BioC 3.2: CHECK report for ballgown on linux1.bioconductor.org

Package: ballgown

Version: 2.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ballgown_2.2.0.tar.gz

StartedAt: 2015-10-27 01:10:59 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:15:06 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 246.7 seconds

RetCode: 0

Status:  OK

CheckDir: ballgown.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ballgown_2.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ballgown.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [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 ... [25s/25s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [34s/34s]
 [34s/34s] 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
  ‘/home/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	4.409	0.096	4.506
ballgown-class	0.065	0.004	0.069
ballgown-constructor	0.258	0.008	0.266
ballgownrsem	3.401	0.020	3.422
bg	0.043	0.000	0.044
checkAssembledTx	0.000	0.000	0.001
clusterTranscripts	0.142	0.000	0.142
collapseTranscripts	0.224	0.000	0.223
contains	2.743	0.007	2.749
dirs	0.042	0.001	0.044
eexpr	0.047	0.000	0.047
expr-replace	0.049	0.000	0.049
expr	0.043	0.000	0.043
exprfilter	0.105	0.000	0.105
geneIDs	0.042	0.004	0.044
geneNames	0.928	0.000	0.933
getAttributeField	0.973	0.000	0.973
getGenes	0.778	0.003	0.782
gexpr	0.132	0.000	0.131
gffRead	0.464	0.000	0.463
gffReadGR	0.903	0.000	0.903
iexpr	0.037	0.000	0.037
indexes-replace	0.043	0.000	0.043
indexes	0.045	0.000	0.045
last	0.001	0.000	0.001
mergedDate	0.043	0.000	0.043
pData-replace	0.046	0.000	0.046
pData	0.041	0.004	0.045
pctOverlap	0.721	0.000	0.722
plotLatentTranscripts	0	0	0
plotMeans	0	0	0
plotTranscripts	0	0	0
sampleNames	0.028	0.000	0.028
seqnames	0.028	0.000	0.028
stattest	0.062	0.004	0.067
structure	0.045	0.003	0.049
subset	0.089	0.005	0.093
tGene	0.032	0.000	0.032
texpr	0.029	0.000	0.029
transcriptIDs	0.037	0.000	0.037
transcriptNames	0.029	0.000	0.029
writeFiles	0	0	0