changing tmp directory buildPhylipLineage
Issue #67
resolved
I don't have write access to the normal /tmp directory on this system, so I changed TMPDIR in the environment before running R.
export TMPDIR=.
I then walk through the example in the docs for lineage reconstruction, but I get this error. I can see that it does create a temporary directory Rtmp5ZXe31
in the current directory, but not sure what file it is complaining about.
> graph <- buildPhylipLineage(clone, dnapars_exec, rm_temp=TRUE)
Error in runPhylip(temp_path, dnapars_exec, verbose = verbose) :
(list) object cannot be coerced to type 'double'
In addition: Warning message:
In file(con, "w") :
cannot open file './Rtmp5ZXe31/fileb6e1c2d7061': No such file or directory
Or maybe actually the error is with the example data...
Comments (2)
-
-
reporter - changed status to resolved
That worked. Also needed dnapars_exec to be an absolute path as well.
- Log in to comment
I had the same error using
TMPDIR=.
. Try an absolute path (egTMPDIR=/home/user/tmp
). That worked for me. It's probably some oddity in howscan
interprets relative file paths.