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BioC 3.5: CHECK report for GenoGAM on malbec2

This page was generated on 2017-10-18 14:17:37 -0400 (Wed, 18 Oct 2017).

Package 531/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 1.4.0
Georg Stricker
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/GenoGAM
Branch: RELEASE_3_5
Last Commit: 28da859
Last Changed Date: 2017-04-24 15:45:44 -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  TIMEOUT  OK 

Summary

Package: GenoGAM
Version: 1.4.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenoGAM_1.4.0.tar.gz
StartedAt: 2017-10-17 23:28:51 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:33:43 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 291.7 seconds
RetCode: 0
Status:  OK 
CheckDir: GenoGAM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenoGAM_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GenoGAM.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 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-view 0.632  0.092   8.437
filterData        0.348  0.100   5.708
GenomicTiles      0.140  0.080   5.662
changeSettings    0.120  0.052   5.537
* 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
  ‘/home/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-methods0.8160.0040.822
GenoGAM-view0.2600.0200.281
GenoGAMDataSet0.7920.1643.818
GenomicTiles-metrics1.6320.0444.506
GenomicTiles-view0.6320.0928.437
GenomicTiles0.1400.0805.662
callPeaks0.7360.0360.773
changeSettings0.1200.0525.537
checkSettings0.1280.0362.877
computeRegionSignificance0.1560.0120.165
computeSignificance0.0600.0040.064
computeSizeFactors0.5760.0803.527
dataRange0.2440.0443.226
design0.1120.0402.972
filterData0.3480.1005.708
fitGenoGAM0.0000.0000.001
getChunkIndex0.2680.0442.855
getCoordinates0.1040.0322.688
getIndex0.1320.0442.810
getIndexCoordinates0.1320.0362.740
getTile0.5160.0603.210
makeTestGenoGAM0.0120.0000.012
makeTestGenoGAMDataSet0.1000.0242.632
makeTestGenomicTiles0.1240.0283.032
sizeFactors0.1280.0402.776
subset-GenoGAM-method0.1520.0000.153
subset-GenoGAMDataSet-method0.6520.0403.440
subset-GenomicTiles-method0.4360.0642.941
subsetByOverlaps-GenoGAM-ANY-method0.0880.0000.088
subsetByOverlaps-GenoGAMDataSet-GRanges-method0.2760.0282.904
subsetByOverlaps-GenomicTiles-GRanges-method0.2360.0443.125
tileSettings-elements0.1000.0162.677
tileSettings0.0840.0402.730
untile0.1960.0242.879