[BioC] NOISeq installation error

[Martin Morgan]

On 10/08/2012 05:32 AM, Sean Davis wrote:
> On Mon, Oct 8, 2012 at 8:14 AM, Fatemehsadat Seyednasrollah
> <fatsey at utu.fi> wrote:
>> Sorry for that, this is my sessionInfo() output:
>>
>>> sessionInfo()
>>
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C/UTF-8/C/C/C/C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] BiocInstaller_1.4.8
>
> It looks like your BiocInstaller package is out-of-date.  In a new R
> session, try:

Actually, BiocInstaller is a sentinel for Bioconductor version; the original 
poster is using BiocInstaller 1.4.x, which corresponds to Bioconductor version 
1.10. Sean is using BiocInstaller 1.8.x, which corresponds to Bioconductor 
version 1.11.

NOISeq is available only in Bioconductor version 1.11, so the original poster 
needs to upgrade to Bioconductor version 1.11, for instance

   source("http://bioconductor.org/biocLite.R")
   biocLite("BiocUpgrade")

Since this is an _upgrade_, the original poster should be prepared for many 
packages to be re-installed, and perhaps some complications from that.

Martin

>
>> source('http://bioconductor.org/biocLite.R')
>> biocLite('NOISeq')
>
> This worked fine for me with this sessionInfo().
>
>> sessionInfo()
> R version 2.15.1 Patched (2012-08-09 r60221)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.8.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.1
>
>> loaded via a namespace (and not attached):
>> [1] tools_2.15.1
>>
>> ________________________________________
>> From: seandavi at gmail.com [seandavi at gmail.com] on behalf of Sean Davis [sdavis2 at mail.nih.gov]
>> Sent: Monday, October 08, 2012 3:11 PM
>> To: Fatemehsadat Seyednasrollah
>> Cc: bioconductor at r-project.org
>> Subject: Re: [BioC] NOISeq installation error
>>
>> On Mon, Oct 8, 2012 at 8:04 AM, Fatemehsadat Seyednasrollah
>> <fatsey at utu.fi> wrote:
>>> Hi all,
>>> I am trying to install NOISeq package from Bioconductor using commands :
>>>   source("http://bioconductor.org/biocLite.R")
>>> biocLite("NOISeq")
>>>
>>> But there is an error when installing: Warning message: package ‘NOISeq’ is not available (for R version 2.15.1)
>>>
>>
>> When reporting errors, be sure to post the output of sessionInfo().
>> Without that, we are all guessing a bit as to what your R setup is.
>>
>> Sean
>>
>>> But in the manual it is mentioned that NOISeq is available for R (>=2.0.3) so why is that?
>>> Thanks in advance
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> _______________________________________________
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>
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>


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