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BioC 3.5: CHECK report for LOLA on toluca2

This page was generated on 2017-04-23 14:40:28 -0400 (Sun, 23 Apr 2017).

Package 724/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOLA 1.5.0
Nathan Sheffield
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LOLA
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 
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: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LOLA_1.5.0.tar.gz
StartedAt: 2017-04-23 05:56:44 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 05:58:38 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 113.4 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LOLA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LOLA/DESCRIPTION’ ... OK
* this is package ‘LOLA’ version ‘1.5.0’
* 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
buildRestrictedUniverse0.6160.0190.640
checkUniverseAppropriateness0.4870.0030.494
extractEnrichmentOverlaps4.2480.0724.476
getRegionSet1.7690.0562.022
listRegionSets0.0400.0140.060
loadRegionDB0.3170.0190.352
mergeRegionDBs0.3440.0220.375
readBed0.0120.0000.012
readCollection0.1760.0060.183
readCollectionAnnotation0.0060.0000.006
readCollectionFiles0.0140.0010.015
readRegionGRL0.2940.0180.313
readRegionSetAnnotation0.0340.0140.050
redefineUserSets1.7060.0481.965
runLOLA1.9250.0442.115
setSharedDataDir0.0010.0000.001
splitFileIntoCollection0.0110.0010.012
userSets0.0010.0010.001
writeCombinedEnrichment1.7270.0391.892