[BioC] Need better quality control for reliable installation of bioconductor packages?

[Glynn, Earl]

Under Windows I just downloaded the new 2.0.1 version of R and installed
all the packages:

	Packages | Install package(s) from CRAN ... 

I select all the packages for installation and that worked fine.  This
took about an hour.

So with the new version of R, I thought I'd re-install all the
Bioconductor packages. Like several times in the past, when I try to
install all the Bioconductor packages I encounter problems:

	Packages | Install package(s) from Bioconductor ...

I select all the packages for installation.  The download take a long
time but then the installation of packages fails.  I wish the name of
the temporary download directory was displayed earlier to make it easier
to find.  But I found the Bioconductor ZIP files and then tried Packages
| Install Package(s) from local zip files ...

Why is the installation of so many Bioconductor packages failing?

For example:

	>
install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
	Error in file(file, "r") : unable to open connection
	In addition: Warning messages: 
	1: error 1 in extracting from zip file 
	2: cannot open file `twilight/DESCRIPTION' 
	>
install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
	Error in file(file, "r") : unable to open connection
	In addition: Warning messages: 
	1: error 1 in extracting from zip file 
	2: cannot open file `iSPlot/DESCRIPTION' 
	>
install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
	Error in file(file, "r") : unable to open connection
	In addition: Warning messages: 
	1: error 1 in extracting from zip file 
	2: cannot open file `affycomp/DESCRIPTION' 
	>
install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
	Error in file(file, "r") : unable to open connection
	In addition: Warning messages: 
	1: error 1 in extracting from zip file 
	2: cannot open file `RdbiPgSQL/DESCRIPTION' 

This installation process is quite frustrating since one selects all the
packages to install and then it fails.  This must be repeated every time
for a failure.  So far I've seen at least 9 failures.  What wrong with
these DESCRIPTION directories?

Why isn't the installation of bioconductor packages more reliable? (I've
seen this same problem several times before).  What quality control
measures can be put in place to catch these problems and fix them
automatically?

efg
--
Earl F. Glynn    
Scientific Programmer
Bioinformatics Department
Stowers Institute for Medical Research


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