Kamal Kishore
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/compEpiTools |
| Branch: RELEASE_3_7 |
| Last Commit: d9d95f0 |
| Last Changed Date: 2018-05-22 07:28:58 -0400 (Tue, 22 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:53:24 -0400 (Wed, 17 Oct 2018).
| Package 294/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| compEpiTools 1.14.1 Kamal Kishore
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: compEpiTools |
| Version: 1.14.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compEpiTools_1.14.1.tar.gz |
| StartedAt: 2018-10-16 20:37:49 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:45:29 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 460.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: compEpiTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compEpiTools_1.14.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/compEpiTools.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compEpiTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compEpiTools’ version ‘1.14.1’
* 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 for sufficient/correct file permissions ... 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
* 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
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 : <anonymous>: no visible global function definition for
'ggplot'
topGOres : <anonymous>: no visible global function definition for 'aes'
topGOres : <anonymous>: no visible binding for global variable
'Significant'
topGOres : <anonymous>: no visible binding for global variable 'P_val'
topGOres : <anonymous>: no visible global function definition for
'geom_bar'
topGOres : <anonymous>: no visible global function definition for
'coord_flip'
topGOres : <anonymous>: 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOres 43.062 1.624 45.105
GRannotate-methods 7.991 0.122 8.175
plotStallingIndex 6.841 0.070 6.974
stallingIndex 6.644 0.070 6.773
GRangesInPromoters-methods 5.303 0.098 5.439
makeGtfFromDb 5.058 0.327 5.819
getPromoterClass-methods 2.861 0.026 20.229
* 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
‘/Users/biocbuild/bbs-3.7-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.
compEpiTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL compEpiTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘compEpiTools’ ... ** R ** inst ** byte-compile and prepare 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. * DONE (compEpiTools)
compEpiTools.Rcheck/compEpiTools-Ex.timings
| name | user | system | elapsed | |
| GR2fasta-methods | 0.550 | 0.011 | 0.566 | |
| GRanges2ucsc-methods | 0.007 | 0.001 | 0.008 | |
| GRangesInPromoters-methods | 5.303 | 0.098 | 5.439 | |
| GRannotate-methods | 7.991 | 0.122 | 8.175 | |
| GRannotateSimple | 0.757 | 0.018 | 0.779 | |
| GRbaseCoverage-methods | 0.091 | 0.001 | 0.092 | |
| GRcoverage-methods | 0.123 | 0.002 | 0.126 | |
| GRcoverageSummit-methods | 0.068 | 0.001 | 0.069 | |
| GRenrichment-methods | 0.093 | 0.001 | 0.098 | |
| GRmidpoint-methods | 0.024 | 0.001 | 0.025 | |
| GRsetwidth | 0.025 | 0.001 | 0.026 | |
| TSS | 1.859 | 0.059 | 1.934 | |
| countOverlapsInBins-methods | 0.139 | 0.001 | 0.141 | |
| distanceFromTSS-methods | 3.473 | 0.049 | 3.556 | |
| enhancers | 0.434 | 0.012 | 0.448 | |
| findLncRNA | 0.987 | 0.050 | 1.054 | |
| getPromoterClass-methods | 2.861 | 0.026 | 20.229 | |
| heatmapData | 1.338 | 0.031 | 1.375 | |
| heatmapPlot | 3.430 | 0.175 | 3.682 | |
| makeGtfFromDb | 5.058 | 0.327 | 5.819 | |
| matchEnhancers | 2.423 | 0.090 | 2.534 | |
| overlapOfGRanges-methods | 0.070 | 0.001 | 0.071 | |
| palette2d | 0.097 | 0.003 | 0.102 | |
| plotStallingIndex | 6.841 | 0.070 | 6.974 | |
| simplifyGOterms | 0.898 | 0.127 | 1.162 | |
| stallingIndex | 6.644 | 0.070 | 6.773 | |
| topGOres | 43.062 | 1.624 | 45.105 | |
| ucsc2GRanges | 0.014 | 0.000 | 0.014 | |
| unionMaxScore-methods | 0.139 | 0.001 | 0.139 | |