Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.3: CHECK report for compEpiTools on moscato2

This page was generated on 2016-10-13 12:52:58 -0700 (Thu, 13 Oct 2016).

Package 232/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.6.4
Kamal Kishore
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/compEpiTools
Last Changed Rev: 120390 / Revision: 122332
Last Changed Date: 2016-08-24 09:16:04 -0700 (Wed, 24 Aug 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: compEpiTools
Version: 1.6.4
Command: rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.6.4.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.6.4.tar.gz
StartedAt: 2016-10-13 02:27:37 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 02:43:24 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 947.3 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 && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.6.4.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.6.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/compEpiTools.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.6.4'
* 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 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<-'
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 as.dendrogram dist distanceToNearest end<-
  hclust layout legend par pie plot points quantile rainbow reduce
  seqlengths seqlengths<- start<- stopCluster trim txdb write.table
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                 32.78   0.04   34.94
makeGtfFromDb             7.70   0.14   34.94
GRannotate-methods        7.29   0.06   11.40
heatmapPlot               5.26   0.03   12.59
simplifyGOterms           1.71   0.22   45.06
getPromoterClass-methods  0.96   0.03   16.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
topGOres                 50.60   0.09   50.70
makeGtfFromDb             8.94   0.16    9.10
GRannotate-methods        8.63   0.03    8.66
heatmapPlot               6.66   0.04    6.72
getPromoterClass-methods  1.51   0.00   19.65
* 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
  'E:/biocbld/bbs-3.3-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_1.6.4.zip
* DONE (compEpiTools)

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

nameusersystemelapsed
GR2fasta-methods0.800.010.84
GRanges2ucsc-methods000
GRangesInPromoters-methods4.870.024.88
GRannotate-methods 7.29 0.0611.40
GRannotateSimple1.140.001.14
GRbaseCoverage-methods0.130.000.12
GRcoverage-methods0.20.00.2
GRcoverageSummit-methods0.080.000.08
GRenrichment-methods0.090.000.10
GRmidpoint-methods0.020.000.01
GRsetwidth0.030.000.03
TSS3.370.053.42
countOverlapsInBins-methods0.160.000.16
distanceFromTSS-methods4.040.024.06
enhancers0.450.000.45
findLncRNA1.220.001.22
getPromoterClass-methods 0.96 0.0316.72
heatmapData2.340.032.37
heatmapPlot 5.26 0.0312.59
makeGtfFromDb 7.70 0.1434.94
matchEnhancers3.520.003.52
overlapOfGRanges-methods0.060.000.06
palette2d0.080.000.08
plotStallingIndex3.650.033.68
simplifyGOterms 1.71 0.2245.06
stallingIndex3.350.053.42
topGOres32.78 0.0434.94
ucsc2GRanges000
unionMaxScore-methods0.110.000.11

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

nameusersystemelapsed
GR2fasta-methods0.680.010.70
GRanges2ucsc-methods0.020.000.02
GRangesInPromoters-methods4.690.034.73
GRannotate-methods8.630.038.66
GRannotateSimple1.310.021.33
GRbaseCoverage-methods0.120.000.16
GRcoverage-methods0.170.000.17
GRcoverageSummit-methods0.130.000.12
GRenrichment-methods0.150.000.16
GRmidpoint-methods0.040.000.03
GRsetwidth0.030.000.03
TSS2.910.032.95
countOverlapsInBins-methods0.240.000.23
distanceFromTSS-methods3.790.034.04
enhancers0.640.000.64
findLncRNA1.980.012.02
getPromoterClass-methods 1.51 0.0019.65
heatmapData3.090.043.12
heatmapPlot6.660.046.72
makeGtfFromDb8.940.169.10
matchEnhancers4.120.014.13
overlapOfGRanges-methods0.080.000.07
palette2d0.110.000.11
plotStallingIndex4.350.044.39
simplifyGOterms1.440.151.60
stallingIndex4.540.024.56
topGOres50.60 0.0950.70
ucsc2GRanges0.020.000.02
unionMaxScore-methods0.150.000.15