BioC 3.5: CHECK report for genphen on oaxaca

Package: genphen

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genphen_1.3.0.tar.gz

StartedAt: 2017-03-04 03:37:04 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:39:31 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 147.1 seconds

RetCode: 0

Status:  OK

CheckDir: genphen.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 genphen_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genphen.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 ‘genphen/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genphen’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘randomForest’ ‘e1071’ ‘ggplot2’ ‘effsize’ ‘Biostrings’ ‘rjags’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘genphen’ 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
getBayesianTtest : getDataList: no visible global function definition
  for ‘sd’
getBayesianTtest : getEss: no visible global function definition for
  ‘effectiveSize’
getBayesianTtest: no visible global function definition for ‘update’
getTTestScore: no visible global function definition for ‘t.test’
plotGenphenBayes: no visible binding for global variable ‘g.1’
plotGenphenBayes: no visible binding for global variable ‘site’
plotGenphenBayes: no visible binding for global variable ‘g.2’
plotGenphenRfSvm: no visible binding for global variable ‘ca.hdi.H’
plotGenphenRfSvm: no visible binding for global variable ‘ca.hdi.L’
plotGenphenRfSvm: no visible global function definition for
  ‘terrain.colors’
plotManhattan: no visible binding for global variable ‘t.test.pvalue’
Undefined global functions or variables:
  ca.hdi.H ca.hdi.L effectiveSize g.1 g.2 sd site t.test t.test.pvalue
  terrain.colors update
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("stats", "sd", "t.test", "update")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
runGenphenRf     13.059  0.154  13.216
plotGenphenBayes 11.720  0.033  13.093
plotGenphenRfSvm 10.152  0.299  10.489
runGenphenBayes  10.291  0.018  10.313
plotManhattan     6.675  0.446   7.122
* 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/genphen.Rcheck/00check.log’
for details.

* installing *source* package ‘genphen’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genphen)

name	user	system	elapsed
genotype.saap	0.008	0.001	0.008
genotype.saap.msa	0.003	0.001	0.003
genotype.snp	0.003	0.001	0.003
genotype.snp.msa	0.002	0.001	0.003
phenotype.saap	0.001	0.001	0.002
phenotype.snp	0.001	0.001	0.002
plotGenphenBayes	11.720	0.033	13.093
plotGenphenRfSvm	10.152	0.299	10.489
plotManhattan	6.675	0.446	7.122
plotSpecificGenotype	0.704	0.005	0.722
runGenphenBayes	10.291	0.018	10.313
runGenphenRf	13.059	0.154	13.216
runGenphenSvm	2.554	0.022	2.586