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BioC 3.2: CHECK report for compEpiTools on moscato1

This page was generated on 2016-04-23 10:20:36 -0700 (Sat, 23 Apr 2016).

Package 215/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.4.0
Kamal Kishore
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/compEpiTools
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (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: 1.4.0
Command: rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && D:\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 && D:\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: 2016-04-23 01:02:27 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:19:10 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1002.8 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 && D:\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  && D:\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
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/compEpiTools.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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' ... [265s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
topGOres                   46.27   0.07   51.61
makeGtfFromDb               8.70   0.26   93.70
GRannotate-methods          6.54   0.02   11.46
GRangesInPromoters-methods  5.12   0.01    9.30
heatmapPlot                 4.96   0.05   18.03
simplifyGOterms             1.76   0.11   12.68
getPromoterClass-methods    1.06   0.00   18.93
** running examples for arch 'x64' ... [158s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
topGOres                 51.87   0.14   52.21
makeGtfFromDb            10.62   0.15   10.78
GRannotate-methods        6.94   0.00    7.36
heatmapPlot               5.57   0.05    5.71
plotStallingIndex         5.05   0.03    5.40
getPromoterClass-methods  1.17   0.03   23.81
* 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
  'D:/biocbld/bbs-3.2-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_1.4.0.zip
* DONE (compEpiTools)

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

nameusersystemelapsed
GR2fasta-methods0.810.030.87
GRanges2ucsc-methods0.020.000.01
GRangesInPromoters-methods5.120.019.30
GRannotate-methods 6.54 0.0211.46
GRannotateSimple1.650.001.66
GRbaseCoverage-methods0.170.000.19
GRcoverage-methods0.240.000.23
GRcoverageSummit-methods0.110.000.11
GRenrichment-methods0.140.000.14
GRmidpoint-methods0.030.000.04
GRsetwidth0.050.000.04
TSS3.010.023.03
countOverlapsInBins-methods0.190.000.19
distanceFromTSS-methods4.490.004.49
enhancers0.50.00.5
findLncRNA0.940.000.94
getPromoterClass-methods 1.06 0.0018.93
heatmapData2.570.012.59
heatmapPlot 4.96 0.0518.03
makeGtfFromDb 8.70 0.2693.70
matchEnhancers4.230.074.29
overlapOfGRanges-methods0.060.000.06
palette2d0.080.000.08
plotStallingIndex4.150.044.23
simplifyGOterms 1.76 0.1112.68
stallingIndex3.640.023.65
topGOres46.27 0.0751.61
ucsc2GRanges0.020.000.02
unionMaxScore-methods0.230.020.25

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

nameusersystemelapsed
GR2fasta-methods0.770.000.77
GRanges2ucsc-methods0.020.000.02
GRangesInPromoters-methods4.520.064.58
GRannotate-methods6.940.007.36
GRannotateSimple0.930.040.97
GRbaseCoverage-methods0.200.000.48
GRcoverage-methods1.000.011.01
GRcoverageSummit-methods0.090.000.10
GRenrichment-methods0.110.000.11
GRmidpoint-methods0.040.000.03
GRsetwidth0.030.000.03
TSS2.060.022.07
countOverlapsInBins-methods0.170.000.18
distanceFromTSS-methods4.070.014.08
enhancers0.530.000.53
findLncRNA1.310.021.33
getPromoterClass-methods 1.17 0.0323.81
heatmapData2.220.002.21
heatmapPlot5.570.055.71
makeGtfFromDb10.62 0.1510.78
matchEnhancers3.280.003.28
overlapOfGRanges-methods0.080.000.08
palette2d0.080.000.08
plotStallingIndex5.050.035.40
simplifyGOterms1.670.051.71
stallingIndex4.230.034.26
topGOres51.87 0.1452.21
ucsc2GRanges0.010.000.02
unionMaxScore-methods0.130.000.12