BioC 3.1: CHECK report for ballgown on petty

Package: ballgown

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ballgown_2.0.0.tar.gz

StartedAt: 2015-10-08 21:33:40 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 21:40:38 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 418.8 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 ballgown_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ballgown.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ballgown/DESCRIPTION’ ... OK
* this is package ‘ballgown’ version ‘2.0.0’
* 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/30s] 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 ... NOTE
subset,ballgown : .local: no visible binding for global variable ‘i_id’
subset,ballgown : .local: no visible binding for global variable ‘e_id’
subset,ballgown : .local: no visible binding for global variable ‘t_id’
* 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 ... [51s/52s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ballgownrsem      8.340  0.053   8.411
annotate_assembly 7.599  0.095   7.697
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [65s/66s]
 [66s/67s] 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/ballgown.Rcheck/00check.log’
for details.

* installing *source* package ‘ballgown’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (ballgown)

name	user	system	elapsed
annotate_assembly	7.599	0.095	7.697
ballgown-class	0.127	0.007	0.134
ballgown-constructor	0.472	0.022	0.734
ballgownrsem	8.340	0.053	8.411
bg	0.051	0.011	0.061
checkAssembledTx	0.001	0.000	0.000
clusterTranscripts	0.275	0.010	0.285
collapseTranscripts	0.449	0.012	0.462
contains	4.810	0.026	4.930
dirs	0.053	0.005	0.060
eexpr	0.056	0.006	0.063
expr-replace	0.048	0.005	0.054
expr	0.044	0.006	0.050
exprfilter	0.134	0.006	0.141
geneIDs	0.055	0.007	0.062
geneNames	1.863	0.014	1.882
getAttributeField	3.016	0.007	3.029
getGenes	1.589	0.009	1.599
gexpr	0.190	0.008	0.197
gffRead	0.616	0.001	0.630
gffReadGR	2.703	0.025	2.786
iexpr	0.057	0.009	0.068
indexes-replace	0.054	0.008	0.062
indexes	0.056	0.007	0.063
last	0.001	0.000	0.001
mergedDate	0.054	0.007	0.060
pData-replace	0.057	0.006	0.063
pData	0.055	0.008	0.061
pctOverlap	2.274	0.014	2.338
plotLatentTranscripts	0.001	0.000	0.001
plotMeans	0.001	0.000	0.001
plotTranscripts	0.001	0.001	0.001
sampleNames	0.052	0.007	0.061
seqnames	0.054	0.006	0.061
stattest	0.142	0.007	0.153
structure	0.111	0.006	0.120
subset	0.213	0.007	0.220
tGene	0.065	0.006	0.073
texpr	0.056	0.005	0.061
transcriptIDs	0.052	0.006	0.058
transcriptNames	0.054	0.007	0.061
writeFiles	0.000	0.001	0.000