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Package 171/419HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicRanges 1.2.3
Biocore Team c/o BioC user list
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/GenomicRanges
Last Changed Rev: 51795 / Revision: 54588
Last Changed Date: 2011-01-06 15:25:01 -0800 (Thu, 06 Jan 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64 [ ERROR ] skipped  skipped 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 

Summary

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

Command output

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