aroma-project.org

The maximum number of symbols in a Windows pathname is 256, including file separators '/' or '\', but excluding the drive letter, and initial file separator (e.g. "C:/"), and the string terminator ('\0'), cf. MSDN - Naming a File or Directory.  In R, the limit is one symbol less, i.e. 255.

Example:

Here is an example of a very long pathname:

# Working directory:
pwd <- getwd();
print(pwd);
[1] "C:/Users/AromaUser/Project_2010/TCGA,GBM,analysis/redundancyTests/"

# Result directory:
path <- "cbsData/broad.mit.edu_GBM.Genome_Wide_SNP_6.4.5.0,pairs/GenomeWideSNP_6/";

# Filename
filename <- "TCGA-06-0208,01A,01D-0236-01,ratios,ref=TCGA-06-0208,10A,01D-0237-01,log2ratio,total,chr09,dbc39899be02529b41df0a9416537f0a.xdr";

# Complete pathname
pathname <- file.path(pwd, path, filename);
print(nchar(pathname));

[1] 267  

Symptom:

This limitation typically reveals itself as "file" errors.  One example is "In gzfile(file, "wb") : cannot open compressed file '<long pathname>', probable reason 'No such file or directory'.  Another example is "Error in dirname(pathname) : file name conversion problem".

Workaround:

1. Use a working directory that is higher up in the directory structure, e.g. instead of C:/way/too/long/path/ use C:/short/path/.
2. The [Windows/MS-DOS] console 'subst' utility makes a drive letter to any Windows directory, e.g. subst Y: 'C:/Documents and Settings/JohnDoe/Documents/My Research/Projects/aroma.affymetrix/ProjectA/'.
3. The following R.utils solution maps the current working directory to 'Y:' (using the above internally) and set new working directory to 'Y:/':
   

   setwd(System$mapDriveOnWindows("Y:"));

Not a workaround:

1. Unfortunately it is not a solution to try to use relative instead of absolute pathnames.  The limitation is deep down in the file system itself and it is the absolute pathname that counts.

Comments:

One could imagine that aroma should detect too long pathname and give a more informative error.  This is still something that has to be implemented. /HB 2010-01-06