BioC 3.1: CHECK report for compEpiTools on petty

Package: compEpiTools

Version: 1.2.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compEpiTools_1.2.6.tar.gz

StartedAt: 2015-10-08 22:16:23 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:27:27 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 663.7 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 --no-vignettes --timings compEpiTools_1.2.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/compEpiTools.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.6’
* 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 ... [45s/45s] 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
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’
TSS: no visible global function definition for ‘end<-’
TSS: no visible global function definition for ‘start<-’
ucsc2GRanges: no visible global function definition for ‘IRanges’
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’
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<-’
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 ... [159s/203s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
topGOres                   69.231  1.781  71.804
GRangesInPromoters-methods 10.628  0.174  10.847
GRannotate-methods          8.425  0.171   8.808
matchEnhancers              5.497  0.123   5.621
heatmapPlot                 4.589  0.127   5.188
makeGtfFromDb               3.404  0.488  24.627
getPromoterClass-methods    1.198  0.010  21.440
* 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-3.1-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	1.243	0.016	1.410
GRanges2ucsc-methods	0.017	0.000	0.018
GRangesInPromoters-methods	10.628	0.174	10.847
GRannotate-methods	8.425	0.171	8.808
GRannotateSimple	1.997	0.043	2.041
GRbaseCoverage-methods	0.266	0.004	0.270
GRcoverage-methods	0.311	0.002	0.314
GRcoverageSummit-methods	0.148	0.001	0.149
GRenrichment-methods	0.133	0.002	0.134
GRmidpoint-methods	0.045	0.001	0.044
GRsetwidth	0.052	0.005	0.057
TSS	3.902	0.104	4.008
countOverlapsInBins-methods	0.280	0.003	0.284
distanceFromTSS-methods	3.986	0.032	4.019
enhancers	1.626	0.023	1.650
findLncRNA	1.444	0.030	1.475
getPromoterClass-methods	1.198	0.010	21.440
heatmapData	2.746	0.029	2.776
heatmapPlot	4.589	0.127	5.188
makeGtfFromDb	3.404	0.488	24.627
matchEnhancers	5.497	0.123	5.621
overlapOfGRanges-methods	0.117	0.001	0.117
palette2d	0.094	0.001	0.095
plotStallingIndex	3.862	0.035	3.896
simplifyGOterms	2.731	0.349	4.494
stallingIndex	3.801	0.043	3.845
topGOres	69.231	1.781	71.804
ucsc2GRanges	0.016	0.000	0.017
unionMaxScore-methods	0.143	0.001	0.144