Package: xmapcore

Version: 1.7.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings xmapcore_1.7.1.tar.gz

StartedAt: 2011-07-07 02:36:11 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:37:38 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 86.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: xmapcore.Rcheck

Warnings: NA

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/xmapcore.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xmapcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘xmapcore’ version ‘1.7.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘xmapcore’ can be installed ... OK
* checking installed package size ... 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 ‘doRUnit.R’
 ERROR
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  Number of failures: 0 
  
   
  1 Test Suite : 
  xmapcore unit testing - 28 test functions, 1 error, 0 failures
  ERROR in test.databases.txt: Error in mysqlNewConnection(drv, ...) : 
    RS-DBI driver: (Failed to connect to database: Error: Can't connect to local MySQL server through socket '/var/run/mysql/mysql.sock' (2)
  )
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted

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

Attaching package: ‘IRanges’

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

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

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘INSTALL.Rnw’ 
   ‘xmapcore.Rnw’ 
** testing if installed package can be loaded

* DONE (xmapcore)

name	user	system	elapsed
xmapcore.all	0	0	0
xmapcore.details	0	0	0
xmapcore.env	0	0	0
xmapcore.filters	0.000	0.000	0.001
xmapcore.range	0	0	0
xmapcore.to	0.000	0.004	0.001
xmapcore.utils	0.000	0.000	0.001
xmapcore.utr	0	0	0