[Bioc-devel] update packages not working

Seth Falcon sfalcon at fhcrc.org
Mon Jan 22 17:52:20 CET 2007

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

> Seth,
> Regarding synching version numbers of R and BioC, I see your point about
> giving the impression that they are the same project, whereas in reality
> they are separate. It seems to me, however, that there are many cases on
> the list that result from a newer BioC version being used with an older
> 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 something only to find that I am working with an outdated package.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 for
> CRAN. At the end of this post is a screen dump with code, error message
> 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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