[BioC] Can't get arrayMagic to work under R 2.0.0?

[Glynn, Earl]

arrayMagic didn't work on Monday right after R 2.0.0 was introduced -- I
thought perhaps one or more of the libraries had not been updated or
propagated.  So I tried re-installing arrrayMagic today and I get the
same error:

Error in library(arrayMagic) : 'arrayMagic' is not a valid package --
installed < 2.0.0?
In addition: Warning messages: 

I can install all the R packages without any problems, but when I try to
install all the Bioconductor packages under R 1.9.1, or now under R
2.0.0, there are multiple errors:

Under Windows 2000 using R 2.0.0:
Packages | Install Package(s) from Bioconductor  ...
<select all packages>
OK

package 'AnnBuilder' successfully unpacked and MD5 sums checked
package 'Biobase' successfully unpacked and MD5 sums checked
package 'Biostrings' successfully unpacked and MD5 sums checked
package 'DNAcopy' successfully unpacked and MD5 sums checked
package 'DynDoc' successfully unpacked and MD5 sums checked
package 'EBarrays' successfully unpacked and MD5 sums checked
package 'GOstats' successfully unpacked and MD5 sums checked
package 'GeneSpring' successfully unpacked and MD5 sums checked
package 'GeneTS' successfully unpacked and MD5 sums checked
package 'Icens' successfully unpacked and MD5 sums checked
package 'LPE' successfully unpacked and MD5 sums checked
package 'MeasurementError.cor' successfully unpacked and MD5 sums
checked
files Test/122402imac40-s-c-192combined,
8c35faef7efd8c7696b730103ecb3cfa, i12.csv,
calibration/060503peptidecalib, 4a1e5042bb765e36c922faf753312d5c,
1_16.csv, calibration/060503peptidecalib,
affbdb67631df9b75d6922239aff3bbf, 1_256.csv,
calibration/060503peptidecalib, b84492123d2ad458c74c68e22bc923f9,
1_4.csv, calibration/060503peptidecalib,
9a655d25045d1a710e3c0cfe4bb3a3d7, 1_8.csv are missing
package 'RBGL' successfully unpacked and MD5 sums checked
package 'RMAGEML' successfully unpacked and MD5 sums checked
package 'ROC' successfully unpacked and MD5 sums checked
package 'RSNPper' successfully unpacked and MD5 sums checked
Error in file(file, "r") : unable to open connection
In addition: Warning messages: 
1: downloaded length 140288 != reported length 71958672 
2: downloaded length 24576 != reported length 13097356 
3: error 1 in extracting from zip file 
4: cannot open file `RdbiPgSQL/DESCRIPTION' 

I re-installed arrayMagic from the downloaded ZIPs (Packages | Install
Packages from Local ZIPs):

> install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
package 'aCGH' successfully unpacked and MD5 sums checked
package 'affy' successfully unpacked and MD5 sums checked
Error in file(file, "r") : unable to open connection
In addition: Warning messages: 
1: error 1 in extracting from zip file 
2: cannot open file `affycomp/DESCRIPTION' 

Any suggestions on how to get all the Bioconductor packages installed,
and specifically arrayMagic, using R 2.0.0?

efg
--
Earl F. Glynn    
Stowers Institute for Medical Research


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