BioC 3.1: CHECK report for ballgown on morelia

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 23:21:22 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:25:47 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 265.7 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_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ballgown.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.0.0’
* 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 ... [19s/19s] 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’ [39s/39s]
 [40s/40s] 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	4.538	0.164	4.705
ballgown-class	0.098	0.005	0.103
ballgown-constructor	0.474	0.027	0.501
ballgownrsem	3.811	0.143	3.957
bg	0.030	0.006	0.037
checkAssembledTx	0	0	0
clusterTranscripts	0.183	0.006	0.189
collapseTranscripts	0.353	0.031	0.386
contains	2.638	0.091	2.730
dirs	0.040	0.008	0.048
eexpr	0.045	0.002	0.047
expr-replace	0.044	0.003	0.047
expr	0.038	0.009	0.047
exprfilter	0.089	0.002	0.092
geneIDs	0.035	0.002	0.037
geneNames	1.055	0.045	1.100
getAttributeField	1.466	0.006	1.472
getGenes	1.439	0.104	1.544
gexpr	0.092	0.003	0.096
gffRead	0.259	0.000	0.259
gffReadGR	1.789	0.057	1.847
iexpr	0.039	0.004	0.043
indexes-replace	0.035	0.002	0.038
indexes	0.036	0.002	0.040
last	0.000	0.000	0.001
mergedDate	0.034	0.003	0.038
pData-replace	0.029	0.004	0.033
pData	0.035	0.004	0.040
pctOverlap	1.177	0.070	1.248
plotLatentTranscripts	0.000	0.001	0.000
plotMeans	0.001	0.000	0.000
plotTranscripts	0.001	0.000	0.000
sampleNames	0.036	0.013	0.049
seqnames	0.037	0.014	0.051
stattest	0.103	0.012	0.114
structure	0.059	0.013	0.072
subset	0.106	0.009	0.115
tGene	0.043	0.011	0.055
texpr	0.038	0.013	0.052
transcriptIDs	0.036	0.011	0.047
transcriptNames	0.039	0.013	0.053
writeFiles	0.001	0.000	0.001