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@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@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
>> 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]]
>>
>>
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>>
>

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