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BioC 3.5: CHECK report for LOLA on veracruz2

This page was generated on 2017-08-16 13:33:34 -0400 (Wed, 16 Aug 2017).

Package 726/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOLA 1.6.0
Nathan Sheffield
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/LOLA
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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: 2017-08-16 04:39:41 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:41:17 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 96.5 seconds
RetCode: 0
Status:  OK 
CheckDir: LOLA.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LOLA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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.


LOLA.Rcheck/00install.out:

* 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)

LOLA.Rcheck/LOLA-Ex.timings:

nameusersystemelapsed
buildRestrictedUniverse0.6840.0140.705
checkUniverseAppropriateness0.3980.0030.407
extractEnrichmentOverlaps4.4290.3673.590
getRegionSet2.0960.2941.436
listRegionSets0.0980.0390.048
loadRegionDB0.4290.0610.277
mergeRegionDBs0.3690.0280.332
readBed0.0090.0000.008
readCollection0.1040.0030.107
readCollectionAnnotation0.0030.0000.004
readCollectionFiles0.0120.0010.013
readRegionGRL0.3640.0200.241
readRegionSetAnnotation0.0520.0130.042
redefineUserSets2.0940.1251.624
runLOLA1.8480.1631.407
setSharedDataDir0.0010.0000.001
splitFileIntoCollection0.0160.0050.013
userSets0.0010.0000.001
writeCombinedEnrichment1.7980.1351.488