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

[Gordon K Smyth]

Glynn, Earl <EFG at Stowers-Institute.org> wrote
>
>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'

The package affycomp does install successfully for me under R 2.0.1 for Windows 2000 using the
drop-down menu.  It is however a very large package indeed and might be subject to download
errors.

The other three packages do not have Windows versions, so they are never going to install for you.
  See http://www.bioconductor.org, click on "Release 1.5 Packages", and then on the relevant
package.

Gordon

>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