[Rd] issue with update.packages()

[Dan Tenenbaum]

Hello,

I see the following issue in R-devel since 'both' has become the default pkgType for binary platforms.

update.packages() fails when you set options(repos). Looks like it is trying to download a tgz file from the src/contrib section of a repository (on a mac).

To reproduce this you need to have an older version of AnnotationDbi installed, which I accomplished by faking it, installing pkgKitten and then doing:

library(pkgKitten)
kitten("AnnotationDbi")

Then exiting R and doing

R CMD INSTALL AnnotationDbi.

Here's the problem:

> packageVersion("AnnotationDbi")
[1] ‘1.0’
> options(repos=structure(c("http://bioconductor.org/packages/3.1/bioc", "http://bioconductor.org/packages/3.1/data/annotation", 
+ "http://bioconductor.org/packages/3.1/data/experiment", "http://bioconductor.org/packages/3.1/extra", 
+ "http://cran.fhcrc.org"), .Names = c("BioCsoft", "BioCann", "BioCexp", 
+ "BioCextra", "CRAN")))
> update.packages(oldPkgs="AnnotationDbi")
AnnotationDbi :
 Version 1.0 installed in /Library/Frameworks/R.framework.develMav/Versions/3.2/Resources/library 
 Version 1.29.17 available at http://bioconductor.org/packages/3.1/bioc
Update (y/N/c)?  y
also installing the dependencies ‘IRanges’, ‘BiocGenerics’, ‘Biobase’, ‘GenomeInfoDb’, ‘DBI’, ‘RSQLite’, ‘S4Vectors’

trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.1.35.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.1.35.tgz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘IRanges’ failed
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocGenerics_0.13.4.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocGenerics_0.13.4.tgz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘BiocGenerics’ failed
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/Biobase_2.27.1.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/Biobase_2.27.1.tgz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘Biobase’ failed
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/GenomeInfoDb_1.3.12.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/GenomeInfoDb_1.3.12.tgz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘GenomeInfoDb’ failed
trying URL 'http://cran.fhcrc.org/src/contrib/DBI_0.3.1.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.fhcrc.org/src/contrib/DBI_0.3.1.tgz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘DBI’ failed
trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_1.0.0.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.fhcrc.org/src/contrib/RSQLite_1.0.0.tgz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘RSQLite’ failed
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/S4Vectors_0.5.16.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/S4Vectors_0.5.16.tgz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘S4Vectors’ failed
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/AnnotationDbi_1.29.17.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/AnnotationDbi_1.29.17.tgz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘AnnotationDbi’ failed
> sessionInfo()
R Under development (unstable) (2015-01-22 r67580)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] tools_3.2.0

Thanks,
Dan