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Package 170/419HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicFeatures 1.2.5
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/GenomicFeatures
Last Changed Rev: 53414 / Revision: 54588
Last Changed Date: 2011-03-03 10:42:18 -0800 (Thu, 03 Mar 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ ERROR ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  OK 

Summary

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

Command output

* 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

GenomicFeatures.Rcheck/00install.out:

* 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)

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings:

nameusersystemelapsed
DEFAULT_CIRC_SEQS0.0000.0000.001
TranscriptDb-class1.0920.0361.142
extractTranscriptsFromGenome55.815 7.39668.064
id2name0.2160.0040.222
makeTranscriptDb0.2730.0040.274
makeTranscriptDbFromBiomart 2.484 0.03619.573
makeTranscriptDbFromUCSC13.196 0.07637.896
regions1.3170.0681.384
saveFeatures0.0560.0000.059
transcripts0.6040.0000.604
transcriptsBy3.5080.0003.513
transcriptsByOverlaps0.6000.0040.601