ArrayExpress: missing cdf environment!
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Daniel Rico ▴ 110
@daniel-rico-2390
Last seen 6.6 years ago
Dear list, I downloaded a dataset from ArrayExpress using ArrayExpress package, and I get an error when I try to see the object created, or a try to normalize it with rma. I am using a Linux Ubuntu. For some reason, a package installation is tried (related with cdf, I guess) but I am not root... Is there a way to overcome this problem installing some cdf package in my home R library folder? I tried installing hgu133a.db, gahgu133acdf and u133x3pcdf, and repeating the operation, but I still get the error. Any help will be really appreciated! Best, Daniel > library("ArrayExpress") > library(affy) > GNF <- ArrayExpress("E-TABM-145") ... The object containing experiment E-TABM-145 has been built. > class(GNF) [1] "AffyBatch" attr(,"package") [1] "affy" > GNF Warning in install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(), : 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable AffyBatch object size of arrays=712x712 features (228 kb) cdf=HG-U133A (??? affyids) number of samples=158 Warning in install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(), : 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable Error in install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(), : unable to install packages In addition: Warning message: missing cdf environment! in show(AffyBatch) > GNFnorm <- rma(GNF) Warning in install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(), : 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable Error in install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(), : unable to install packages > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.26.0 ArrayExpress_1.8.0 Biobase_2.8.0 loaded via a namespace (and not attached): [1] XML_2.8-1 affyio_1.16.0 limma_3.4.0 [4] preprocessCore_1.10.0 tools_2.11.0 ******************************************** Daniel Rico Rodriguez, PhD. Structural Computational Biology Group Spanish National Cancer Research Center, CNIO Melchor Fernandez Almagro, 3. 28029 Madrid, Spain. Phone: +34 91 224 69 00 #3015 drico at cnio.es http://www.cnio.es ******************************************** **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y ...{{dropped:3}}
Cancer hgu133a cdf ArrayExpress Cancer hgu133a cdf ArrayExpress • 1.2k views
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@wolfgang-huber-3550
Last seen 9 days ago
EMBL European Molecular Biology Laborat…
Dear Daniel have you tried with installing the hgu133acdf package manually beforehand? (After that, please try to load it to verify it's really there.) What you see is because the 'print' method for 'AffyBatch' objects from the 'affy' package requires the array's CDF package (hgu133acdf in your case), and if it does not find it on your computer, it tries to be helpful and install it from the Bioconductor repository on the web. Btw, it should never be necessary to be 'root' to install R packages on any sane system configuration. Best wishes Wolfgang Il Oct/15/10 5:50 PM, Daniel Rico Rodriguez ha scritto: > Dear list, > > I downloaded a dataset from ArrayExpress using ArrayExpress package, and > I get an error when I try to see the object created, or a try to > normalize it with rma. > > I am using a Linux Ubuntu. For some reason, a package installation is > tried (related with cdf, I guess) but I am not root... Is there a way to > overcome this problem installing some cdf package in my home R library > folder? I tried installing hgu133a.db, gahgu133acdf and u133x3pcdf, and > repeating the operation, but I still get the error. > > Any help will be really appreciated! > > Best, > Daniel > > > library("ArrayExpress") > > library(affy) > > GNF <- ArrayExpress("E-TABM-145") > ... > The object containing experiment E-TABM-145 has been built. > > class(GNF) > [1] "AffyBatch" > attr(,"package") > [1] "affy" > > GNF > Warning in install.packages(cdfname, lib = lib, repos = > Biobase:::biocReposList(), : > 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable > AffyBatch object > size of arrays=712x712 features (228 kb) > cdf=HG-U133A (??? affyids) > number of samples=158 > Warning in install.packages(cdfname, lib = lib, repos = > Biobase:::biocReposList(), : > 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable > Error in install.packages(cdfname, lib = lib, repos = > Biobase:::biocReposList(), : > unable to install packages > In addition: Warning message: > missing cdf environment! in show(AffyBatch) > > GNFnorm <- rma(GNF) > Warning in install.packages(cdfname, lib = lib, repos = > Biobase:::biocReposList(), : > 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable > Error in install.packages(cdfname, lib = lib, repos = > Biobase:::biocReposList(), : > unable to install packages > > > sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.26.0 ArrayExpress_1.8.0 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] XML_2.8-1 affyio_1.16.0 limma_3.4.0 > [4] preprocessCore_1.10.0 tools_2.11.0 > > ******************************************** > > Daniel Rico Rodriguez, PhD. > Structural Computational Biology Group > Spanish National Cancer Research Center, CNIO > Melchor Fernandez Almagro, 3. > 28029 Madrid, Spain. > Phone: +34 91 224 69 00 #3015 > drico at cnio.es > http://www.cnio.es > > ******************************************** > > > > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y ...{{dropped:3}} > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thanks Wolfgang!! It is very nice that the method tries to install the package. As "cdfname" is not shown, it is not clear which package is missing. Maybe the package name could be printed in the error message? Thank you guys for the excelent sofware!! Best, Daniel On Oct 16, 2010, at 5:51 PM, Wolfgang Huber wrote: > > Dear Daniel > > have you tried with installing the hgu133acdf package manually > beforehand? (After that, please try to load it to verify it's really > there.) > > What you see is because the 'print' method for 'AffyBatch' objects > from the 'affy' package requires the array's CDF package (hgu133acdf > in your case), and if it does not find it on your computer, it tries > to be helpful and install it from the Bioconductor repository on the > web. > > Btw, it should never be necessary to be 'root' to install R packages > on any sane system configuration. > > Best wishes > Wolfgang > > Il Oct/15/10 5:50 PM, Daniel Rico Rodriguez ha scritto: >> Dear list, >> >> I downloaded a dataset from ArrayExpress using ArrayExpress >> package, and >> I get an error when I try to see the object created, or a try to >> normalize it with rma. >> >> I am using a Linux Ubuntu. For some reason, a package installation is >> tried (related with cdf, I guess) but I am not root... Is there a >> way to >> overcome this problem installing some cdf package in my home R >> library >> folder? I tried installing hgu133a.db, gahgu133acdf and u133x3pcdf, >> and >> repeating the operation, but I still get the error. >> >> Any help will be really appreciated! >> >> Best, >> Daniel >> >> > library("ArrayExpress") >> > library(affy) >> > GNF <- ArrayExpress("E-TABM-145") >> ... >> The object containing experiment E-TABM-145 has been built. >> > class(GNF) >> [1] "AffyBatch" >> attr(,"package") >> [1] "affy" >> > GNF >> Warning in install.packages(cdfname, lib = lib, repos = >> Biobase:::biocReposList(), : >> 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable >> AffyBatch object >> size of arrays=712x712 features (228 kb) >> cdf=HG-U133A (??? affyids) >> number of samples=158 >> Warning in install.packages(cdfname, lib = lib, repos = >> Biobase:::biocReposList(), : >> 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable >> Error in install.packages(cdfname, lib = lib, repos = >> Biobase:::biocReposList(), : >> unable to install packages >> In addition: Warning message: >> missing cdf environment! in show(AffyBatch) >> > GNFnorm <- rma(GNF) >> Warning in install.packages(cdfname, lib = lib, repos = >> Biobase:::biocReposList(), : >> 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable >> Error in install.packages(cdfname, lib = lib, repos = >> Biobase:::biocReposList(), : >> unable to install packages >> >> > sessionInfo() >> R version 2.11.0 (2010-04-22) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] affy_1.26.0 ArrayExpress_1.8.0 Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] XML_2.8-1 affyio_1.16.0 limma_3.4.0 >> [4] preprocessCore_1.10.0 tools_2.11.0 >> >> ******************************************** >> >> Daniel Rico Rodriguez, PhD. >> Structural Computational Biology Group >> Spanish National Cancer Research Center, CNIO >> Melchor Fernandez Almagro, 3. >> 28029 Madrid, Spain. >> Phone: +34 91 224 69 00 #3015 >> drico at cnio.es >> http://www.cnio.es >> >> ******************************************** >> >> >> >> >> >> >> **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y ... >> {{dropped:3}} >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ******************************************** Daniel Rico Rodriguez, PhD. Structural Computational Biology Group Spanish National Cancer Research Center, CNIO Melchor Fernandez Almagro, 3. 28029 Madrid, Spain. Phone: +34 91 224 69 00 #3015 drico at cnio.es http://www.cnio.es ******************************************** **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y ...{{dropped:3}}
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