[BioC] Error with read.SMD() of marray
Ignacio Lopez de Ullibarri [guest]
guest at bioconductor.org
Thu Oct 27 12:36:43 CEST 2011
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 <- grep(regName.Gf, readLines(fullnames[i], n = 100))
and could be avoided by replacing it with
comment <- grep(regName.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:
[1] LC_CTYPE=C LC_NUMERIC=C
[3] LC_TIME=C LC_COLLATE=C
[5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] marray_1.30.0 limma_3.8.3
loaded via a namespace (and not attached):
[1] tools_2.13.2
--
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