Package: chimera

Version: 1.0.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chimera_1.0.6.tar.gz

StartedAt: 2013-03-24 03:28:33 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 03:39:01 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 628.6 seconds

RetCode: 0

Status:  OK

CheckDir: chimera.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/chimera.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'chimera/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chimera' version '1.0.6'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'chimera' can be installed ... [30s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 installed files from 'inst/doc' ... OK
* checking examples ... [327s/332s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotCoverage     135.820  1.696 138.269
chimeraSeqs       45.621  0.821  46.876
fusionPeptides    44.223  0.970  48.005
class.fSet        43.111  0.855  44.153
filterList        11.156  0.195  11.382
fusionName        10.186  0.170  10.416
supportingReads    8.408  0.160   8.601
importFusionData   8.142  0.157   8.455
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'chimera' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'chimera.Rnw' 
** testing if installed package can be loaded
* DONE (chimera)

name	user	system	elapsed
chimeraSeqs	45.621	0.821	46.876
class.fSet	43.111	0.855	44.153
filterList	11.156	0.195	11.382
fusionName	10.186	0.170	10.416
fusionPeptides	44.223	0.970	48.005
importFusionData	8.142	0.157	8.455
plotCoverage	135.820	1.696	138.269
supportingReads	8.408	0.160	8.601
tophatInstallation	0.002	0.004	0.007
tophatRun	0.002	0.005	0.008