[BioC] how to revert to an older limma version?

[Marcus Davy]

Also if installing a previous version check in R that it is installed with
sessionInfo().

You might want to check the changeLog(n=100) to see if readGenericHeader has
been changed in recent package releases.

You can obtain some old archived releases at;

http://bioinf.wehi.edu.au/limma/

and

http://www.bioconductor.org/download/oldrelease

for some past BioC stable releases.


Marcus


On 9/7/07 4:42 AM, "Kasper Daniel Hansen" <khansen at stat.berkeley.edu> wrote:

> 
> On Jul 8, 2007, at 6:54 AM, Maya Bercovich wrote:
> 
>> Dear Sirs,
>> 
>> How can I revert to an older limma version?
>> 
>> Typing "install.packages("limma")"  in R gives a list of mirrors. How
>> can I install the version I want after I obtain and untar the file
>> (e.g,
>> limma_2.9.1.tar.gz)?
> 
> Not every version is kept around. You could try to see if 2.9.1 is
> part of a stable Bioc release. But in general I am not aware of how
> you can get any arbitrary old version of a package. When you have the
> tarball use
> # R CMD INSTALL limma....
> from the command line (and if that is not enough, look in this email
> list, the manual and the faqs for the numerous help available on this
> subject).
> 
>> I am running R 2.5.0 on a Linux machine (CentOS 5).  When using
>> limma it
>> will not go past the read.maimages command.
>> 
>> I get this error:
>> 
>> Error in readGenericHeader(fullname, columns = columns, sep = sep) :
>>          Specified column headings not found in file
> 
> If you read this message carefully it seems that limma is looking for
> some columns in the file which does not exists.
> 
>>  In addition: Warning message:
>> input string 1 is invalid in this locale in: grep(pattern, x,
>> ignore.case, extended, value, fixed, useBytes)
> 
> Coupled with this warning I guess that the first characters in your
> file are non-standard for example using a different alphabet or
> whatever.
> 
> You should look carefully at the file in order to see what the error is.
> 
> It could also be the local you are using: is he using english and you
> are using a different language?
> 
>> I was told by a colleague that this may be due to my limma version.
>> 
>> I try to use limma 2.10.5 and he uses 2.9.1
>> 
>> Could this be the reason?
> 
> Perhaps, but I doubt it.
> 
>> 
>> Thanks in advance
>> 
>> Maya
>> 
>> 
>> 
>> 
>> [[alternative HTML version deleted]]
>> 
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