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BioC 3.5: CHECK report for GenoGAM on veracruz2

This page was generated on 2017-08-16 13:34:28 -0400 (Wed, 16 Aug 2017).

Package 531/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 1.4.0
Georg Stricker
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GenoGAM
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -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: GenoGAM
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenoGAM_1.4.0.tar.gz
StartedAt: 2017-08-16 03:17:07 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:22:36 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 328.6 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GenoGAM.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.4.0’
* 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 ‘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
Examples with CPU or elapsed time > 5s
                      user system elapsed
GenomicTiles-metrics 1.934  0.138   5.121
GenomicTiles-view    0.582  0.253   9.396
filterData           0.432  0.206   6.639
GenomicTiles         0.156  0.149   5.897
changeSettings       0.140  0.132   5.834
* 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-3.5-bioc/meat/GenoGAM.Rcheck/00check.log’
for details.


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)

GenoGAM.Rcheck/GenoGAM-Ex.timings:

nameusersystemelapsed
GenoGAM-methods0.9910.0041.025
GenoGAM-view0.2360.0050.245
GenoGAMDataSet0.8440.1723.957
GenomicTiles-metrics1.9340.1385.121
GenomicTiles-view0.5820.2539.396
GenomicTiles0.1560.1495.897
callPeaks1.0060.0611.102
changeSettings0.1400.1325.834
checkSettings0.0820.0752.840
computeRegionSignificance0.1380.0150.153
computeSignificance0.0420.0040.045
computeSizeFactors0.4870.1133.426
dataRange0.1740.0973.167
design0.1060.0793.155
filterData0.4320.2066.639
fitGenoGAM0.0010.0010.001
getChunkIndex0.2840.1143.452
getCoordinates0.1080.0833.257
getIndex0.1100.0863.210
getIndexCoordinates0.1890.1063.093
getTile0.5870.1133.414
makeTestGenoGAM0.0150.0010.015
makeTestGenoGAMDataSet0.1250.0883.180
makeTestGenomicTiles0.0930.0763.119
sizeFactors0.1170.0993.127
subset-GenoGAM-method0.1130.0150.127
subset-GenoGAMDataSet-method0.6420.1233.606
subset-GenomicTiles-method0.5140.1103.611
subsetByOverlaps-GenoGAM-ANY-method0.0900.0020.093
subsetByOverlaps-GenoGAMDataSet-GRanges-method0.2910.1033.468
subsetByOverlaps-GenomicTiles-GRanges-method0.2500.0933.308
tileSettings-elements0.0990.0903.235
tileSettings0.0990.0753.227
untile0.2410.1133.382