LOLA 1.6.0
Nathan Sheffield
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/LOLA | | Branch: RELEASE_3_5 | | Last Commit: a5242f6 | | Last Changed Date: 2017-04-24 15:45:44 -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 | |
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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 3.4.2 Patched (2017-10-07 r73498)
* 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 3.05 0.04 16.80
redefineUserSets 1.58 0.03 11.22
getRegionSet 1.48 0.04 8.54
runLOLA 1.52 0.00 6.56
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
extractEnrichmentOverlaps 3.91 0.11 6.64
loadRegionDB 0.35 0.00 5.37
* 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.
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)