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 was built before R 3.0.0: please this says that the AnnotationDbi package is out of date. try biocLite() and respond 'y' when asked if you'd like to update out-of-date packages.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/AnnotationD bi_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/AnnotationD bi_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/AnnotationD bi_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