Question: Error with read.SMD() of marray
6.8 years ago by
Guest User • 12k
Guest User • 12k wrote:
Dear list, I get an error when I try to import an xls file obtained from the SMD database using the read.SMD function of the marray package. The error occurs only if the file is not placed in the working directory. More in detail, if the file 'myfile.xls' is placed on the 'path/to/dir' directory and the command: read.SMD(fnames = "myfile.xls", path = "path/to/dir") is run, the output is: Generating target sample info from all files Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : cannot open file 'myfile.xls': No such file or directory After checking the function code, I think that the error is due to the following line (line 51) of the function body comment <- grepregName.Gf, readLines(fullnames[i], n = 100)) and could be avoided by replacing it with comment <- grepregName.Gf, readLines(paste(path, "/", fullnames[i], sep = ""), n = 100)) Regards, Ignacio L. de Ullibarri -- output of sessionInfo(): R version 2.13.2 (2011-09-30) Platform: x86_64-pc-linux-gnu (64-bit) locale:  LC_CTYPE=C LC_NUMERIC=C  LC_TIME=C LC_COLLATE=C  LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8  LC_PAPER=en_GB.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  marray_1.30.0 limma_3.8.3 loaded via a namespace (and not attached):  tools_2.13.2 -- Sent via the guest posting facility at bioconductor.org.
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