BioC 3.2: CHECK report for ballgown on oaxaca

Package: ballgown

Version: 2.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ballgown_2.1.1.tar.gz

StartedAt: 2015-08-23 21:47:50 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 21:53:06 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 316.1 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_2.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘2.1.1’
* 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 ... [24s/24s] 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 ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
annotate_assembly 5.828  0.115   6.014
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [47s/47s]
 [47s/47s] 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	5.828	0.115	6.014
ballgown-class	0.101	0.004	0.105
ballgown-constructor	0.592	0.015	0.615
ballgownrsem	4.199	0.046	4.368
bg	0.039	0.004	0.043
checkAssembledTx	0	0	0
clusterTranscripts	0.221	0.004	0.226
collapseTranscripts	0.362	0.007	0.382
contains	2.831	0.020	2.887
dirs	0.039	0.003	0.042
eexpr	0.042	0.003	0.045
expr-replace	0.045	0.004	0.049
expr	0.040	0.003	0.042
exprfilter	0.103	0.004	0.107
geneIDs	0.039	0.003	0.043
geneNames	1.463	0.025	1.489
getAttributeField	1.790	0.004	1.801
getGenes	1.424	0.016	1.444
gexpr	0.126	0.005	0.133
gffRead	0.433	0.002	0.435
gffReadGR	1.803	0.015	1.822
iexpr	0.040	0.005	0.045
indexes-replace	0.039	0.005	0.044
indexes	0.040	0.005	0.045
last	0.001	0.000	0.001
mergedDate	0.035	0.006	0.040
pData-replace	0.401	0.011	0.414
pData	0.039	0.006	0.044
pctOverlap	1.401	0.017	1.420
plotLatentTranscripts	0.000	0.000	0.001
plotMeans	0.001	0.000	0.001
plotTranscripts	0.001	0.000	0.001
sampleNames	0.040	0.005	0.045
seqnames	0.038	0.006	0.043
stattest	0.095	0.006	0.101
structure	0.077	0.006	0.083
subset	0.144	0.005	0.150
tGene	0.046	0.005	0.051
texpr	0.040	0.006	0.046
transcriptIDs	0.038	0.006	0.044
transcriptNames	0.040	0.006	0.046
writeFiles	0.000	0.000	0.001