I can see this has been addressed, thanks!
I found a couple more issues with installed.packages().
The values returned in the Archs column don't seem to really make
sense on Unix:
> installed.packages()[1:5, c("Version", "Archs", "Built")]
Version Archs Built
affxparser "1.22.0" "affxparser.so" "2.12.0"
affy "1.28.0" "affy.so" "2.12.0"
affydata "1.11.10" NA "2.12.0"
affyILM "1.2.0" "affyILM.so" "2.12.0"
affyio "1.18.0" "affyio.so" "2.12.0"
Also the man page for installed.packages would need to be updated to
list this new Archs column (Value section).
Thanks,
H.
On 11/10/2010 01:13 PM, Hervé Pagès wrote:
Hi,
Today we've seen the following problem with the R-2.12 that we use
for our Windows builds:
> installed.packages()
Error: subscript out of bounds
After some investigation we discovered that the cause of this failure
was that 1 of the 890 packages currently installed on the machine
(Windows Server 2003 R2) had its DESCRIPTION file empty:
E:\biocbld\bbs-2.7-bioc\R\library>ls -al DLBCL
total 1
drwxr-xr-x+ 1 biocbuild2 root 0 2010-11-08 14:11 .
drwxr-xr-x+ 1 biocbuild2 root 0 2010-11-10 00:14 ..
-rwxr-xr-x+ 1 biocbuild2 root 0 2010-11-08 14:11 DESCRIPTION
-rwxr-xr-x+ 1 biocbuild2 root 357 2010-11-08 14:11 INDEX
drwxr-xr-x+ 1 biocbuild2 root 0 2010-11-08 14:11 data
drwxr-xr-x+ 1 biocbuild2 root 0 2010-11-08 14:11 help
drwxr-xr-x+ 1 biocbuild2 root 0 2010-11-08 14:11 html
Then from R:
> library(DLBCL)
Error in library(DLBCL) : there is no package called 'DLBCL'
> packageDescription("DLBCL")
Error in packageDescription("DLBCL") :
DESCRIPTION file of package 'DLBCL' is corrupt
> installed.packages()
Error: subscript out of bounds
I have no idea how this DESCRIPTION file ended up empty. I've never
seen this before. Probably a very rare race condition that would be
very hard to reproduce.
Anyway would it be possible to have installed.packages() give
a more informative error message when this happens? That would
make it behave more consistently with packageDescription().
Does something like this sound reasonable?
hpa...@latitude:~/svn/R-trunk$ svn diff src/library/utils/R/packages.R
Index: src/library/utils/R/packages.R
===================================================================
--- src/library/utils/R/packages.R (revision 53546)
+++ src/library/utils/R/packages.R (working copy)
@@ -453,6 +453,11 @@
domain = NA, call. = FALSE)
next
}
+ if (NROW(desc) < 1L) {
+ warning(gettextf("file '%s' is corrupt", pkgpath),
+ domain = NA, call. = FALSE)
+ next
+ }
desc <- desc[1,]
Rver <- strsplit(strsplit(desc["Built"], ";")[[1L]][1L],
"[ \t]+")[[1L]][2L]
Thanks,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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