R help - Jul 2007 - how to revert to an older limma version?

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)?
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
 In addition: Warning message:
input string 1 is invalid in this locale in: grep(pattern, x,
ignore.case, extended, value, fixed, useBytes)
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?
Thanks in advance
Maya


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"Maya Bercovich" <MayaB at tauex.tau.ac.il> writes:
> Dear Sirs,
Please post to the Bioconductor list (see http://bioconductor.org for
instructions)
> 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)?
> 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
>  In addition: Warning message:
> input string 1 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
Please provide a short section of code that shows how you invoke the
function. It is very hard to tell what the cause of your problem is
without this.

read.maimages has a 'columns' argument. Do you supply it? If so, does
it contain the correct column names for the file type you are reading?
For instance, is the capitalization correct? The help page for
read.maimages provides some guidance.
> 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
Specific Bioconductor package versions work with specific R
versions. Instead of using install.packages, use
> source("http://bioconductor.org/biocLite.R")
> biocLite("limma")
to get the right version for your R. For R 2.5.0, limma 2.10.5 is the
correct version. The limma author is very responsive to bug reports, so
seek additional help and if necessary report bugs rather than revert
to previous versions.
> Could this be the reason?
Please always provide the output of the command
> sessionInfo()
to provide a concise summary of your system.
> Thanks in advance
> Maya
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org

That sounds as if you are running in a UTF-8 locale and your colleague is 
not.  We do ask for the results of sessionInfo(), which would have helped.

I suggest you try an English 8-bit locale and see what happens.

On Sun, 8 Jul 2007, 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)?
> 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
> In addition: Warning message:
> input string 1 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 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?
> Thanks in advance
> Maya
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595