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BioC 3.5: CHECK report for LOLA on tokay2

This page was generated on 2017-08-16 13:24:54 -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: rm -rf LOLA.buildbin-libdir LOLA.Rcheck && mkdir LOLA.buildbin-libdir LOLA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LOLA.buildbin-libdir LOLA_1.6.0.tar.gz >LOLA.Rcheck\00install.out 2>&1 && cp LOLA.Rcheck\00install.out LOLA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=LOLA.buildbin-libdir --install="check:LOLA-install.out" --force-multiarch --no-vignettes --timings LOLA_1.6.0.tar.gz
StartedAt: 2017-08-16 00:52:20 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:57:04 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 283.2 seconds
RetCode: 0
Status:  OK  
CheckDir: LOLA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf LOLA.buildbin-libdir LOLA.Rcheck && mkdir LOLA.buildbin-libdir LOLA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LOLA.buildbin-libdir LOLA_1.6.0.tar.gz >LOLA.Rcheck\00install.out 2>&1 && cp LOLA.Rcheck\00install.out LOLA-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=LOLA.buildbin-libdir --install="check:LOLA-install.out" --force-multiarch --no-vignettes --timings LOLA_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/LOLA.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
extractEnrichmentOverlaps 3.17   0.05   11.25
runLOLA                   1.81   0.01   10.06
writeCombinedEnrichment   1.58   0.04    9.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
extractEnrichmentOverlaps 3.60   0.09    9.92
getRegionSet              2.06   0.00    8.09
writeCombinedEnrichment   1.84   0.03    7.69
redefineUserSets          1.72   0.02    6.98
runLOLA                   1.66   0.03    6.52
listRegionSets            0.02   0.00    6.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/LOLA.Rcheck/00check.log'
for details.


LOLA.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'LOLA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LOLA' as LOLA_1.6.0.zip
* DONE (LOLA)

LOLA.Rcheck/examples_i386/LOLA-Ex.timings:

nameusersystemelapsed
buildRestrictedUniverse0.340.010.36
checkUniverseAppropriateness0.280.000.28
extractEnrichmentOverlaps 3.17 0.0511.25
getRegionSet1.610.003.92
listRegionSets0.040.001.01
loadRegionDB0.480.001.60
mergeRegionDBs0.330.021.45
readBed000
readCollection0.130.010.14
readCollectionAnnotation0.010.000.01
readCollectionFiles0.020.000.02
readRegionGRL0.340.001.44
readRegionSetAnnotation0.020.001.11
redefineUserSets1.410.023.62
runLOLA 1.81 0.0110.06
setSharedDataDir000
splitFileIntoCollection0.010.000.02
userSets000
writeCombinedEnrichment1.580.049.28

LOLA.Rcheck/examples_x64/LOLA-Ex.timings:

nameusersystemelapsed
buildRestrictedUniverse0.390.020.41
checkUniverseAppropriateness0.320.000.33
extractEnrichmentOverlaps3.600.099.92
getRegionSet2.060.008.09
listRegionSets0.020.006.47
loadRegionDB0.360.001.57
mergeRegionDBs0.340.031.48
readBed0.010.000.02
readCollection0.160.000.15
readCollectionAnnotation000
readCollectionFiles0.000.020.02
readRegionGRL0.340.014.20
readRegionSetAnnotation0.020.001.13
redefineUserSets1.720.026.98
runLOLA1.660.036.52
setSharedDataDir000
splitFileIntoCollection0.010.000.01
userSets000
writeCombinedEnrichment1.840.037.69