could not find function "makeProbePackage"
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@merja-heinaniemi-5982
Last seen 9.6 years ago
Hi! I am trying to build a custom probe package using the AnnotationDBI library and the function makeProbePackage. The script worked earlier (with R.2.12 at least) but now I get an error. Error in eval(expr, envir, enclos) : could not find function "makeProbePackage" I get the error with R2.15.2 and Biobase_2.18.0 (see more details in session info below) Did the function get replaced / removed ? What should I do? Any other alternative than going back to earlier R and Bioconductor versions? (in the same setting, building custom cdf worked but I would need the probe package for gcrma) kind regards, Merja > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-redhat-linux-gnu (64-bit) 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C 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] AnnotationDbi_1.20.7 Biobase_2.18.0 BiocGenerics_0.4.0 [4] makecdfenv_1.36.0 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] affy_1.36.1 affyio_1.26.0 DBI_0.2-7 [4] IRanges_1.16.6 parallel_2.15.2 preprocessCore_1.20.0 [7] RSQLite_0.11.4 stats4_2.15.2 tools_2.15.2 [10] zlibbioc_1.4.0
cdf probe cdf probe • 671 views
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@james-w-macdonald-5106
Last seen 14 hours ago
United States
Hi Merja, On 6/9/2013 11:33 AM, Merja Hein?niemi wrote: > Hi! > > I am trying to build a custom probe package using the AnnotationDBI library and the function makeProbePackage. The script worked earlier (with R.2.12 at least) but now I get an error. > Error in eval(expr, envir, enclos) : > could not find function "makeProbePackage" > > I get the error with R2.15.2 and Biobase_2.18.0 (see more details in session info below) > > Did the function get replaced / removed ? What should I do? Any other alternative than going back to earlier R and Bioconductor versions? You want the AnnotationForge package. Best, Jim > > (in the same setting, building custom cdf worked but I would need the probe package for gcrma) > > kind regards, > Merja > > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-redhat-linux-gnu (64-bit) > > 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C 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] AnnotationDbi_1.20.7 Biobase_2.18.0 BiocGenerics_0.4.0 > [4] makecdfenv_1.36.0 BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] affy_1.36.1 affyio_1.26.0 DBI_0.2-7 > [4] IRanges_1.16.6 parallel_2.15.2 preprocessCore_1.20.0 > [7] RSQLite_0.11.4 stats4_2.15.2 tools_2.15.2 > [10] zlibbioc_1.4.0 > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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