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

[Robert Gentleman]

On Dec 10, 2004, at 10:21 AM, Glynn, Earl 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:
>

  But you have not shown us what commands you are using?
  You can (and possibly should) use the reposTools library and the tools  
that we have built for dealing with the package dependencies that exist  
in and between many Bioconductor packages.

> 	>
> 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'
> 	>

   Did you look to see what the problem is? Try just installing a single  
package, giving the correct path. These are just zip files open them  
and see if they are complete (it isn't very hard).
Do you have Gtk properly installed? If not why would you want a package  
that relies on it?

> 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'
>

   Do you have Postgres properly installed on your computer? If not, why  
would you expect this package to install or work? I don't think that  
blindly trying to install every package, regardless of whether you want  
or need to use it makes very much sense. As for why these particular  
ones have failed, one needs to look and see if they downloaded (maybe  
there was a time out), what the name of the downloaded file is, does it  
match the name in the command you issued, and then you can look at the  
zip file and see if it is ok. I suspect that there is a failure  
somewhere in one of those three places (but I could be wrong).

> 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?
>

   You have chosen to install the development version of these packages,  
that means that you are working with unstable software. If you want  
stable software you can use the release version, or you can pay someone  
(like Insightful for that). But as I noted above, I suspect that the  
problem lies with the downloaded files, and that is the first place to  
start looking.

> 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?

   Well, we would like to make it more stable, and accurate and  
informative user reports help us to do that. You could help, by trying  
to find out just what the problem is, and no we can't tell what is  
happening on your computer, so you have to be slightly more  
descriptive.

   As for what could make things easier, well, contributing money is one  
if you send us a lot we can fix it really fast. Otherwise, you can  
supply informative bug reports that can be used to figure out what has  
gone wrong.

   Robert

>
> efg
> --
> Earl F. Glynn
> Scientific Programmer
> Bioinformatics Department
> Stowers Institute for Medical Research
>
>
> 	[[alternative HTML version deleted]]
>
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>
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