Package: GenoGAM

Version: 1.8.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GenoGAM.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GenoGAM_1.8.0.tar.gz

StartedAt: 2018-10-16 00:42:03 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:45:11 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 187.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenoGAM.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GenoGAM.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GenoGAM_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/GenoGAM.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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 ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/biocbuild/bbs-3.7-bioc/meat/GenoGAM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 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 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/GenoGAM.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL GenoGAM
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘GenoGAM’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenoGAM)

name	user	system	elapsed
GenoGAM-methods	0.180	0.000	0.181
GenoGAM-view	0.088	0.000	0.089
GenoGAMDataSet	1.364	0.296	1.440
GenomicTiles-metrics	1.972	0.292	2.055
GenomicTiles-view	1.648	0.648	1.659
GenomicTiles	0.692	0.300	0.694
callPeaks	0.600	0.036	0.650
changeSettings	0.744	0.368	0.747
checkSettings	0.488	0.176	0.489
computeRegionSignificance	0.188	0.020	0.210
computeSignificance	0.020	0.004	0.025
computeSizeFactors	0.732	0.216	0.791
dataRange	0.376	0.148	0.363
design	0.404	0.152	0.384
filterData	1.016	0.384	0.971
fitGenoGAM	0	0	0
getChunkIndex	0.560	0.136	0.553
getCoordinates	0.556	0.192	0.494
getIndex	0.512	0.224	0.515
getIndexCoordinates	0.576	0.236	0.566
getTile	0.816	0.200	0.788
makeTestGenoGAM	0.012	0.000	0.011
makeTestGenoGAMDataSet	0.516	0.220	0.473
makeTestGenomicTiles	0.412	0.184	0.401
sizeFactors	0.480	0.220	0.469
subset-GenoGAM-method	0.068	0.000	0.068
subset-GenoGAMDataSet-method	0.932	0.216	0.932
subset-GenomicTiles-method	0.716	0.180	0.707
subsetByOverlaps-GenoGAM-ANY-method	0.040	0.004	0.047
subsetByOverlaps-GenoGAMDataSet-GRanges-method	0.552	0.224	0.559
subsetByOverlaps-GenomicTiles-GRanges-method	0.56	0.20	0.53
tileSettings-elements	0.408	0.156	0.393
tileSettings	0.396	0.160	0.369
untile	0.516	0.196	0.517