[BioC] Follow-up to: [R] Annotation metadata "kills" help.search

[Gerard Tromp]

Greetings,

this is a follow-up to the mailing below. Seth Falcon replied and indicated
that he and several others were unable to replicate the problem.
Specifically he requested:

============
We are not able to reproduce this issue.  If you reinstall the
annotation packages does the error reappear?

If so, an exact transcript of the commands entered, their output, and
the output of traceback() right after the error would be helpful ---
and it would be best to move the discussion to the bioconductor list.
=======

The answers are: Yes, the problem is reproducible. I did a complete
reinstall of R and bioconductor end everything worked fine until I installed
an annotation package.

I had previously (3/20/2005) used ReposTools to download annotation packages
to a local directory.

1. Installing GO from the local zip file (GO_1.7.0.zip)
> install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
package 'GO' successfully unpacked and MD5 sums checked
updating HTML package descriptions


2. Performing help.search for something in the R base package
> help.search("Control")
Error in rbind(...) : number of columns of matrices must match (see arg 203)
In addition: Warning messages:
1: No Rd contents for package 'gregmisc' in 'C:/Program Files/R/library' in:
help.search("Control")
2: No Rd contents for package 'nlrq' in 'C:/Program Files/R/library' in:
help.search("Control")
3: No Rd contents for package 'nprq' in 'C:/Program Files/R/library' in:
help.search("Control")

+++ Note that GO is the 203rd directory in the library directory


3. traceback of the latest error produces a very long list (aprox. 1.7MB) I
am attaching a zipped version.


4. Removing the GO directory restores the help.search function.
> help.search("Control")
Warning messages:
1: No Rd contents for package 'gregmisc' in 'C:/Program Files/R/library' in:
help.search("Control")
2: No Rd contents for package 'nlrq' in 'C:/Program Files/R/library' in:
help.search("Control")
3: No Rd contents for package 'nprq' in 'C:/Program Files/R/library' in:
help.search("Control")

+++ Note warning messages but no errors


I can reproduce the error with each of the annotation packages I listed in
my initial message, i.e., each individually produces the same error. The
only difference is the arg number in the error message since the argument
number is based on the position of the package directory in the list of
directories under the "library" directory.

Gerard


-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch]On Behalf Of Gerard Tromp
Sent: Monday, March 28, 2005 22:09
To: R-help list
Subject: [R] Annotation metadata "kills" help.search


Greetings!

OS: Windows
R 2.0.1

Before anyone flames -- I tried to query this on the R searchable web site
and using google and did not find anything applicable.

As of about a week ago the help.search function dies when used in the simple
help.search("something") usage.
The error is
Error in rbind(...) : number of columns of matrices must match (see arg 203)

After some effort I have traced it down to the annotation packages. I
installed
GO, KEGG, mgu74[abc]v2 and hgu133plus2 all version 1.7.0

When I move these out of the library directory, help.search() functions
correctly again.

I have not tracked it any further -- just wanted to know if anyone else had
noticed it.


Gerard Tromp

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