Old packages: 'GenomicRanges', 'hugene10stv1cdf', 'illuminaHumanv4.db', 'mogene10stv1cdf',
  'mogene10stv1probe', 'mouse.db0', 'VariantAnnotation'
Update all/some/none? [a/s/n]:a
...............
## From here on the dependencies org.Hs.eg.db do not get installed as well. Error message is given below:
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  cannot open the connection
In addition: Warning messages:
1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'org.Hs.eg.db/DESCRIPTION', probable reason 'No such file or directory'

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252   
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.15.0




-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] 
Sent: 04 May 2012 09:25
To: Ekta Jain
Cc: bioconductor at r-project.org
Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows?

On Thu, May 3, 2012 at 8:35 PM, Ekta Jain <Ekta_Jain at jubilantbiosys.com> wrote:
> Dear Dan,
> That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it.
>

What is the exact error message, and the output of sessionInfo()?

Also what is the output of
 getOption("BioC_mirror")
?

> I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available.
>


The .gz file is available, see the you emailed. However, biocLite() is
the preferred way to install it, so let's figure out why that is not
working.
Dan


> Any help would be great !!!
>
> Thanks,
> Ekta
>
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
> Sent: 03 May 2012 23:22
> To: Ekta Jain
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows?
>
> On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <Ekta_Jain at jubilantbiosys.com> wrote:
>> Dear All,
>> The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.bioconductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.html
>>
>> Can anyone please tell me where i can get the same .gz package from?
>
> I'll look into why this is not available for windows, but in the
> meantime you can install it as follows:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("lumiHumanIDMapping", type="source")
>
> Dan
>
>>
>> Many Thanks,
>> Ekta
>> Senior Research Associate
>> Bioinformatics Department
>> Jubilant Biosys Pvt Ltd,
>> #96, Industrial Suburb, 2nd Stage
>> Yeshwantpur, Bangalore 560 022
>> Ph No : +91-80-66628346
>>
>>
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