BioC 3.2: CHECK report for ballgown on perceval

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: 2015-11-10 02:20:19 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:25:42 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 323.3 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 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [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 ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ballgownrsem      6.763  0.033   6.797
annotate_assembly 5.291  0.113   5.428
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [43s/43s]
 [44s/44s] 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	5.291	0.113	5.428
ballgown-class	0.098	0.003	0.102
ballgown-constructor	0.309	0.013	0.321
ballgownrsem	6.763	0.033	6.797
bg	0.038	0.005	0.042
checkAssembledTx	0.001	0.000	0.001
clusterTranscripts	0.223	0.005	0.228
collapseTranscripts	0.298	0.003	0.301
contains	3.314	0.011	3.325
dirs	0.039	0.005	0.045
eexpr	0.041	0.006	0.046
expr-replace	0.044	0.005	0.049
expr	0.038	0.005	0.043
exprfilter	0.094	0.006	0.099
geneIDs	0.039	0.006	0.045
geneNames	1.433	0.010	1.444
getAttributeField	1.649	0.001	1.651
getGenes	1.901	0.010	1.910
gexpr	0.120	0.006	0.126
gffRead	0.359	0.001	0.360
gffReadGR	1.869	0.009	1.878
iexpr	0.039	0.006	0.045
indexes-replace	0.038	0.006	0.043
indexes	0.040	0.005	0.045
last	0.001	0.000	0.000
mergedDate	0.037	0.006	0.044
pData-replace	0.039	0.006	0.045
pData	0.038	0.006	0.045
pctOverlap	1.466	0.009	1.476
plotLatentTranscripts	0.000	0.000	0.001
plotMeans	0.001	0.000	0.001
plotTranscripts	0.000	0.000	0.001
sampleNames	0.037	0.005	0.043
seqnames	0.038	0.005	0.043
stattest	0.097	0.007	0.104
structure	0.068	0.006	0.076
subset	0.150	0.006	0.156
tGene	0.045	0.007	0.051
texpr	0.040	0.006	0.046
transcriptIDs	0.037	0.006	0.045
transcriptNames	0.039	0.006	0.046
writeFiles	0	0	0