I have been trying to install bioconductor 2.5 packages using biocLite and
keep receiving the following error message:

package 'KEGG.db' successfully unpacked and MD5 sums checked
package 'AnnotationDbi' successfully unpacked and MD5 sums checked
Error in normalizePath(path) :
  path[1]="C:\Program Files\R\R-2.10.1\library/AnnotationDbi": The system
cannot find the file specified

In going through the archives, I found and tried this:

Elliot Kleiman <kleiman at rohan.sdsu.edu
<https://stat.ethz.ch/mailman/listinfo/bioconductor>> writes:

>* Hi BioC,
*>*
*>* I am unable to install the new BioC 2.4
*>* as I am receiving the following error,
*
>* Error in normalizePath(path) :
*>* path[1]="C:\Program Files\R\R-2.9.0\library/GO.db": The system cannot
*>* find the file specified
*
Hi Elliot --

The R-help and R-devel lists suggest this might be related to
anti-virus software, especially if the failure changes over time. One
useful possibility is to say

trace(normalizePath, quote(cat("path=", path, "\n")))

before biocLite(). You'll see the arguments called each time
normalizePath() is invoked, and it'll likely rule out a number of
possibilities, e.g., spaces in the path name or use of \ and /

HTH, Martin

I tried the solution and am not sure what to do with it.  Here is the
recent attempt:

Tracing normalizePath(lib) on entry
path= C:/PROGRA~1/R/R-210~1.1/library
package 'AnnotationDbi' successfully unpacked and MD5 sums checked
Tracing normalizePath(file.path(tmpDir, curPkg)) on entry
path= C:\Program Files\R\R-2.10.1\library\file54de1547/AnnotationDbi
Tracing normalizePath(instPath) on entry
path= C:\Program Files\R\R-2.10.1\library/AnnotationDbi
Error in normalizePath(path) :
  path[1]="C:\Program Files\R\R-2.10.1\library/AnnotationDbi": The
system cannot find the file specified

Thanks for any help or suggestions!

-- 
Eric Bremer, PhD
Chief Scientific Officer
Precision Biomarker Resources, Inc.
820 Davis St.,  Suite 216
Evanston, Illinois  60201

Office: 847.866.0406
Mobile: 708.267.2052
Skype: egbremer

www.precisionbiomarker.com

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