BioC 3.2: CHECK report for ballgown on perceval

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 22:21:30 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:27:35 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 364.7 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_2.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ballgown.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘2.1.1’
* 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 ... [26s/26s] 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 ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ballgownrsem      6.224  0.061   6.327
annotate_assembly 5.668  0.194   5.875
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [45s/45s]
 [46s/46s] 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	5.668	0.194	5.875
ballgown-class	0.084	0.010	0.093
ballgown-constructor	0.289	0.023	0.313
ballgownrsem	6.224	0.061	6.327
bg	0.802	0.012	0.821
checkAssembledTx	0.001	0.000	0.001
clusterTranscripts	0.180	0.006	0.186
collapseTranscripts	0.309	0.005	0.315
contains	2.556	0.016	2.579
dirs	0.037	0.008	0.046
eexpr	0.037	0.004	0.041
expr-replace	0.040	0.004	0.044
expr	0.032	0.004	0.036
exprfilter	0.107	0.005	0.111
geneIDs	0.034	0.005	0.039
geneNames	1.250	0.009	1.262
getAttributeField	1.564	0.006	1.597
getGenes	1.329	0.007	1.338
gexpr	0.111	0.004	0.114
gffRead	0.328	0.001	0.331
gffReadGR	1.725	0.009	1.737
iexpr	0.034	0.004	0.038
indexes-replace	0.033	0.005	0.038
indexes	0.034	0.005	0.040
last	0.000	0.000	0.001
mergedDate	0.032	0.005	0.037
pData-replace	0.036	0.005	0.041
pData	0.033	0.005	0.039
pctOverlap	2.157	0.012	2.170
plotLatentTranscripts	0.000	0.000	0.001
plotMeans	0.001	0.000	0.000
plotTranscripts	0	0	0
sampleNames	0.033	0.004	0.037
seqnames	0.033	0.004	0.037
stattest	0.095	0.005	0.100
structure	0.061	0.005	0.066
subset	0.133	0.005	0.137
tGene	0.043	0.005	0.049
texpr	0.033	0.004	0.037
transcriptIDs	0.034	0.005	0.040
transcriptNames	0.034	0.005	0.039
writeFiles	0.001	0.000	0.001