BioC 3.2: CHECK report for compEpiTools on windows1.bioconductor.org

Package: compEpiTools

Version: 1.4.0

Command: rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.4.0.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.4.0.tar.gz

StartedAt: 2015-10-27 00:50:53 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:00:10 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 556.8 seconds

RetCode: 0

Status:  OK

CheckDir: compEpiTools.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.4.0.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.4.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/compEpiTools.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'compEpiTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compEpiTools' version '1.4.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
* 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 ...
** running examples for arch 'i386' ... [113s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
topGOres                   28.69   0.03   32.50
makeGtfFromDb               4.89   0.19   13.03
heatmapPlot                 2.96   0.05    7.04
GRangesInPromoters-methods  2.63   0.02    5.91
getPromoterClass-methods    0.87   0.01   10.61
simplifyGOterms             0.61   0.09   11.21
** running examples for arch 'x64' ... [99s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
topGOres                 34.44   0.05   34.48
makeGtfFromDb             5.28   0.11    5.39
getPromoterClass-methods  0.97   0.00   12.78
* 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
  'C:/biocbld/bbs-3.2-bioc/meat/compEpiTools.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'compEpiTools' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'graph::.__C__dist' when loading 'topGO'

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'graph::.__C__dist' when loading 'topGO'

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

install for x64

* installing *source* package 'compEpiTools' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'graph::.__C__dist' when loading 'topGO'

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'compEpiTools' as compEpiTools_1.4.0.zip
* DONE (compEpiTools)

name	user	system	elapsed
GR2fasta-methods	0.56	0.00	0.56
GRanges2ucsc-methods	0.01	0.00	0.01
GRangesInPromoters-methods	2.63	0.02	5.91
GRannotate-methods	4.59	0.04	4.81
GRannotateSimple	0.56	0.00	0.56
GRbaseCoverage-methods	0.1	0.0	0.1
GRcoverage-methods	0.17	0.00	0.17
GRcoverageSummit-methods	0.06	0.00	0.06
GRenrichment-methods	0.08	0.00	0.08
GRmidpoint-methods	0.02	0.00	0.02
GRsetwidth	0.01	0.00	0.01
TSS	1.6	0.0	1.6
countOverlapsInBins-methods	0.10	0.00	0.09
distanceFromTSS-methods	2.85	0.03	2.90
enhancers	0.38	0.02	0.39
findLncRNA	0.72	0.00	0.71
getPromoterClass-methods	0.87	0.01	10.61
heatmapData	1.41	0.00	1.41
heatmapPlot	2.96	0.05	7.04
makeGtfFromDb	4.89	0.19	13.03
matchEnhancers	2.48	0.00	2.48
overlapOfGRanges-methods	0.05	0.00	0.05
palette2d	0.05	0.00	0.05
plotStallingIndex	2.64	0.03	2.67
simplifyGOterms	0.61	0.09	11.21
stallingIndex	2.63	0.05	2.68
topGOres	28.69	0.03	32.50
ucsc2GRanges	0	0	0
unionMaxScore-methods	0.1	0.0	0.1

name	user	system	elapsed
GR2fasta-methods	0.55	0.03	0.58
GRanges2ucsc-methods	0	0	0
GRangesInPromoters-methods	3.14	0.00	3.14
GRannotate-methods	4.80	0.08	4.87
GRannotateSimple	1.06	0.00	1.07
GRbaseCoverage-methods	0.11	0.00	0.11
GRcoverage-methods	0.14	0.01	0.15
GRcoverageSummit-methods	0.08	0.00	0.08
GRenrichment-methods	0.09	0.00	0.09
GRmidpoint-methods	0.02	0.00	0.02
GRsetwidth	0.03	0.00	0.03
TSS	2.14	0.02	2.15
countOverlapsInBins-methods	0.14	0.00	0.14
distanceFromTSS-methods	2.81	0.03	2.85
enhancers	0.42	0.00	0.43
findLncRNA	0.72	0.00	0.71
getPromoterClass-methods	0.97	0.00	12.78
heatmapData	2.37	0.00	2.37
heatmapPlot	4.41	0.06	4.47
makeGtfFromDb	5.28	0.11	5.39
matchEnhancers	2.57	0.00	2.57
overlapOfGRanges-methods	0.07	0.00	0.07
palette2d	0.04	0.00	0.04
plotStallingIndex	2.79	0.03	2.82
simplifyGOterms	1.06	0.06	1.12
stallingIndex	2.84	0.00	2.85
topGOres	34.44	0.05	34.48
ucsc2GRanges	0.01	0.00	0.02
unionMaxScore-methods	0.10	0.00	0.09