Kamal Kishore
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/compEpiTools |
| Branch: RELEASE_3_6 |
| Last Commit: af9edf3 |
| Last Changed Date: 2017-10-30 12:40:23 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:12:34 -0400 (Thu, 12 Apr 2018).
| Package 281/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| compEpiTools 1.12.0 Kamal Kishore
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: compEpiTools |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings compEpiTools_1.12.0.tar.gz |
| StartedAt: 2018-04-11 22:29:29 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:36:03 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 394.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: compEpiTools.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings compEpiTools_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/compEpiTools.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOres 28.056 0.040 28.188
heatmapPlot 5.288 0.104 5.414
GRannotate-methods 5.156 0.040 5.312
makeGtfFromDb 4.712 0.084 5.085
getPromoterClass-methods 1.140 0.032 15.687
* 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
‘/home/biocbuild/bbs-3.6-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.
compEpiTools.Rcheck/00install.out
* 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. * DONE (compEpiTools)
compEpiTools.Rcheck/compEpiTools-Ex.timings
| name | user | system | elapsed | |
| GR2fasta-methods | 1.228 | 0.004 | 1.877 | |
| GRanges2ucsc-methods | 0.004 | 0.000 | 0.007 | |
| GRangesInPromoters-methods | 3.904 | 0.040 | 3.946 | |
| GRannotate-methods | 5.156 | 0.040 | 5.312 | |
| GRannotateSimple | 0.860 | 0.008 | 0.869 | |
| GRbaseCoverage-methods | 0.184 | 0.000 | 0.233 | |
| GRcoverage-methods | 0.420 | 0.000 | 0.422 | |
| GRcoverageSummit-methods | 0.052 | 0.000 | 0.050 | |
| GRenrichment-methods | 0.068 | 0.004 | 0.073 | |
| GRmidpoint-methods | 0.020 | 0.004 | 0.024 | |
| GRsetwidth | 0.032 | 0.000 | 0.031 | |
| TSS | 1.496 | 0.004 | 1.502 | |
| countOverlapsInBins-methods | 0.120 | 0.000 | 0.121 | |
| distanceFromTSS-methods | 2.224 | 0.008 | 2.236 | |
| enhancers | 0.476 | 0.004 | 0.482 | |
| findLncRNA | 0.816 | 0.000 | 0.817 | |
| getPromoterClass-methods | 1.140 | 0.032 | 15.687 | |
| heatmapData | 1.372 | 0.024 | 1.398 | |
| heatmapPlot | 5.288 | 0.104 | 5.414 | |
| makeGtfFromDb | 4.712 | 0.084 | 5.085 | |
| matchEnhancers | 2.712 | 0.012 | 2.726 | |
| overlapOfGRanges-methods | 0.060 | 0.000 | 0.058 | |
| palette2d | 0.076 | 0.000 | 0.076 | |
| plotStallingIndex | 2.676 | 0.000 | 2.680 | |
| simplifyGOterms | 1.764 | 0.044 | 2.962 | |
| stallingIndex | 2.644 | 0.008 | 2.653 | |
| topGOres | 28.056 | 0.040 | 28.188 | |
| ucsc2GRanges | 0.008 | 0.000 | 0.010 | |
| unionMaxScore-methods | 0.096 | 0.000 | 0.100 | |