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: 2013-03-25 01:41:27 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:51:11 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 583.3 seconds

RetCode: 0

Status:  OK

CheckDir: chimera.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/chimera.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [25s/25s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [337s/337s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotCoverage     150.159  1.578 151.881
fusionPeptides    55.172  1.010  56.254
class.fSet        42.447  0.849  43.330
chimeraSeqs       42.041  0.832  42.919
fusionName         8.562  0.249   8.823
filterList         8.056  0.257   8.320
importFusionData   6.616  0.265   6.954
supportingReads    6.187  0.225   6.670
* 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	42.041	0.832	42.919
class.fSet	42.447	0.849	43.330
filterList	8.056	0.257	8.320
fusionName	8.562	0.249	8.823
fusionPeptides	55.172	1.010	56.254
importFusionData	6.616	0.265	6.954
plotCoverage	150.159	1.578	151.881
supportingReads	6.187	0.225	6.670
tophatInstallation	0.003	0.005	0.008
tophatRun	0.003	0.005	0.010