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Radek Blatny ▴ 60
@radek-blatny-2983
Last seen 10.2 years ago
Hi, I'm getting the error, although my connection is OK. R> ai<-compute.affinities(cdfName(Data)) Computing affinitiesError in getCDF(cdfpackagename) : The current operation could not access the Bioconductor repository. Please check your internet connection, and report further problems to bioconductor at stat.math.ethz.ch In addition: Warning message: In readLines(biocURL) : cannot open: HTTP status was '404 Not Found' Regards, Radek Blatny Radek Blatny, MSc. Institute of Molecular Genetics Department of Mouse Molecular Genetics (Jiri Forejt unit) Czech Academy of Sciences Videnska 1083 142 20, Prague Czech Republic Tel. (+420) 241 062 260 Fax (+420) 241 062 154 http://www.img.cas.cz/mmg email: blatny at img.cas.cz Skype name: blatny
Genetics Genetics • 1.3k views
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@sean-davis-490
Last seen 3 months ago
United States
On Tue, Aug 12, 2008 at 10:58 AM, Radek Blatny <blatny at="" img.cas.cz=""> wrote: > Hi, I'm getting the error, although my connection is OK. > > R> ai<-compute.affinities(cdfName(Data)) > Computing affinitiesError in getCDF(cdfpackagename) : > The current operation could not access the Bioconductor repository. Please > check your internet connection, and report further problems to > bioconductor at stat.math.ethz.ch > In addition: Warning message: > In readLines(biocURL) : cannot open: HTTP status was '404 Not Found' Hi, Radek. Folks will probably need to see the output of sessionInfo() to help more. Sean
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R> sessionInfo() R version 2.6.0 Patched (2007-10-22 r43252) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .U TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UT F- 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ ID ENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] mouse4302_2.0.1 mm430mmentrezgprobe_10.0.0 [3] mm430mmentrezg_10.0.0 mouse4302probe_2.0.0 [5] mouse4302cdf_2.0.0 geneplotter_1.16.0 [7] lattice_0.17-12 annotate_1.16.1 [9] xtable_1.5-2 AnnotationDbi_1.0.6 [11] RSQLite_0.6-9 DBI_0.2-4 [13] vsn_3.2.1 limma_2.12.0 [15] affyPLM_1.14.0 RColorBrewer_1.0-2 [17] simpleaffy_2.14.05 gcrma_2.10.0 [19] matchprobes_1.10.0 genefilter_1.16.0 [21] survival_2.34-1 affy_1.16.0 [23] preprocessCore_1.0.0 affyio_1.6.1 [25] Biobase_1.16.3 loaded via a namespace (and not attached): [1] grid_2.6.0 KernSmooth_2.22-22 rcompgen_0.1-17 #################################################### # I am trying to change the cdf file from Mouse430_2 to mm430mmentrezg7: AffyBatch at cdfName<-"mm430mmentrezg7" # and afterwards to initiate the affinity computation and continue with gcrma, but I am getting the error: R> ai<-compute.affinities(cdfName(Data)) Computing affinitiesError in getCDF(cdfpackagename) : The current operation could not access the Bioconductor repository. Please check your internet connection, and report further problems to bioconductor at stat.math.ethz.ch In addition: Warning message: In readLines(biocURL) : cannot open: HTTP status was '404 Not Found' Regards, Radek On Aug 12, 2008, at 5:43 PM, Sean Davis wrote: On Tue, Aug 12, 2008 at 10:58 AM, Radek Blatny <blatny at="" img.cas.cz=""> wrote: > Hi, I'm getting the error, although my connection is OK. > > R> ai<-compute.affinities(cdfName(Data)) > Computing affinitiesError in getCDF(cdfpackagename) : > The current operation could not access the Bioconductor > repository. Please > check your internet connection, and report further problems to > bioconductor at stat.math.ethz.ch > In addition: Warning message: > In readLines(biocURL) : cannot open: HTTP status was '404 Not Found' Hi, Radek. Folks will probably need to see the output of sessionInfo() to help more. Sean
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Oh, I've figured it out, the command must be: AffyBatch at cdfName<-"mm430mmentrezg" not AffyBatch at cdfName<-"mm430mmentrezg7" I thought I can choose the genome version by appending the number. Anyway, is there a way to choose the version? Regards, Radek On Aug 12, 2008, at 6:07 PM, Radek Blatny wrote: R> sessionInfo() R version 2.6.0 Patched (2007-10-22 r43252) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .U TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UT F- 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ ID ENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] mouse4302_2.0.1 mm430mmentrezgprobe_10.0.0 [3] mm430mmentrezg_10.0.0 mouse4302probe_2.0.0 [5] mouse4302cdf_2.0.0 geneplotter_1.16.0 [7] lattice_0.17-12 annotate_1.16.1 [9] xtable_1.5-2 AnnotationDbi_1.0.6 [11] RSQLite_0.6-9 DBI_0.2-4 [13] vsn_3.2.1 limma_2.12.0 [15] affyPLM_1.14.0 RColorBrewer_1.0-2 [17] simpleaffy_2.14.05 gcrma_2.10.0 [19] matchprobes_1.10.0 genefilter_1.16.0 [21] survival_2.34-1 affy_1.16.0 [23] preprocessCore_1.0.0 affyio_1.6.1 [25] Biobase_1.16.3 loaded via a namespace (and not attached): [1] grid_2.6.0 KernSmooth_2.22-22 rcompgen_0.1-17 #################################################### # I am trying to change the cdf file from Mouse430_2 to mm430mmentrezg7: AffyBatch at cdfName<-"mm430mmentrezg7" # and afterwards to initiate the affinity computation and continue with gcrma, but I am getting the error: R> ai<-compute.affinities(cdfName(Data)) Computing affinitiesError in getCDF(cdfpackagename) : The current operation could not access the Bioconductor repository. Please check your internet connection, and report further problems to bioconductor at stat.math.ethz.ch In addition: Warning message: In readLines(biocURL) : cannot open: HTTP status was '404 Not Found' Regards, Radek On Aug 12, 2008, at 5:43 PM, Sean Davis wrote: On Tue, Aug 12, 2008 at 10:58 AM, Radek Blatny <blatny at="" img.cas.cz=""> wrote: > Hi, I'm getting the error, although my connection is OK. > > R> ai<-compute.affinities(cdfName(Data)) > Computing affinitiesError in getCDF(cdfpackagename) : > The current operation could not access the Bioconductor > repository. Please > check your internet connection, and report further problems to > bioconductor at stat.math.ethz.ch > In addition: Warning message: > In readLines(biocURL) : cannot open: HTTP status was '404 Not Found' Hi, Radek. Folks will probably need to see the output of sessionInfo() to help more. Sean
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The only way to choose the version is to go to the MBNI website and download the one you want. BioC only carries the most current version. Best, Jim Radek Blatny wrote: > Oh, I've figured it out, the command must be: > > AffyBatch at cdfName<-"mm430mmentrezg" > > not > > AffyBatch at cdfName<-"mm430mmentrezg7" > > I thought I can choose the genome version by appending the number. > Anyway, is there a way to choose the version? > > Regards, Radek > > On Aug 12, 2008, at 6:07 PM, Radek Blatny wrote: > > R> sessionInfo() > R version 2.6.0 Patched (2007-10-22 r43252) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] mouse4302_2.0.1 mm430mmentrezgprobe_10.0.0 > [3] mm430mmentrezg_10.0.0 mouse4302probe_2.0.0 > [5] mouse4302cdf_2.0.0 geneplotter_1.16.0 > [7] lattice_0.17-12 annotate_1.16.1 > [9] xtable_1.5-2 AnnotationDbi_1.0.6 > [11] RSQLite_0.6-9 DBI_0.2-4 > [13] vsn_3.2.1 limma_2.12.0 > [15] affyPLM_1.14.0 RColorBrewer_1.0-2 > [17] simpleaffy_2.14.05 gcrma_2.10.0 > [19] matchprobes_1.10.0 genefilter_1.16.0 > [21] survival_2.34-1 affy_1.16.0 > [23] preprocessCore_1.0.0 affyio_1.6.1 > [25] Biobase_1.16.3 > > loaded via a namespace (and not attached): > [1] grid_2.6.0 KernSmooth_2.22-22 rcompgen_0.1-17 > > #################################################### > > # I am trying to change the cdf file from Mouse430_2 to mm430mmentrezg7: > > AffyBatch at cdfName<-"mm430mmentrezg7" > > # and afterwards to initiate the affinity computation and continue with > gcrma, but I am getting the error: > > R> ai<-compute.affinities(cdfName(Data)) > > Computing affinitiesError in getCDF(cdfpackagename) : > The current operation could not access the Bioconductor repository. > Please check your internet connection, and report further problems to > bioconductor at stat.math.ethz.ch > In addition: Warning message: > In readLines(biocURL) : cannot open: HTTP status was '404 Not Found' > > > > > Regards, Radek > > > > On Aug 12, 2008, at 5:43 PM, Sean Davis wrote: > > On Tue, Aug 12, 2008 at 10:58 AM, Radek Blatny <blatny at="" img.cas.cz=""> wrote: >> Hi, I'm getting the error, although my connection is OK. >> >> R> ai<-compute.affinities(cdfName(Data)) >> Computing affinitiesError in getCDF(cdfpackagename) : >> The current operation could not access the Bioconductor repository. >> Please >> check your internet connection, and report further problems to >> bioconductor at stat.math.ethz.ch >> In addition: Warning message: >> In readLines(biocURL) : cannot open: HTTP status was '404 Not Found' > > Hi, Radek. Folks will probably need to see the output of > sessionInfo() to help more. > > Sean > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
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