BioC 3.5: CHECK report for GenoGAM on oaxaca

Package: GenoGAM

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenoGAM_1.3.1.tar.gz

StartedAt: 2017-03-04 03:24:57 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:31:01 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 363.8 seconds

RetCode: 0

Status:  OK

CheckDir: GenoGAM.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenoGAM_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GenoGAM.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.1’
* 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
subset-GenomicTiles-method 128.663 31.105   3.778
GenomicTiles-metrics         1.847  0.148   5.162
GenomicTiles-view            0.657  0.285   9.960
filterData                   0.560  0.223   8.507
GenomicTiles                 0.172  0.150   5.862
changeSettings               0.143  0.141   6.285
* 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.

* 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)

name	user	system	elapsed
GenoGAM-methods	0.885	0.002	0.887
GenoGAM-view	0.232	0.001	0.234
GenoGAMDataSet	0.573	0.120	3.970
GenomicTiles-metrics	1.847	0.148	5.162
GenomicTiles-view	0.657	0.285	9.960
GenomicTiles	0.172	0.150	5.862
callPeaks	0.887	0.050	0.938
changeSettings	0.143	0.141	6.285
checkSettings	0.127	0.103	3.304
computeRegionSignificance	0.134	0.017	0.152
computeSignificance	0.067	0.007	0.074
computeSizeFactors	0.534	0.122	3.873
dataRange	0.223	0.102	3.636
design	0.161	0.096	3.561
filterData	0.560	0.223	8.507
fitGenoGAM	0.001	0.000	0.002
getChunkIndex	0.317	0.111	3.757
getCoordinates	0.124	0.090	3.741
getIndex	0.173	0.124	3.935
getIndexCoordinates	0.212	0.103	3.772
getTile	0.836	0.146	4.026
makeTestGenoGAM	0.015	0.001	0.016
makeTestGenoGAMDataSet	0.105	0.088	3.197
makeTestGenomicTiles	0.100	0.092	3.268
sizeFactors	0.106	0.076	3.149
subset-GenoGAM-method	0.099	0.012	0.111
subset-GenoGAMDataSet-method	0.801	0.141	3.983
subset-GenomicTiles-method	128.663	31.105	3.778
subsetByOverlaps-GenoGAM-ANY-method	0.104	0.001	0.105
subsetByOverlaps-GenoGAMDataSet-GRanges-method	0.294	0.111	3.470
subsetByOverlaps-GenomicTiles-GRanges-method	0.283	0.116	3.176
tileSettings-elements	0.115	0.099	2.975
tileSettings	0.110	0.085	2.930
untile	0.197	0.104	3.050