make.cdf.package: Error: cannot allocate vector of size 1 Kb
1
0
Entering edit mode
Peng Yu ▴ 940
@peng-yu-3586
Last seen 9.6 years ago
I run the following example. The cdf file is downloaded from the following link. I'm wondering what the problem is with make.cdf.package. http://www.affymetrix.com/Auth/support/downloads/library_files/MoEx- 1_0-st-v1.text.cdf.zip $ Rscript MoEx-1_0-st-v1.cdf.R > library(makecdfenv) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affy Loading required package: affyio > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] makecdfenv_1.24.0 affyio_1.14.0 affy_1.24.2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] preprocessCore_1.8.0 > make.cdf.package('MoEx-1_0-st-v1.text.cdf', species='Mus_musculus') Reading CDF file. Error: cannot allocate vector of size 1 Kb Execution halted
cdf cdf • 936 views
ADD COMMENT
0
Entering edit mode
@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Peng Yu how big is the RAM of your computer? You could try with closing all other applications before running this script. You could try on a server with more RAM. I tried downloading the file whose URL who give below, but gave up after some failed rounds with the extraordinarily annoying and intrusive registration procedure that Affymetrix has set up for this. Let us know how it goes with the suggestions above, if they don't help, I'd try again with that. Best wishes Wolfgang > I run the following example. The cdf file is downloaded from the > following link. I'm wondering what the problem is with > make.cdf.package. > > http://www.affymetrix.com/Auth/support/downloads/library_files/MoEx- 1_0-st-v1.text.cdf.zip > > $ Rscript MoEx-1_0-st-v1.cdf.R >> library(makecdfenv) > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affy > Loading required package: affyio >> sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] makecdfenv_1.24.0 affyio_1.14.0 affy_1.24.2 Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] preprocessCore_1.8.0 >> make.cdf.package('MoEx-1_0-st-v1.text.cdf', species='Mus_musculus') > Reading CDF file. > Error: cannot allocate vector of size 1 Kb > Execution halted > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact
ADD COMMENT

Login before adding your answer.

Traffic: 950 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6