[Bioc-devel] Problem accessing annotation packages in R2.4.0

I need to access annotation packages under R2.4.0 to test my program.
I have just installed the latest R2.4.0 binary available for Windows. I 
also had the same problem with a vesion of R2.4.0 I installed in May 
this year.

I run the following code under R2.3.1 and R2.4.0

 >===========

cu=contrib.url(Biobase::biocReposList())
cu
ap<-available.packages(contriburl=cu)
length(ap)
mi<-match("mouse4302",ap[,"Package"])
mi
sessionInfo()

 >============

Output Using R2.3.1

 > cu=contrib.url(Biobase::biocReposList())
 > cu

[1] "http://bioconductor.org/packages/1.8/bioc/bin/windows/contrib/2.3" 

[2] 
"http://bioconductor.org/packages/1.8/data/annotation/bin/windows/contrib/2.3"
[3] 
"http://bioconductor.org/packages/1.8/data/experiment/bin/windows/contrib/2.3"
[4] 
"http://bioconductor.org/packages/1.8/omegahat/bin/windows/contrib/2.3" 

[5] 
"http://bioconductor.org/packages/1.8/lindsey/bin/windows/contrib/2.3" 

[6] "http://cran.fhcrc.org/bin/windows/contrib/2.3" 

 > ap<-available.packages(contriburl=cu)
 > length(ap)

[1] 14517

 > mi<-match("mouse4302",ap[,"Package"])
 > mi

[1] 619

 > sessionInfo()

Version 2.3.1 (2006-06-01)
i386-pc-mingw32

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils" 
"datasets"  "base"

---------------

Output Using R2.4.0

 > cu=contrib.url(Biobase::biocReposList())
 > cu

[1] "http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4" 

[2] 
"http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4"
[3] 
"http://bioconductor.org/packages/1.9/data/experiment/bin/windows/contrib/2.4"
[4] 
"http://bioconductor.org/packages/1.9/omegahat/bin/windows/contrib/2.4" 

[5] 
"http://bioconductor.org/packages/1.9/monograph/bin/windows/contrib/2.4" 

[6] "http://cran.fhcrc.org/bin/windows/contrib/2.4" 

 > ap<-available.packages(contriburl=cu)

Warning: unable to access index for repository 
http://bioconductor.org/packages/1.9/monograph/bin/windows/contrib/2.4

 > length(ap)

[1] 8676

 > mi<-match("mouse4302",ap[,"Package"])
 > mi

[1] NA

 > sessionInfo()

R version 2.4.0 Under development (unstable) (2006-08-14 r38872)
i386-pc-mingw32

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils" 
"datasets"  "base"

 >

-------------

Questions:
1. Is the warning from R2.4.0 being unable to access the monograph 
repository expected.

2. I do not have any of the annotation packages in the output from 
R2.4.0, whereas I do under R2.3.1. Can the windows binary versions of 
these packages be made available?

3. Alternatively will the R2.3.1 windows binary versions of the 
annotation packages work for R2.4.0?

Note also that when running bioclite(), it reports:
Warning: unable to access index for repository 
http://bioconductor.org/packages/1.9/monograph/bin/windows/contrib/2.4
dependency ''hgu95av2'' is not available

thanks for any response,

Keith Satterley
Bioinformatics
WEHI

Hi Keith,

As James W. MacDonald posted here recently:

    The binary metaData packages are typically not built until close to
    release time for the devel branch. For those using
    R-devel/BioC-devel, a
    certain level of expertise is assumed, which (in this case) includes
    the
    ability to compile source packages.

You might try to use BioC 1.8 windows binary versions of the annotation packages with
R 2.4.0 though and they will probably work... (but we can't
guarantee it)

After some discussion here, we are going to try and build Windows
binaries for the devel experiment and annotation packages to encourage
developers to use R-devel earlier rather than later.