BioC 3.2: CHECK report for ballgown on oaxaca

Package: ballgown

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ballgown_2.2.0.tar.gz

StartedAt: 2016-04-22 21:57:48 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:02:29 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 280.2 seconds

RetCode: 0

Status:  OK

CheckDir: ballgown.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ballgown_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ballgown.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘2.2.0’
* 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 ... [21s/21s] 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 ... [31s/31s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [37s/37s]
 [37s/37s] 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-3.2-bioc/meat/ballgown.Rcheck/00check.log’
for details.

* 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	4.442	0.104	4.550
ballgown-class	0.091	0.006	0.098
ballgown-constructor	0.529	0.017	0.548
ballgownrsem	4.131	0.068	4.200
bg	0.037	0.004	0.040
checkAssembledTx	0	0	0
clusterTranscripts	0.179	0.004	0.183
collapseTranscripts	0.347	0.005	0.352
contains	2.703	0.031	2.736
dirs	0.033	0.005	0.038
eexpr	0.038	0.005	0.042
expr-replace	0.043	0.005	0.048
expr	0.036	0.005	0.040
exprfilter	0.081	0.004	0.085
geneIDs	0.039	0.006	0.045
geneNames	0.877	0.009	0.886
getAttributeField	1.468	0.001	1.470
getGenes	0.893	0.007	0.900
gexpr	0.140	0.006	0.146
gffRead	0.398	0.001	0.400
gffReadGR	0.912	0.007	0.918
iexpr	0.036	0.005	0.041
indexes-replace	0.033	0.005	0.039
indexes	0.038	0.006	0.044
last	0.001	0.000	0.001
mergedDate	0.038	0.006	0.045
pData-replace	0.052	0.007	0.059
pData	0.036	0.004	0.040
pctOverlap	1.088	0.032	1.120
plotLatentTranscripts	0	0	0
plotMeans	0.000	0.000	0.001
plotTranscripts	0.000	0.000	0.001
sampleNames	0.038	0.005	0.043
seqnames	0.037	0.005	0.042
stattest	0.100	0.006	0.106
structure	0.064	0.005	0.069
subset	0.136	0.005	0.141
tGene	0.040	0.005	0.045
texpr	0.044	0.005	0.050
transcriptIDs	0.037	0.005	0.043
transcriptNames	0.035	0.006	0.042
writeFiles	0.001	0.000	0.000