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Hi Lana, Lana Schaffer wrote: > Hi, > I am trying to create a cdf package in R2.3.1 and Bioconductor 1.8 and using > the windows compiled version. > I have previously created this cdf package in R2.2.0 with success. > The package does not get compressed even though compress=TRUE > is the directive so I have to compress it myself. I think you are misunderstanding something here. The compress argument is TRUE if the cdf file you are reading is compressed. It doesn't have anything to do with the output. > > glycov2a520086f = make.cdf.package("GLYCOv2a520086F.CDF", > cdf.path=system.file("extdata", package="makecdfenv"), > compress=TRUE, species = "Homo_sapiens", > package.path = pkgpath) Is your cdf file really in R_HOME/library/makecdfenv/extdata? That is sort of an odd place to put things. Anyway, I don't have the same problem with the example file in that directory: > make.cdf.package("hu6800.CDF.gz", cdf.path = system.file("extdata", package="makecdfenv"),compress=TRUE, species = "Homo_sapiens") Reading CDF file. Creating CDF environment Wait for about 71 dots.................................................................. ....... Creating package in C:/rw2030beta/hu6800.cdf.gzcdf [1] "hu6800.cdf.gzcdf" I tried un-gzipping the cdf as well, and used compress = TRUE, and that still worked. > make.cdf.package("hu6800.CDF", cdf.path = system.file("extdata", package="makecdfenv"),compress=TRUE, species = "Homo_sapiens") Reading CDF file. Creating CDF environment Wait for about 71 dots.................................................................. ............. Creating package in C:/rw2030beta/hu6800cdf [1] "hu6800cdf" You should also always give your sessionInfo()! > sessionInfo() Version 2.3.0 RC (2006-04-17 r37823) i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [8] "base" other attached packages: makecdfenv affy affyio Biobase "1.9.3" "1.10.0" "0.99.3" "1.10.1" What versions of makecdfenv, and more importantly, affyio are you using? Also, if you download the Rtools and put them in your PATH, does the problem go away? http://www.murdoch-sutherland.com/Rtools/tools.zip Best, Jim > > Error in gzfile(file, "r") : unable to open connection > In addition: Warning messages: > 1: error -1 in extracting from zip file > 2: cannot open compressed file 'glycov2a520086fcdf/DESCRIPTION' > > I know this is a popular problem, so does anyone know the solution? > Thanks. > > Lana Schaffer > Biostatistics/Informatics > The Scripps Research Institute > DNA Array Core Facility > La Jolla, CA 92037 > (858) 784-2263 > (858) 784-2994 > schaffer at scripps.edu > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.