Package: GenomicFeatures

Version: 1.2.5

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.2.5.tar.gz

StartedAt: 2011-04-07 06:39:37 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 06:44:50 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 313.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: GenomicFeatures.Rcheck

Warnings: NA

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/GenomicFeatures.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.2.5’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘GenomicFeatures’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’
 ERROR
Running the tests in ‘tests/GenomicFeatures_unit_tests.R’ failed.
Last 13 lines of output:
  GenomicFeatures RUnit Tests - 14 test functions, 0 errors, 1 failure
  FAILURE in test_makeTranscriptDbFromBiomart: Error in checkTrue(ok) : Test not TRUE
  
  
  Test files with failing tests
  
     test_makeTranscriptDbFromBiomart.R 
       test_makeTranscriptDbFromBiomart 
  
  
  Error in GenomicFeatures:::.test() : 
    unit tests failed for package GenomicFeatures
  Execution halted

* installing *source* package ‘GenomicFeatures’ ...
** R
** inst
** preparing package for lazy loading

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

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GenomicFeatures)

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0.000	0.000	0.001
TranscriptDb-class	1.092	0.036	1.142
extractTranscriptsFromGenome	55.815	7.396	68.064
id2name	0.216	0.004	0.222
makeTranscriptDb	0.273	0.004	0.274
makeTranscriptDbFromBiomart	2.484	0.036	19.573
makeTranscriptDbFromUCSC	13.196	0.076	37.896
regions	1.317	0.068	1.384
saveFeatures	0.056	0.000	0.059
transcripts	0.604	0.000	0.604
transcriptsBy	3.508	0.000	3.513
transcriptsByOverlaps	0.600	0.004	0.601