[Bioc-devel] update packages not working

[Kimpel, Mark William]

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. 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? It might be a more visible
warning that putting a warning up when packages are loaded as these can
get lost in the jumble of scrolling screen output. 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working with an outdated package.

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



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> 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" 
> update.packages(ask='graphics')
--- Please select a CRAN mirror for use in this session ---

Mark W. Kimpel MD 

 

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-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
Sent: Monday, January 22, 2007 12:18 AM
To: Kimpel, Mark William
Cc: bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] update packages not working

Hi Mark,

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
> I'm having difficulty auto-updating packages in R 2.5/BioC 2.0. R
> packages update without problem, BioC packages result in following
> error. 

CRAN packages update because:

   a) the CRAN URL is essentially hard-coded into R

   b) CRAN packages, in general, have very few dependencies and those
      that they have are all in the CRAN.

> It seems this happened with BioC 1.9 development also.  What is the
> acceptable protocol for updating BioC development packages?

Here's one way to upgrade all of your installed CRAN _and_
Bioconductor packages:

    library("Biobase")
    update.packages(repos=biocReposList())

> While I'm on a tear here, has anyone ever thought of synching the
> version numbers for BioC and R? I don't have a problem with it, but it
> might help newbies keep things straight. I frequently see problems on
> the BioC list caused by non-synched versions of BioC and R.

I can recall some recent cases where folks have had out of date
packages, but version number syncing is not going to help with that.
My impression is that there have been very few, if any, recent cases
of release/devel mixups.

Syncing R and BioC version numbers would not, IMO, solve package
install/upgrade issues and it would lead to confusion that the R and
Bioconductor projects were the same (they are not).

> update.packages(ask='graphics')

If the above doesn't work, send along the error messages and we'll go
from there.  But perhaps the bioconductor list is a better forum at
that point.

+ seth