Back to Multiple platform build/check report for BioC 3.6
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GenoGAM on veracruz1

This page was generated on 2018-04-12 13:42:40 -0400 (Thu, 12 Apr 2018).

Package 556/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 1.6.0
Georg Stricker
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GenoGAM
Branch: RELEASE_3_6
Last Commit: ca798bc
Last Changed Date: 2017-10-30 12:41:15 -0400 (Mon, 30 Oct 2017)
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  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GenoGAM
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenoGAM_1.6.0.tar.gz
StartedAt: 2018-04-12 04:14:41 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 04:18:50 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 249.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GenoGAM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenoGAM_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GenoGAM.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenoGAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenoGAM’ version ‘1.6.0’
* 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 ‘GenoGAM’ 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
* 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
.doCrossValidation: no visible global function definition for ‘optim’
.loglik : <anonymous>: no visible global function definition for
  ‘dnbinom’
.pvals: no visible global function definition for ‘pnorm’
.updateFormula: no visible global function definition for ‘as.formula’
callBroadPeaks: no visible binding for global variable ‘pval’
callPeaks: no visible binding for global variable ‘fdr’
computeBroadPeakSignificance: no visible global function definition for
  ‘p.adjust’
computeBroadPeakSignificance: no visible binding for global variable
  ‘pval’
computeBroadPeakSignificance: no visible binding for global variable
  ‘region’
computeBroadPeakSignificance: no visible binding for global variable
  ‘estimate’
computePeakSignificance: no visible binding for global variable
  ‘zscore’
computePeakSignificance: no visible global function definition for
  ‘pnorm’
computeRegionSignificance: no visible global function definition for
  ‘p.adjust’
computeRegionSignificance: no visible binding for global variable
  ‘pvalue’
computeRegionSignificance: no visible binding for global variable
  ‘gene’
computeTileExtremes: no visible binding for global variable ‘id’
computeZscore: no visible global function definition for ‘pnorm’
extractSplines: no visible global function definition for
  ‘coefficients’
genogam: no visible global function definition for ‘as.formula’
getExtremes: no visible binding for global variable ‘position’
getFunctions: no visible global function definition for ‘coefficients’
makeTestGenoGAM: no visible global function definition for ‘runif’
parsePeaks : <anonymous>: no visible binding for global variable
  ‘position’
parsePeaks: no visible binding for global variable ‘zscore’
plot.GenoGAM: no visible binding for global variable ‘fit’
plotQC_GenoGAMDataSet: no visible global function definition for ‘png’
plotQC_GenoGAMDataSet: no visible global function definition for ‘par’
plotQC_GenoGAMDataSet: no visible global function definition for
  ‘abline’
plotQC_GenoGAMDataSet: no visible global function definition for
  ‘dev.off’
plotQC_hist: no visible global function definition for ‘png’
plotQC_hist: no visible global function definition for ‘par’
plotQC_hist: no visible global function definition for ‘hist’
plotQC_hist: no visible global function definition for ‘abline’
plotQC_hist: no visible global function definition for ‘axis’
plotQC_hist: no visible global function definition for ‘dev.off’
plot_base: no visible global function definition for ‘par’
plot_base: no visible global function definition for ‘plot’
plot_base: no visible global function definition for ‘lines’
plot_base: no visible global function definition for ‘abline’
plot_base: no visible global function definition for ‘mtext’
writeToBroadPeaks: no visible global function definition for
  ‘write.table’
writeToNarrowPeaks: no visible global function definition for
  ‘write.table’
xsd : <anonymous>: no visible binding for global variable ‘position’
xsd: no visible binding for global variable ‘position’
Undefined global functions or variables:
  abline as.formula axis coefficients dev.off dnbinom estimate fdr fit
  gene hist id lines mtext optim p.adjust par plot png pnorm position
  pval pvalue region runif write.table zscore
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "axis", "hist", "lines", "mtext",
             "par", "plot")
  importFrom("stats", "as.formula", "coefficients", "dnbinom", "optim",
             "p.adjust", "pnorm", "runif")
  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 ... NOTE
S3 methods shown with full name in documentation object 'plot.GenoGAM':
  ‘plot.GenoGAM’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/GenoGAM.Rcheck/00check.log’
for details.



Installation output

GenoGAM.Rcheck/00install.out

* installing *source* package ‘GenoGAM’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenoGAM)

Tests output


Example timings

GenoGAM.Rcheck/GenoGAM-Ex.timings

nameusersystemelapsed
GenoGAM-methods0.3510.0080.362
GenoGAM-view0.1970.0020.201
GenoGAMDataSet0.7160.1101.409
GenomicTiles-metrics1.8540.1292.492
GenomicTiles-view0.5750.2112.243
GenomicTiles0.1840.1131.149
callPeaks1.2640.1001.401
changeSettings0.1310.0910.988
checkSettings0.0960.0560.553
computeRegionSignificance0.1170.0170.146
computeSignificance0.0520.0070.059
computeSizeFactors0.5230.1111.124
dataRange0.1980.0650.738
design0.1120.0610.577
filterData0.4130.1431.512
fitGenoGAM0.0010.0000.001
getChunkIndex0.2700.0800.788
getCoordinates0.1170.0600.623
getIndex0.1190.0550.637
getIndexCoordinates0.2000.0780.740
getTile0.7870.1201.401
makeTestGenoGAM0.0130.0010.013
makeTestGenoGAMDataSet0.1180.0550.645
makeTestGenomicTiles0.1030.0580.656
sizeFactors0.1310.0670.646
subset-GenoGAM-method0.0790.0090.094
subset-GenoGAMDataSet-method0.7370.1161.336
subset-GenomicTiles-method0.4910.0970.945
subsetByOverlaps-GenoGAM-ANY-method0.0930.0040.099
subsetByOverlaps-GenoGAMDataSet-GRanges-method0.2550.0820.769
subsetByOverlaps-GenomicTiles-GRanges-method0.3140.0830.820
tileSettings-elements0.1240.0630.647
tileSettings0.1270.0650.639
untile0.2960.0850.776