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BioC 3.2: CHECK report for compEpiTools on linux1.bioconductor.org

This page was generated on 2015-10-27 17:26:39 -0400 (Tue, 27 Oct 2015).

Package 215/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.4.0
Kamal Kishore
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/compEpiTools
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings compEpiTools_1.4.0.tar.gz
StartedAt: 2015-10-27 02:25:30 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 02:31:43 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 373.2 seconds
RetCode: 0
Status:  OK 
CheckDir: compEpiTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings compEpiTools_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/compEpiTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘compEpiTools’ can be installed ... [30s/30s] 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
* 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 ... [91s/105s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
topGOres                 36.784  0.056  36.883
GRannotate-methods        5.862  0.043   5.913
makeGtfFromDb             4.763  0.053   5.643
getPromoterClass-methods  0.858  0.027  14.154
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.


compEpiTools.Rcheck/00install.out:

* 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.
* DONE (compEpiTools)

compEpiTools.Rcheck/compEpiTools-Ex.timings:

nameusersystemelapsed
GR2fasta-methods0.5520.0040.558
GRanges2ucsc-methods0.010.000.01
GRangesInPromoters-methods3.9050.0243.929
GRannotate-methods5.8620.0435.913
GRannotateSimple1.3300.0121.345
GRbaseCoverage-methods0.140.000.14
GRcoverage-methods0.2130.0000.214
GRcoverageSummit-methods0.1110.0000.111
GRenrichment-methods0.1260.0000.126
GRmidpoint-methods0.0240.0040.027
GRsetwidth0.0500.0040.054
TSS2.7710.0162.794
countOverlapsInBins-methods0.1680.0000.169
distanceFromTSS-methods2.9610.0042.966
enhancers0.4010.0080.409
findLncRNA0.6730.0000.674
getPromoterClass-methods 0.858 0.02714.154
heatmapData2.5430.0762.619
heatmapPlot4.2680.0724.380
makeGtfFromDb4.7630.0535.643
matchEnhancers2.8970.0002.901
overlapOfGRanges-methods0.080.000.08
palette2d0.0760.0000.076
plotStallingIndex2.9680.0162.989
simplifyGOterms0.9210.0600.982
stallingIndex2.3990.0082.410
topGOres36.784 0.05636.883
ucsc2GRanges0.0090.0000.010
unionMaxScore-methods0.0860.0000.086