[R] Make.cdf.package error
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
Hi Elodie, First, this isn't a question for R-help, but should be directed to the Bioconductor help list (redirected). It also appears that you cross-posted, but I don't see any evidence for that in the header to this email (just in the subject). If you did in fact post to both lists, please don't do that either. On 2/17/2011 10:14 AM, elodiem wrote: > > Hi everybody, > > I tried to analyze a custom Affymetrix 3'-biased Array. So I wanted to make > a cdf package. (My CDF file size is 1.12Go). > > I tried several methods but the same error occured > > Method 1 > >> #Set the working directory >> setwd("D:/Analyse R/Cel files") >> #library to create cdf env >> library("makecdfenv") >> #Create cdf environment >> pkgpath<- tempdir() >> make.cdf.package("file.cdf", > cdf.path=getwd(), > compress=FALSE, species = "Homo_sapiens", > package.path = pkgpath, > verbose=TRUE) > dir(pkgpath) > > Method 2 > #Set the working directory > setwd("D:/Analyse R/Cel files") > #library to create cdf env > library("makecdfenv") > #Create cdf environment > env<- make.cdf.env("file.cdf") > > >> Reading CDF file. >> Error in .Call("reaD file", as.character(file), as.integer(3), > as.integer(compress), :promise already under evaluation: recursive default > argument reference or earlier problems? > > The two methods take about one hour and use all the RAM of my computer > (8Go). > > Is it a limit of memory? Possibly. That is a gigantic CDF file; the largest 'stock' cdf I have seen is about an order of magnitude smaller. This is for sure a 3' biased array? > Is it a non appropriated method for my array? If in fact it is a 3' biased array, then this is the software to use. It may be some other incompatibility however. Please send us the output from sessionInfo(). Best, Jim > > Thanks in advance for your response, > Elodie -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
cdf cdf • 769 views
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@elodie-marquand-4499
Last seen 9.6 years ago
Hi everybody, I tried to analyze a custom Affymetrix 3'-biased Array. So I wanted to make a cdf package. (My CDF file size is 1.12Go). I tried several methods but the same error occured Method 1 > #Set the working directory > setwd("D:/Analyse R/Cel files") > #library to create cdf env > library("makecdfenv") > #Create cdf environment > pkgpath<- tempdir() > make.cdf.package("file.cdf", cdf.path=getwd(), compress=FALSE, species = "Homo_sapiens", package.path = pkgpath, verbose=TRUE) > dir(pkgpath) Method 2 > #Set the working directory > setwd("D:/Analyse R/Cel files") > #library to create cdf env > library("makecdfenv") > #Create cdf environment > env<- make.cdf.env("file.cdf") > > > Reading CDF file. > Error in .Call("reaD file", as.character(file), as.integer(3), > as.integer(compress), :promise already under evaluation: recursive > default argument reference or earlier problems? > The two methods take about one hour and use all the RAM of my computer (8Go). I am using R on Windows. Is it a limit of memory? Thanks in adavance for your answer. Elodie MARQUAND [[alternative HTML version deleted]]
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