Package: GenomicRanges

Version: 1.2.3

Command: chmod a+r GenomicRanges -R && E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD build --keep-empty-dirs GenomicRanges

StartedAt: 2011-04-07 05:02:57 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 05:05:30 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 152.6 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

Warning: unknown option '--keep-empty-dirs'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* preparing 'GenomicRanges':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, table

Loading required package: Biostrings
Loading required package: ShortRead
Loading required package: lattice
Loading required package: rtracklayer
Loading required package: RCurl
Loading required package: bitops
Download the sgdGene table ... OK
Download the sgdIsoforms table ... OK
Download the sgdCanonical table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... 
Error: processing vignette 'GenomicRangesUseCases.Rnw' failed with diagnostics:
 chunk 20 (label=GetAnnoations) 
Error in download.file(url, destfile, quiet = TRUE) : 
  cannot open URL 'http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/database/chromInfo.txt.gz'
In addition: Warning messages:
1: In `start<-`(`*tmp*`, value = c(8L, -8L, -7L, 17L)) :
  trimmed start values to be positive
2: In `start<-`(`*tmp*`, value = c(-9L, 9L, 10L, 0L)) :
  trimmed start values to be positive
3: In `start<-`(`*tmp*`, value = c(-22L, 2L, 3L, -13L)) :
  trimmed start values to be positive
4: In `end<-`(`*tmp*`, check = FALSE, value = c(139L, 142L, 143L, 149L,  :
  trimmed end values to be <= seqlengths
5: In `end<-`(`*tmp*`, value = c(200L, 203L, 204L, 210L, 215L, 219L,  :
  trimmed end values to be <= seqlengths
6: In download.file(url, destfile, quiet = TRUE) :
  cannot open: HTTP status was '0 (nil)'
Execution halted