BioC 3.6: CHECK report for MultiDataSet on veracruz1

Package: MultiDataSet

Version: 1.5.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiDataSet_1.5.4.tar.gz

StartedAt: 2017-08-16 06:02:36 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:06:07 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 211.1 seconds

RetCode: 0

Status:  OK

CheckDir: MultiDataSet.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 MultiDataSet_1.5.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MultiDataSet.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiDataSet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiDataSet’ version ‘1.5.4’
* 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 ‘MultiDataSet’ 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘Biobase:::assayDataEnvLock’ ‘Biobase:::assayDataStorageMode’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
lambdaClayton: no visible global function definition for ‘qnorm’
lambdaClayton: no visible global function definition for ‘qchisq’
qq_plot: no visible global function definition for ‘qbeta’
add_methy,MultiDataSet-RatioSet: no visible global function definition
  for ‘rowData’
Undefined global functions or variables:
  qbeta qchisq qnorm rowData
Consider adding
  importFrom("stats", "qbeta", "qchisq", "qnorm")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getMs-methods 11.914  1.421  13.755
add_methy      7.919  0.924   9.086
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/MultiDataSet.Rcheck/00check.log’
for details.

* installing *source* package ‘MultiDataSet’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
in method for ‘add_methy’ with signature ‘"MultiDataSet","RatioSet"’: no definition for class “RatioSet”
in method for ‘add_methy’ with signature ‘"MultiDataSet","GenomicRatioSet"’: no definition for class “GenomicRatioSet”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MultiDataSet)

name	user	system	elapsed
MethylationSet-class	0.002	0.000	0.003
MultiDataSet-class	0.002	0.000	0.003
ResultSet-class	0.002	0.001	0.002
add_eset	0.204	0.003	0.212
add_genexp	0.534	0.004	0.549
add_methy	7.919	0.924	9.086
add_rnaseq-methods	0.087	0.000	0.086
add_rse	0.220	0.016	0.246
add_se	0.224	0.010	0.239
add_snps	0.052	0.000	0.059
add_table	0.010	0.001	0.010
chrNumToChar	0.001	0.000	0.001
commonIds	0.105	0.001	0.106
commonSamples	0.275	0.001	0.283
getAssociation-methods	0.056	0.005	0.064
getMs-methods	11.914	1.421	13.755
lambdaClayton	0.002	0.000	0.002
opt-methods	0.002	0.001	0.003
qq_plot	2.749	0.206	3.030
rowRangesElements	0.124	0.001	0.133
volcano_plot	0.602	0.016	0.636