[BioC] .cel file processing is not working for an old array

[Martin Morgan]

On 07/27/2014 01:20 PM, Maria Kesa wrote:
> Thank you, but I still get the same error message! My friend's computer has
> no problem with my script. There seems to be a problem with
>
> ‘hgu95av2cdf’ library. Further advice would be greatly aporeciated!
>
>
> Maria
>
>
>
> On Sun, Jul 27, 2014 at 1:58 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> Looks like your DBI package is broken. Try remove.packages("DBI") and try
>> again.
>>
>> Sean
>> On Jul 27, 2014 1:53 AM, "Maria Kesa" <maria.kesa at gmail.com> wrote:
>>
>>> *Hello,*
>>>
>>>
>>> *I am trying to process very old .cel files from here:
>>>
>>> http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75
>>> <
>>> http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75
>>>> *
>>>
>>> *I have the newest version of R and updated BiocLite. *
>>>
>>> With the following code I get the error:
>>> library(affy)
>>> setwd("/home/maria/Documents/Work with Pietro/Prostate Cancer")
>>> for (i in 1:9) {
>>>    obj_name<-paste('N0',i,'__normal.CEL',sep="")
>>>    Data<-ReadAffy(filenames=obj_name)
>>>    eset<-rma(Data)
>>>    filename<-paste('sample',i,'.txt',sep="",collapse="")
>>>    write.exprs(eset, file=filename, sep="\t")
>>> }
>>>
>>> trying URL '
>>>
>>> http://bioconductor.org/packages/2.13/data/annotation/src/contrib/hgu95av2cdf_2.13.0.tar.gz
>>> '
>>> Content type 'application/x-gzip' length 1341545 bytes (1.3 Mb)
>>> opened URL
>>> ==================================================
>>> downloaded 1.3 Mb
>>>
>>> * installing *source* package ‘hgu95av2cdf’ ...
>>> ** R
>>> ** data
>>> ** preparing package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** testing if installed package can be loaded
>>> Error : .onLoad failed in loadNamespace() for 'hgu95av2cdf', details:
>>>    call: NULL
>>>    error: package ‘AnnotationDbi’ was built before R 3.0.0: please

this says that the AnnotationDbi package is out of date. try

   biocLite()

and respond 'y' when asked if you'd like to update out-of-date packages.

If you continue to have problems, then post the entire session where the 
biocLite() command is executed.

Martin

>>> re-install it
>>> Error: loading failed
>>> Execution halted
>>> ERROR: loading failed
>>> * removing ‘/home/maria/R/x86_64-pc-linux-gnu-library/3.0/hgu95av2cdf’
>>>
>>> The downloaded source packages are in
>>>      ‘/tmp/RtmpRETXHh/downloaded_packages’
>>>   Show Traceback
>>>
>>>   Rerun with Debug
>>>   Error in getCdfInfo(object) :
>>>    Could not obtain CDF environment, problems encountered:
>>> Specified environment does not contain HG_U95Av2
>>> Library - package hgu95av2cdf not installed
>>> Library - package hgu95av2cdf not installed In addition: Warning message:
>>> In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
>>>    installation of package ‘hgu95av2cdf’ had non-zero exit status
>>>
>>> *When I try to install HG_U95Av2, I get the message:*
>>>
>>>
>>> biocLite("HG_U95Av2")
>>> BioC_mirror: http://bioconductor.org
>>> Using Bioconductor version 2.13 (BiocInstaller 1.12.1),
>>>    R version 3.0.2.
>>> Installing package(s) 'HG_U95Av2'
>>> Old packages: 'AnnotationDbi'
>>> Update all/some/none? [a/s/n]:
>>> a
>>> trying URL '
>>>
>>> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1.24.0.tar.gz
>>> '
>>> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb)
>>> opened URL
>>> ==================================================
>>> downloaded 4.1 Mb
>>>
>>> * installing *source* package ‘AnnotationDbi’ ...
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> Error : package ‘DBI’ was built before R 3.0.0: please re-install it
>>> ERROR: lazy loading failed for package ‘AnnotationDbi’
>>> * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’
>>> * restoring previous ‘/usr/local/lib/R/site-library/AnnotationDbi’
>>>
>>> The downloaded source packages are in
>>>      ‘/tmp/RtmpRETXHh/downloaded_packages’
>>> Warning messages:
>>> 1: package ‘HG_U95Av2’ is not available (for R version 3.0.2)
>>> 2: In install.packages(update[instlib == l, "Package"], l, contriburl =
>>> contriburl,  :
>>>    installation of package ‘AnnotationDbi’ had non-zero exit status
>>>
>>> *When I try to install 'AnnotationDbi' I get*.
>>>
>>>
>>>> biocLite("AnnotationDbi")
>>> BioC_mirror: http://bioconductor.org
>>> Using Bioconductor version 2.13 (BiocInstaller 1.12.1),
>>>    R version 3.0.2.
>>> Installing package(s) 'AnnotationDbi'
>>> trying URL '
>>>
>>> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1.24.0.tar.gz
>>> '
>>> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb)
>>> opened URL
>>> ==================================================
>>> downloaded 4.1 Mb
>>>
>>> * installing *source* package ‘AnnotationDbi’ ...
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> Error : package ‘DBI’ was built before R 3.0.0: please re-install it
>>> ERROR: lazy loading failed for package ‘AnnotationDbi’
>>> * removing ‘/home/maria/R/x86_64-pc-linux-gnu-library/3.0/AnnotationDbi’
>>>
>>> The downloaded source packages are in
>>>      ‘/tmp/RtmpRETXHh/downloaded_packages’
>>> Old packages: 'AnnotationDbi'
>>> Update all/some/none? [a/s/n]:
>>> a
>>> trying URL '
>>>
>>> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1.24.0.tar.gz
>>> '
>>> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb)
>>> opened URL
>>> ==================================================
>>> downloaded 4.1 Mb
>>>
>>> * installing *source* package ‘AnnotationDbi’ ...
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> Error : package ‘DBI’ was built before R 3.0.0: please re-install it
>>> ERROR: lazy loading failed for package ‘AnnotationDbi’
>>> * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’
>>> * restoring previous ‘/usr/local/lib/R/site-library/AnnotationDbi’
>>>
>>> The downloaded source packages are in
>>>      ‘/tmp/RtmpRETXHh/downloaded_packages’
>>> Warning messages:
>>> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>>>    installation of package ‘AnnotationDbi’ had non-zero exit status
>>> 2: In install.packages(update[instlib == l, "Package"], l, contriburl =
>>> contriburl,  :
>>>    installation of package ‘AnnotationDbi’ had non-zero exit status
>>>>
>>> *I would really aporeciate the help! *Is there any chance that I can parse
>>>
>>> these old .cel files?
>>>
>>> Thank you,
>>> Maria Kesa
>>>
>>>          [[alternative HTML version deleted]]
>>>
>>>
>>> _______________________________________________
>>> 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
>>>
>>
>
> 	[[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> 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
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793