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BioC 3.4: CHECK report for compEpiTools on tokay1

This page was generated on 2017-04-15 16:19:02 -0400 (Sat, 15 Apr 2017).

Package 250/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.8.0
Kamal Kishore
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/compEpiTools
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: compEpiTools
Version: 1.8.0
Command: rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.8.0.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.8.0.tar.gz
StartedAt: 2017-04-14 21:40:12 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:50:51 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 638.9 seconds
RetCode: 0
Status:  OK  
CheckDir: compEpiTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.8.0.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/compEpiTools.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.8.0'
* 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'
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
topGOres                 26.62   0.07   26.90
makeGtfFromDb             5.25   0.26   23.48
GRannotate-methods        4.38   0.11    6.53
heatmapPlot               3.50   0.09    8.17
simplifyGOterms           0.95   0.11   18.16
getPromoterClass-methods  0.97   0.00   16.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
topGOres                 37.69   0.03   37.72
GRannotate-methods        5.35   0.06    5.42
getPromoterClass-methods  1.08   0.00   14.78
* 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:/Users/biocbuild/bbs-3.4-bioc/meat/compEpiTools.Rcheck/00check.log'
for details.


compEpiTools.Rcheck/00install.out:


install for i386

* 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.

install for x64

* installing *source* package 'compEpiTools' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'compEpiTools' as compEpiTools_1.8.0.zip
* DONE (compEpiTools)

compEpiTools.Rcheck/examples_i386/compEpiTools-Ex.timings:

nameusersystemelapsed
GR2fasta-methods0.490.030.52
GRanges2ucsc-methods0.010.000.02
GRangesInPromoters-methods2.690.112.79
GRannotate-methods4.380.116.53
GRannotateSimple0.770.000.76
GRbaseCoverage-methods0.090.000.10
GRcoverage-methods0.130.000.12
GRcoverageSummit-methods0.060.000.07
GRenrichment-methods0.080.000.07
GRmidpoint-methods0.010.000.02
GRsetwidth0.030.000.03
TSS2.530.002.53
countOverlapsInBins-methods0.130.000.13
distanceFromTSS-methods2.700.022.72
enhancers0.460.000.45
findLncRNA0.750.000.75
getPromoterClass-methods 0.97 0.0016.13
heatmapData1.390.001.39
heatmapPlot3.500.098.17
makeGtfFromDb 5.25 0.2623.48
matchEnhancers3.430.023.46
overlapOfGRanges-methods0.070.000.06
palette2d0.060.000.06
plotStallingIndex3.030.033.06
simplifyGOterms 0.95 0.1118.16
stallingIndex3.050.063.11
topGOres26.62 0.0726.90
ucsc2GRanges000
unionMaxScore-methods0.090.000.09

compEpiTools.Rcheck/examples_x64/compEpiTools-Ex.timings:

nameusersystemelapsed
GR2fasta-methods0.660.010.67
GRanges2ucsc-methods0.010.000.02
GRangesInPromoters-methods3.910.053.95
GRannotate-methods5.350.065.42
GRannotateSimple0.750.050.80
GRbaseCoverage-methods0.080.000.10
GRcoverage-methods0.140.000.14
GRcoverageSummit-methods0.080.000.08
GRenrichment-methods0.080.000.07
GRmidpoint-methods0.010.000.02
GRsetwidth0.030.000.03
TSS1.860.031.89
countOverlapsInBins-methods0.140.000.14
distanceFromTSS-methods2.640.062.71
enhancers0.530.000.53
findLncRNA0.820.020.82
getPromoterClass-methods 1.08 0.0014.78
heatmapData1.550.001.55
heatmapPlot4.730.084.84
makeGtfFromDb4.360.074.44
matchEnhancers2.390.022.40
overlapOfGRanges-methods0.060.000.06
palette2d0.060.000.07
plotStallingIndex2.960.032.98
simplifyGOterms1.480.141.62
stallingIndex3.120.013.14
topGOres37.69 0.0337.72
ucsc2GRanges0.010.000.01
unionMaxScore-methods0.210.000.21