compEpiTools 1.10.0
Kamal Kishore
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/compEpiTools | | Branch: RELEASE_3_5 | | Last Commit: 944c62a | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.10.0.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/compEpiTools.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 'compEpiTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compEpiTools' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'compEpiTools' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
TSS: no visible global function definition for 'end<-'
TSS: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'end<-'
findLncRNA: no visible global function definition for 'IRanges'
findLncRNA: no visible binding for global variable 'quantile'
heatmapPlot: no visible global function definition for 'quantile'
heatmapPlot: no visible global function definition for 'hclust'
heatmapPlot: no visible global function definition for 'dist'
heatmapPlot: no visible global function definition for 'as.dendrogram'
plotStallingIndex: no visible global function definition for 'rainbow'
plotStallingIndex: no visible global function definition for 'layout'
plotStallingIndex: no visible global function definition for 'par'
plotStallingIndex: no visible global function definition for 'plot'
plotStallingIndex: no visible global function definition for 'points'
plotStallingIndex: no visible global function definition for 'legend'
stallingIndex : getBound: no visible global function definition for
'start<-'
stallingIndex : getBound: no visible global function definition for
'end<-'
stallingIndex: no visible global function definition for 'IRanges'
topGOres: no visible global function definition for 'ggplot'
topGOres: no visible global function definition for 'aes'
topGOres: no visible binding for global variable 'Significant'
topGOres: no visible binding for global variable 'P_val'
topGOres: no visible global function definition for 'geom_bar'
topGOres: no visible global function definition for 'coord_flip'
topGOres: no visible global function definition for 'ylab'
ucsc2GRanges: no visible global function definition for 'IRanges'
GR2fasta,GRanges: no visible global function definition for
'seqlengths'
GR2fasta,GRanges: no visible global function definition for
'seqlengths<-'
GR2fasta,GRanges: no visible global function definition for 'trim'
GRangesInPromoters,GRanges: no visible global function definition for
'start<-'
GRannotate,GRanges: no visible global function definition for 'start<-'
GRannotate,GRanges: no visible global function definition for 'end<-'
GRannotateSimple,GRanges: no visible global function definition for
'pie'
GRcoverageSummit,GRanges: no visible global function definition for
'start<-'
GRcoverageSummit,GRanges: no visible global function definition for
'end<-'
GRmidpoint,GRanges: no visible global function definition for 'start<-'
GRmidpoint,GRanges: no visible global function definition for 'end<-'
GRsetwidth,GRanges: no visible global function definition for 'start<-'
GRsetwidth,GRanges: no visible global function definition for 'end<-'
countOverlapsInBins,GRanges: no visible global function definition for
'IRanges'
featuresLength,TxDb: no visible global function definition for 'reduce'
getPromoterClass,TxDb: no visible binding for global variable 'txdb'
getPromoterClass,TxDb: no visible global function definition for
'start<-'
getPromoterClass,TxDb: no visible global function definition for
'stopCluster'
makeGtfFromDb,TxDb: no visible global function definition for 'reduce'
makeGtfFromDb,TxDb: no visible global function definition for
'write.table'
matchEnhancers,GRanges: no visible global function definition for
'distanceToNearest'
matchEnhancers,GRanges: no visible global function definition for
'IRanges'
Undefined global functions or variables:
IRanges P_val Significant aes as.dendrogram coord_flip dist
distanceToNearest end<- geom_bar ggplot hclust layout legend par pie
plot points quantile rainbow reduce seqlengths seqlengths<- start<-
stopCluster trim txdb write.table ylab
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "layout", "legend", "par", "pie", "plot",
"points")
importFrom("stats", "as.dendrogram", "dist", "hclust", "quantile")
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 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
topGOres 29.22 0.11 29.34
makeGtfFromDb 6.84 0.36 25.29
GRannotate-methods 5.15 0.05 5.20
heatmapPlot 4.41 0.06 8.93
simplifyGOterms 1.41 0.10 19.44
getPromoterClass-methods 1.17 0.03 15.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOres 31.87 0.12 32.00
GRannotate-methods 5.97 0.03 6.00
makeGtfFromDb 5.61 0.10 5.70
heatmapPlot 5.17 0.08 5.25
getPromoterClass-methods 1.17 0.02 17.80
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/compEpiTools.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'compEpiTools' ...
** R
** inst
** preparing package for lazy loading
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
install for x64
* installing *source* package 'compEpiTools' ...
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'compEpiTools' as compEpiTools_1.10.0.zip
* DONE (compEpiTools)