Package: chimera

Version: 1.0.6

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings chimera_1.0.6.tar.gz

StartedAt: 2013-03-25 00:41:20 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:52:13 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 652.7 seconds

RetCode: 0

Status:  OK

CheckDir: chimera.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/chimera.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [38s/38s] 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 ... [287s/292s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotCoverage     101.215  0.596 103.033
chimeraSeqs       42.558  0.668  44.196
fusionPeptides    39.355  0.360  40.482
class.fSet        37.587  0.432  39.047
filterList        11.956  0.052  12.477
importFusionData  11.220  0.028  11.541
fusionName        11.129  0.028  11.283
supportingReads   10.076  0.036  10.118
* 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	42.558	0.668	44.196
class.fSet	37.587	0.432	39.047
filterList	11.956	0.052	12.477
fusionName	11.129	0.028	11.283
fusionPeptides	39.355	0.360	40.482
importFusionData	11.220	0.028	11.541
plotCoverage	101.215	0.596	103.033
supportingReads	10.076	0.036	10.118
tophatInstallation	0.004	0.000	0.005
tophatRun	0.036	0.000	0.034