BioC 3.3: CHECK report for GenoGAM on oaxaca

Package: GenoGAM

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenoGAM_1.0.3.tar.gz

StartedAt: 2016-10-13 01:53:38 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:58:08 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 269.9 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_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GenoGAM.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.0.3’
* 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’
.extractSplines: no visible global function definition for
  ‘coefficients’
.getFunctions: no visible global function definition for ‘coefficients’
.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’
genogam: no visible global function definition for ‘as.formula’
makeTestGenoGAM: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as.formula coefficients dnbinom optim pnorm runif
Consider adding
  importFrom("stats", "as.formula", "coefficients", "dnbinom", "optim",
             "pnorm", "runif")
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 ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-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-view	0.258	0.003	0.263
GenoGAMDataSet	0.001	0.000	0.001
GenomicTiles-metrics	1.717	0.007	1.726
GenomicTiles-view	1.021	0.004	1.028
GenomicTiles	0.415	0.001	0.417
changeSettings	0.493	0.001	0.494
checkSettings	0.273	0.001	0.327
computeSizeFactors	0.653	0.002	0.655
dataRange	0.305	0.001	0.306
design	0.276	0.001	0.277
fitGenoGAM	0.001	0.000	0.000
getChunkIndex	0.414	0.000	0.415
getCoordinates	0.291	0.001	0.292
getFits	0.028	0.000	0.028
getIndex	0.323	0.001	0.326
getIndexCoordinates	0.422	0.002	0.517
getTile	0.671	0.001	0.673
makeTestGenoGAM	0.019	0.000	0.019
makeTestGenoGAMDataSet	0.263	0.000	0.264
makeTestGenomicTiles	0.287	0.000	0.289
sizeFactors	0.264	0.001	0.264
subset-GenoGAM-method	0.453	0.001	0.454
subset-GenoGAMDataSet-method	0.572	0.029	0.602
subset-GenomicTiles-method	0.538	0.002	0.541
subsetByOverlaps-GenoGAM-ANY-method	0.089	0.001	0.090
subsetByOverlaps-GenoGAMDataSet-GRanges-method	0.446	0.001	0.447
subsetByOverlaps-GenomicTiles-GRanges-method	0.465	0.001	0.467
tileSettings-elements	0.275	0.001	0.276
tileSettings	0.291	0.001	0.291
untile	0.378	0.001	0.380