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BioC 3.5: CHECK report for compEpiTools on tokay2

This page was generated on 2017-10-18 14:23:49 -0400 (Wed, 18 Oct 2017).

Package 266/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.10.0
Kamal Kishore
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/compEpiTools
Branch: RELEASE_3_5
Last Commit: 944c62a
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: compEpiTools
Version: 1.10.0
Command: rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.10.0.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.10.0.tar.gz
StartedAt: 2017-10-17 22:57:22 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:09:17 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 715.2 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.10.0.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/compEpiTools.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.10.0'
* 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                 29.22   0.11   29.34
makeGtfFromDb             6.84   0.36   25.29
GRannotate-methods        5.15   0.05    5.20
heatmapPlot               4.41   0.06    8.93
simplifyGOterms           1.41   0.10   19.44
getPromoterClass-methods  1.17   0.03   15.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
topGOres                 31.87   0.12   32.00
GRannotate-methods        5.97   0.03    6.00
makeGtfFromDb             5.61   0.10    5.70
heatmapPlot               5.17   0.08    5.25
getPromoterClass-methods  1.17   0.02   17.80
* 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-3.5-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_1.10.0.zip
* DONE (compEpiTools)

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

nameusersystemelapsed
GR2fasta-methods1.780.021.84
GRanges2ucsc-methods000
GRangesInPromoters-methods3.210.123.33
GRannotate-methods5.150.055.20
GRannotateSimple1.390.001.39
GRbaseCoverage-methods0.160.000.16
GRcoverage-methods0.330.050.38
GRcoverageSummit-methods0.040.010.06
GRenrichment-methods0.100.040.12
GRmidpoint-methods0.010.000.02
GRsetwidth0.050.000.05
TSS1.410.091.50
countOverlapsInBins-methods0.090.000.09
distanceFromTSS-methods2.130.062.19
enhancers0.890.000.89
findLncRNA0.870.000.87
getPromoterClass-methods 1.17 0.0315.83
heatmapData1.450.021.46
heatmapPlot4.410.068.93
makeGtfFromDb 6.84 0.3625.29
matchEnhancers2.730.082.81
overlapOfGRanges-methods0.040.000.04
palette2d0.080.000.08
plotStallingIndex2.800.012.81
simplifyGOterms 1.41 0.1019.44
stallingIndex2.850.012.88
topGOres29.22 0.1129.34
ucsc2GRanges0.020.000.02
unionMaxScore-methods0.120.000.12

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

nameusersystemelapsed
GR2fasta-methods3.360.033.39
GRanges2ucsc-methods000
GRangesInPromoters-methods4.060.034.10
GRannotate-methods5.970.036.00
GRannotateSimple1.080.021.10
GRbaseCoverage-methods0.240.020.25
GRcoverage-methods0.480.000.48
GRcoverageSummit-methods0.060.000.06
GRenrichment-methods0.080.010.10
GRmidpoint-methods0.020.000.01
GRsetwidth0.030.000.03
TSS1.730.031.77
countOverlapsInBins-methods0.160.000.16
distanceFromTSS-methods3.730.033.76
enhancers0.580.000.58
findLncRNA0.840.000.84
getPromoterClass-methods 1.17 0.0217.80
heatmapData1.440.001.44
heatmapPlot5.170.085.25
makeGtfFromDb5.610.105.70
matchEnhancers2.710.002.71
overlapOfGRanges-methods0.10.00.1
palette2d0.180.000.18
plotStallingIndex3.230.043.29
simplifyGOterms1.310.031.35
stallingIndex3.020.043.04
topGOres31.87 0.1232.00
ucsc2GRanges000
unionMaxScore-methods0.090.000.09