BioC 3.1: CHECK report for compEpiTools on zin2

Package: compEpiTools

Version: 1.2.6

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings compEpiTools_1.2.6.tar.gz

StartedAt: 2015-10-08 23:53:13 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-09 00:00:44 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 451.2 seconds

RetCode: 0

Status:  OK

CheckDir: compEpiTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings compEpiTools_1.2.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/compEpiTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.6’
* 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 ... [24s/37s] 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 binding for global variable ‘Significant’
topGOres: no visible binding for global variable ‘P_val’
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’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [78s/113s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
topGOres                   33.726  0.028  41.408
GRangesInPromoters-methods  5.218  0.007   6.927
getPromoterClass-methods    1.148  0.024  14.860
* 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-3.1-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.

* installing *source* package ‘compEpiTools’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (compEpiTools)

name	user	system	elapsed
GR2fasta-methods	0.588	0.000	0.835
GRanges2ucsc-methods	0.008	0.000	0.020
GRangesInPromoters-methods	5.218	0.007	6.927
GRannotate-methods	3.500	0.018	4.747
GRannotateSimple	1.156	0.004	1.306
GRbaseCoverage-methods	0.099	0.000	0.174
GRcoverage-methods	0.151	0.000	0.152
GRcoverageSummit-methods	0.074	0.000	0.075
GRenrichment-methods	0.089	0.000	0.117
GRmidpoint-methods	0.020	0.000	0.036
GRsetwidth	0.026	0.000	0.052
TSS	2.078	0.012	2.684
countOverlapsInBins-methods	0.116	0.000	0.143
distanceFromTSS-methods	2.106	0.012	2.994
enhancers	0.530	0.000	0.575
findLncRNA	0.771	0.000	1.127
getPromoterClass-methods	1.148	0.024	14.860
heatmapData	1.249	0.024	1.522
heatmapPlot	2.393	0.019	3.401
makeGtfFromDb	1.665	0.051	3.357
matchEnhancers	2.939	0.023	3.988
overlapOfGRanges-methods	0.057	0.000	0.058
palette2d	0.052	0.000	0.052
plotStallingIndex	2.189	0.012	2.964
simplifyGOterms	1.454	0.051	1.964
stallingIndex	2.194	0.000	3.296
topGOres	33.726	0.028	41.408
ucsc2GRanges	0.010	0.000	0.011
unionMaxScore-methods	0.101	0.000	0.101