[Bioc-devel] update packages not working

Kimpel, Mark William mkimpel at iupui.edu
Mon Jan 22 18:11:52 CET 2007


My thoughts on version numbers were really just an aside. You are
certainly correct that if new users do everything correctly they will
have no problems. Here, however, is one scenario where I can see someone
screwing something up. User only used R/BioC intermittently and has
version R 2.1 on his machine. He reads about a new package in
Bioinformatics, goes to the BioC website, downloads this new package
(created to run in R 2.4.1) and installs from zip file. Couldn't this
cause problems for the user? Perhaps this is just theoretical and never
happens in practice. The next time I see what I think is a real world
example, I'll forward it to you. Unless someone else has something to
add, let's just drop this for now.

My real problem is that I am not sure if the update packages code is
working in R 2.5.0. Is the warning message itself a bug or is the update
not working? So far I haven't been prompted to enter "y" to update a
BioC package, whereas I have for CRAN packages.


Mark W. Kimpel MD 


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-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
Sent: Monday, January 22, 2007 11:52 AM
To: Kimpel, Mark William
Cc: Seth Falcon; bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] update packages not working

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:

> Seth,
> Regarding synching version numbers of R and BioC, I see your point
> giving the impression that they are the same project, whereas in
> they are separate. It seems to me, however, that there are many cases
> the list that result from a newer BioC version being used with an
> R version.

Please post links to posts where you think this is happening.  When
users follow the directions for installing Bioconductor packages using
biocLite it is virtually impossible to get a mismatch.

Have there been cases of such mixups?  Yes.  But the ones that I can
recall were the result of users being confused about how to install
BioC packages in the first place -- I just fail to see how version
numbers would help these users.

> I think that the bioinformatics folks focus in on getting the latest
> and greatest packages for BioC and forget that R is also
> evolving. On start-up, could R run a quick check of version numbers
> of all packages to see if they are supported by the base R version
> and, if not, give a list of those that are not? 

If the packages were installed using any of the recommended methods,
then I don't think it is possible to have a package that isn't
supported by your version of R.  Adding such a feature to R is
something for the R email lists and not something we can do much about
here at BioC HQ ;-)

> For myself, I simply have the commands you gave me in .Rprofile and
> I update every time R starts up. It makes the process a little
> slower, but it was the only way I could make myself remember to do
> it on a regular basis and it certainly beats spending time debugging
> something only to find that I am working with an outdated package.

I'm glad you've found a solution that works for you.  The code in your
.Rprofile file keeps packages updated with respect to bug fixes,
etc. -- that's fine, but it leaves me a bit confused about how this
relates to arguments about R <-> BioC version number syncing or
mismatches between R version and package version.

> Well, now onto a real-world problem that I am having. I could not get
> your code to work for updating my BioC devel packages. It does work
> CRAN. At the end of this post is a screen dump with code, error
> and sessionInfo(). Any thoughts?
> Mark
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>> library("Biobase")
> Loading required package: tools
> Welcome to Bioconductor
>     Vignettes contain introductory material. To view, type
>     'openVignette()' or start with 'help(Biobase)'. For details
>     on reading vignettes, see the openVignette help page.
>>     update.packages(repos=biocReposList())
> Warning: unable to access index for repository
> http://bioconductor.org/packages/2.0/monograph/bin/windows/contrib/2.5
>> sessionInfo()
> R version 2.5.0 Under development (unstable) (2007-01-19 r40528) 
> i386-pc-mingw32 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"
> "datasets"  "methods"   "base"     
> other attached packages:
>   Biobase 
> "1.13.34" 

Aside from the warning message (which will be fixed, but hey, you are
using devel), what didn't work?

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