[BioC] Error with read.SMD() of marray

[Ignacio Lopez de Ullibarri [guest]]

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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