BioC 3.5: CHECK report for LOLA on veracruz2

Package: LOLA

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LOLA_1.6.0.tar.gz

StartedAt: 2017-10-18 05:24:59 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:26:29 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 90.4 seconds

RetCode: 0

Status:  OK

CheckDir: LOLA.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 LOLA_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LOLA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LOLA/DESCRIPTION’ ... OK
* this is package ‘LOLA’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘simpleCache’
* 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 ‘LOLA’ can be installed ... 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
readCollectionAnnotation: no visible global function definition for
  ‘setNames’
readCollectionFiles: no visible global function definition for
  ‘write.table’
runLOLA: no visible global function definition for ‘fisher.test’
write.tsv: no visible global function definition for ‘write.table’
writeCombinedEnrichment: no visible global function definition for
  ‘write.table’
writeDataTableSplitByColumn : <anonymous>: no visible global function
  definition for ‘write.table’
Undefined global functions or variables:
  fisher.test setNames write.table
Consider adding
  importFrom("stats", "fisher.test", "setNames")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/LOLA.Rcheck/00check.log’
for details.

* installing *source* package ‘LOLA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LOLA)

name	user	system	elapsed
buildRestrictedUniverse	0.594	0.016	0.624
checkUniverseAppropriateness	0.373	0.004	0.397
extractEnrichmentOverlaps	4.549	0.385	3.641
getRegionSet	2.161	0.263	1.456
listRegionSets	0.093	0.035	0.048
loadRegionDB	0.500	0.091	0.272
mergeRegionDBs	0.401	0.023	0.282
readBed	0.007	0.000	0.008
readCollection	0.127	0.008	0.142
readCollectionAnnotation	0.004	0.001	0.004
readCollectionFiles	0.011	0.000	0.012
readRegionGRL	0.385	0.019	0.257
readRegionSetAnnotation	0.052	0.014	0.041
redefineUserSets	1.978	0.186	1.366
runLOLA	2.088	0.257	1.315
setSharedDataDir	0.002	0.001	0.000
splitFileIntoCollection	0.029	0.004	0.009
userSets	0.002	0.001	0.001
writeCombinedEnrichment	2.328	0.247	1.522