BioC 3.0: CHECK report for ballgown on oaxaca

Package: ballgown

Version: 1.0.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ballgown_1.0.4.tar.gz

StartedAt: 2015-04-09 21:33:08 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:40:03 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 415.3 seconds

RetCode: 0

Status:  OK

CheckDir: ballgown.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ballgown_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ballgown.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ballgown/DESCRIPTION’ ... OK
* this is package ‘ballgown’ version ‘1.0.4’
* 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 ‘ballgown’ can be installed ... [30s/32s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [42s/43s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
annotate_assembly 6.236   0.07   6.441
ballgownrsem      4.923   0.04   5.152
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [55s/59s]
 [55s/59s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

* installing *source* package ‘ballgown’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘structure’ in package ‘ballgown’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ballgown)

name	user	system	elapsed
annotate_assembly	6.236	0.070	6.441
ballgown-class	0.106	0.006	0.113
ballgown-constructor	0.587	0.012	0.736
ballgownrsem	4.923	0.040	5.152
bg	0.047	0.005	0.052
checkAssembledTx	0.001	0.000	0.001
clusterTranscripts	0.248	0.005	0.257
collapseTranscripts	0.396	0.010	0.408
contains	3.403	0.034	3.505
dirs	0.039	0.006	0.046
eexpr	0.045	0.005	0.054
expr-replace	0.045	0.005	0.053
expr	0.037	0.006	0.045
exprfilter	0.105	0.007	0.113
geneIDs	0.040	0.007	0.048
geneNames	1.592	0.013	1.622
getAttributeField	2.297	0.009	2.371
getGenes	1.547	0.013	1.563
gexpr	0.141	0.005	0.147
gffRead	0.420	0.001	0.424
gffReadGR	2.172	0.014	2.188
iexpr	0.041	0.003	0.044
indexes-replace	0.037	0.003	0.041
indexes	0.039	0.003	0.043
last	0.002	0.001	0.002
mergedDate	0.038	0.003	0.041
pData-replace	0.040	0.003	0.042
pData	0.039	0.003	0.042
pctOverlap	1.494	0.008	1.506
plotLatentTranscripts	0.001	0.000	0.000
plotMeans	0.000	0.000	0.001
plotTranscripts	0.000	0.000	0.001
sampleNames	0.039	0.003	0.042
seqnames	0.039	0.003	0.042
stattest	0.102	0.005	0.108
structure	0.085	0.004	0.089
subset	0.155	0.003	0.159
texpr	0.039	0.003	0.043
transcriptIDs	0.038	0.003	0.041
transcriptNames	0.040	0.003	0.043
writeFiles	0	0	0