BioC 3.4: CHECK report for GenoGAM on morelia

Package: GenoGAM

Version: 1.1.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenoGAM_1.1.4.tar.gz

StartedAt: 2016-09-20 07:03:16 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:06:11 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 175.0 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_1.1.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘1.1.4’
* 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’
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’
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 gene optim p.adjust pnorm pvalue
  runif
Consider adding
  importFrom("stats", "as.formula", "coefficients", "dnbinom", "optim",
             "p.adjust", "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-3.4-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	0.208	0.004	0.211
GenoGAMDataSet	0	0	0
GenomicTiles-metrics	1.568	0.027	1.594
GenomicTiles-view	0.662	0.002	0.664
GenomicTiles	0.299	0.001	0.299
changeSettings	0.284	0.000	0.285
checkSettings	0.181	0.001	0.182
computeSizeFactors	0.357	0.001	0.358
dataRange	0.189	0.000	0.189
design	0.184	0.001	0.185
fitGenoGAM	0.001	0.000	0.001
getChunkIndex	0.256	0.001	0.257
getCoordinates	0.169	0.000	0.169
getFits	0.015	0.001	0.015
getIndex	0.188	0.000	0.189
getIndexCoordinates	0.229	0.000	0.228
getTile	0.413	0.001	0.414
makeTestGenoGAM	0.023	0.000	0.023
makeTestGenoGAMDataSet	0.151	0.000	0.152
makeTestGenomicTiles	0.166	0.000	0.165
sizeFactors	0.169	0.000	0.170
subset-GenoGAM-method	0.084	0.001	0.084
subset-GenoGAMDataSet-method	0.316	0.000	0.316
subset-GenomicTiles-method	0.330	0.001	0.331
subsetByOverlaps-GenoGAM-ANY-method	0.049	0.000	0.049
subsetByOverlaps-GenoGAMDataSet-GRanges-method	0.360	0.001	0.360
subsetByOverlaps-GenomicTiles-GRanges-method	0.254	0.000	0.255
tileSettings-elements	0.177	0.000	0.177
tileSettings	0.179	0.000	0.179
untile	0.231	0.000	0.232