Kamal Kishore
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/compEpiTools |
| Branch: RELEASE_3_8 |
| Last Commit: bfc46e8 |
| Last Changed Date: 2018-10-30 11:41:54 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:57:53 -0400 (Tue, 16 Apr 2019).
| Package 312/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| compEpiTools 1.16.0 Kamal Kishore
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: compEpiTools |
| Version: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2019-04-15 23:10:14 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:17:52 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 457.8 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/compEpiTools.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.0’
* 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 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'
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<-'
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'
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 coord_flip distanceToNearest end<-
geom_bar ggplot reduce seqlengths seqlengths<- start<- stopCluster
trim txdb ylab
* 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 43.628 1.692 45.718
makeGtfFromDb 5.271 0.213 5.521
getPromoterClass-methods 0.812 0.033 17.810
* 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-3.8-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 | 0.593 | 0.014 | 0.610 | |
| GRanges2ucsc-methods | 0.009 | 0.001 | 0.011 | |
| GRangesInPromoters-methods | 3.394 | 0.100 | 3.516 | |
| GRannotate-methods | 4.228 | 0.100 | 4.339 | |
| GRannotateSimple | 0.645 | 0.018 | 0.664 | |
| GRbaseCoverage-methods | 0.119 | 0.001 | 0.121 | |
| GRcoverage-methods | 0.115 | 0.001 | 0.116 | |
| GRcoverageSummit-methods | 0.041 | 0.000 | 0.042 | |
| GRenrichment-methods | 0.063 | 0.002 | 0.065 | |
| GRmidpoint-methods | 0.015 | 0.000 | 0.015 | |
| GRsetwidth | 0.026 | 0.000 | 0.025 | |
| TSS | 1.489 | 0.048 | 1.539 | |
| countOverlapsInBins-methods | 0.104 | 0.000 | 0.105 | |
| distanceFromTSS-methods | 3.189 | 0.060 | 3.259 | |
| enhancers | 0.407 | 0.028 | 0.437 | |
| findLncRNA | 0.872 | 0.033 | 0.912 | |
| getPromoterClass-methods | 0.812 | 0.033 | 17.810 | |
| heatmapData | 1.297 | 0.021 | 1.321 | |
| heatmapPlot | 3.398 | 0.171 | 3.593 | |
| makeGtfFromDb | 5.271 | 0.213 | 5.521 | |
| matchEnhancers | 2.061 | 0.085 | 2.164 | |
| overlapOfGRanges-methods | 0.059 | 0.000 | 0.060 | |
| palette2d | 0.093 | 0.002 | 0.096 | |
| plotStallingIndex | 2.722 | 0.066 | 2.818 | |
| simplifyGOterms | 0.850 | 0.128 | 1.119 | |
| stallingIndex | 2.887 | 0.071 | 2.975 | |
| topGOres | 43.628 | 1.692 | 45.718 | |
| ucsc2GRanges | 0.009 | 0.000 | 0.009 | |
| unionMaxScore-methods | 0.122 | 0.001 | 0.122 | |