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).
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 | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Package: LOLA
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Version: 1.6.0
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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
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StartedAt: 2017-08-16 00:52:20 -0400 (Wed, 16 Aug 2017)
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EndedAt: 2017-08-16 00:57:04 -0400 (Wed, 16 Aug 2017)
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EllapsedTime: 283.2 seconds
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RetCode: 0
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Status: OK
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CheckDir: LOLA.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### 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
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* 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:
name | user | system | elapsed
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buildRestrictedUniverse | 0.34 | 0.01 | 0.36 |
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checkUniverseAppropriateness | 0.28 | 0.00 | 0.28 |
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extractEnrichmentOverlaps | 3.17 | 0.05 | 11.25 |
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getRegionSet | 1.61 | 0.00 | 3.92 |
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listRegionSets | 0.04 | 0.00 | 1.01 |
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loadRegionDB | 0.48 | 0.00 | 1.60 |
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mergeRegionDBs | 0.33 | 0.02 | 1.45 |
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readBed | 0 | 0 | 0 |
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readCollection | 0.13 | 0.01 | 0.14 |
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readCollectionAnnotation | 0.01 | 0.00 | 0.01 |
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readCollectionFiles | 0.02 | 0.00 | 0.02 |
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readRegionGRL | 0.34 | 0.00 | 1.44 |
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readRegionSetAnnotation | 0.02 | 0.00 | 1.11 |
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redefineUserSets | 1.41 | 0.02 | 3.62 |
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runLOLA | 1.81 | 0.01 | 10.06 |
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setSharedDataDir | 0 | 0 | 0 |
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splitFileIntoCollection | 0.01 | 0.00 | 0.02 |
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userSets | 0 | 0 | 0 |
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writeCombinedEnrichment | 1.58 | 0.04 | 9.28 |
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LOLA.Rcheck/examples_x64/LOLA-Ex.timings:
name | user | system | elapsed
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buildRestrictedUniverse | 0.39 | 0.02 | 0.41 |
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checkUniverseAppropriateness | 0.32 | 0.00 | 0.33 |
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extractEnrichmentOverlaps | 3.60 | 0.09 | 9.92 |
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getRegionSet | 2.06 | 0.00 | 8.09 |
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listRegionSets | 0.02 | 0.00 | 6.47 |
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loadRegionDB | 0.36 | 0.00 | 1.57 |
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mergeRegionDBs | 0.34 | 0.03 | 1.48 |
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readBed | 0.01 | 0.00 | 0.02 |
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readCollection | 0.16 | 0.00 | 0.15 |
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readCollectionAnnotation | 0 | 0 | 0 |
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readCollectionFiles | 0.00 | 0.02 | 0.02 |
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readRegionGRL | 0.34 | 0.01 | 4.20 |
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readRegionSetAnnotation | 0.02 | 0.00 | 1.13 |
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redefineUserSets | 1.72 | 0.02 | 6.98 |
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runLOLA | 1.66 | 0.03 | 6.52 |
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setSharedDataDir | 0 | 0 | 0 |
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splitFileIntoCollection | 0.01 | 0.00 | 0.01 |
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userSets | 0 | 0 | 0 |
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writeCombinedEnrichment | 1.84 | 0.03 | 7.69 |
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