[BioC] error in getMonograph() - many packages not available

[Jenny Drnevich]

Hi Robert and others,

Your new book looks great, and I can't wait until I can get a copy - 
literally. About a month ago, I downloaded all the packages using 
getMonograph(), version 1.2.2, although I then got so busy I couldn't check 
it out. I just now tried running through an R script from the first 
chapter, and ran into the same problem that was posted on the list serve on 
July 25, 2005, but there was no response:

 > library("RbcBook1")
Error in open.connection(con, "rb") : unable to open connection
In addition: Warning message:
cannot open compressed file 'C:/PROGRA~1/R/rw2011/library/RbcBook1/R/all.rda'
Error in library("RbcBook1") : .First.lib failed for 'RbcBook1'
 > sessionInfo()
R version 2.1.1, 2005-06-20, i386-pc-mingw32

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

other attached packages:
  RColorBrewer SpikeInSubset          affy    reposTools       Biobase
       "0.2-3"       "1.0.1"       "1.6.7"      "1.5.19"      "1.5.12"


I also have R 2.2 and Bioconductor 1.7, so today I tried using 
getMonograph(), version 1.3 to download the newest versions of the 
packages. However, most of the packages are no longer available from the 
specified repositories:

 > source("http://www.bioconductor.org/getMonograph.R")
 > getMonograph()
Running getMonograph version 1.3.0  with R version  2.2.0
Warning: unable to access index for repository 
http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.2
Warning: unable to access index for repository 
http://www.bioconductor.org/packages/data/experiment/stable/bin/windows/contrib/2.2
Warning: unable to access index for repository 
http://www.bioconductor.org/packages/omegahat/stable/bin/windows/contrib/2.2
Warning: unable to access index for repository 
http://www.bioconductor.org/packages/lindsey/stable/bin/windows/contrib/2.2
Warning: unable to access index for repository 
http://www.bioconductor.org/packages/monograph/1.1/bin/windows/contrib/2.2
dependencies ''affycomp'' are not availabledependencies ''affydata'' are 
not availabledependencies ''affypdnn'' are not availabledependencies 
''affyPLM'' are not availabledependencies ''ALL'' are not 
availabledependencies ''ALLMLL'' are not availabledependencies 
''AmpAffyExample'' are not availabledependencies ''annaffy'' are not 
availabledependencies ''AnnBuilder'' are not availabledependencies 
''annotate'' are not availabledependencies ''arrayMagic'' are not 
availabledependencies ''arrayQuality'' are not availabledependencies 
''beta7'' are not availabledependencies ''Biobase'' are not 
availabledependencies ''bioDist'' are not availabledependencies 
''Biostrings'' are not availabledependencies ''CoCiteStats'' are not 
availabledependencies ''convert'' are not availabledependencies ''edd'' are 
not availabledependencies ''estrogen'' are not availabledependencies 
''facsDorit'' are not availabledependencies ''factDesign'' are not 
availabledependencies ''gcrma'' are not availabledependencies 
''geneplotter'' are not availabledependencies ''golubEsets'' are not 
availabledependencies ''GOstats'' are not availabledependencies ''graph'' 
are not availabledependencies ''hexbin'' are not availabledependencies 
''hgu2beta7'' are not availabledependencies ''KEGGSOAP'' are not 
availabledependencies ''kidpack'' are not availabledependencies 
''LogitBoost'' are not availabledependencies ''matchprobes'' are not 
availabledependencies ''MLInterfaces'' are not availabledependencies 
''prada'' are not availabledependencies ''PROcess'' are not 
availabledependencies ''ProData'' are not availabledependencies 
''RbcBook1'' are not availabledependencies ''RBGL'' are not 
availabledependencies ''RCurl'' are not availabledependencies 
''reposTools'' are not availabledependencies ''Rgraphviz'' are not 
availabledependencies ''simpleaffy'' are not availabledependencies 
''SpikeInSubset'' are not availabledependencies ''SSOAP'' are not 
availabledependencies ''vsn'' are not availabledependencies 
''yeastExpData'' are not available

 > sessionInfo()
R version 2.2.0, 2005-10-06, i386-pc-mingw32

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

other attached packages:
RColorBrewer         affy      Biobase      RWinEdt   hgu133acdf
      "0.2-3"      "1.8.1"      "1.8.0"      "1.7-3"      "1.5.1"


Is this a problem related to the new release of Bioconductor? What can be 
done to get getMonograph() to work?

Thanks,
Jenny



Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu