BioC 3.3: CHECK report for compEpiTools on linux2.bioconductor.org

Package: compEpiTools

Version: 1.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings compEpiTools_1.5.0.tar.gz

StartedAt: 2015-10-27 02:52:50 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:58:27 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 337.9 seconds

RetCode: 0

Status:  OK

CheckDir: compEpiTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings compEpiTools_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/compEpiTools.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.5.0’
* 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 ... [22s/22s] 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’
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<-’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [84s/97s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
topGOres                 34.423  0.048  34.502
makeGtfFromDb             5.854  0.033   6.599
getPromoterClass-methods  1.139  0.033  12.763
* 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-3.3-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
GR2fasta-methods	0.417	0.008	0.427
GRanges2ucsc-methods	0.007	0.000	0.006
GRangesInPromoters-methods	2.550	0.012	2.569
GRannotate-methods	4.835	0.040	4.875
GRannotateSimple	0.564	0.008	0.574
GRbaseCoverage-methods	0.086	0.000	0.086
GRcoverage-methods	0.159	0.000	0.159
GRcoverageSummit-methods	0.067	0.000	0.068
GRenrichment-methods	0.079	0.000	0.079
GRmidpoint-methods	0.017	0.000	0.017
GRsetwidth	0.022	0.000	0.022
TSS	3.168	0.012	3.195
countOverlapsInBins-methods	0.163	0.000	0.164
distanceFromTSS-methods	3.608	0.012	3.647
enhancers	0.513	0.000	0.518
findLncRNA	1.227	0.004	1.231
getPromoterClass-methods	1.139	0.033	12.763
heatmapData	1.242	0.024	1.267
heatmapPlot	3.578	0.036	3.650
makeGtfFromDb	5.854	0.033	6.599
matchEnhancers	1.886	0.004	1.892
overlapOfGRanges-methods	0.045	0.000	0.045
palette2d	0.044	0.000	0.045
plotStallingIndex	3.296	0.012	3.312
simplifyGOterms	0.934	0.072	1.007
stallingIndex	3.436	0.016	3.472
topGOres	34.423	0.048	34.502
ucsc2GRanges	0.01	0.00	0.01
unionMaxScore-methods	0.084	0.000	0.085