BioC 3.3: CHECK report for ballgown on linux2.bioconductor.org

Package: ballgown

Version: 2.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ballgown_2.3.0.tar.gz

StartedAt: 2015-10-27 01:50:52 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:54:42 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 230.2 seconds

RetCode: 0

Status:  OK

CheckDir: ballgown.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ballgown_2.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ballgown.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.3.0’
* 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 ... [18s/18s] 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: no visible binding for global variable ‘i_id’
subset,ballgown: no visible binding for global variable ‘e_id’
subset,ballgown: no visible binding for global variable ‘t_id’
Undefined global functions or variables:
  e_id i_id 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 ... [27s/27s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [33s/33s]
 [33s/33s] 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-3.3-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	3.963	0.056	4.018
ballgown-class	0.089	0.000	0.088
ballgown-constructor	0.327	0.008	0.334
ballgownrsem	3.915	0.016	3.929
bg	0.033	0.008	0.044
checkAssembledTx	0.000	0.000	0.001
clusterTranscripts	0.207	0.000	0.207
collapseTranscripts	0.221	0.000	0.221
contains	2.358	0.052	2.410
dirs	0.043	0.000	0.043
eexpr	0.046	0.000	0.047
expr-replace	0.047	0.000	0.047
expr	0.039	0.000	0.039
exprfilter	0.097	0.000	0.098
geneIDs	0.045	0.000	0.044
geneNames	1.069	0.004	1.073
getAttributeField	1.883	0.000	1.884
getGenes	1.059	0.000	1.059
gexpr	0.075	0.000	0.075
gffRead	0.386	0.004	0.390
gffReadGR	1.117	0.004	1.121
iexpr	0.040	0.004	0.044
indexes-replace	0.044	0.000	0.043
indexes	0.041	0.004	0.044
last	0.001	0.000	0.001
mergedDate	0.043	0.000	0.043
pData-replace	0.046	0.000	0.045
pData	0.040	0.004	0.045
pctOverlap	1.112	0.004	1.116
plotLatentTranscripts	0.000	0.000	0.001
plotMeans	0	0	0
plotTranscripts	0.000	0.000	0.001
sampleNames	0.042	0.000	0.043
seqnames	0.043	0.000	0.044
stattest	0.104	0.000	0.104
structure	0.072	0.004	0.077
subset	0.147	0.000	0.148
tGene	0.049	0.000	0.049
texpr	0.055	0.004	0.058
transcriptIDs	0.04	0.00	0.04
transcriptNames	0.044	0.000	0.043
writeFiles	0.000	0.000	0.001