BioC 3.5: CHECK report for MultiDataSet on veracruz2

Package: MultiDataSet

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiDataSet_1.4.0.tar.gz

StartedAt: 2017-08-16 05:45:54 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:49:34 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 220.0 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.4.0’
* 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
add_methy,MultiDataSet-RatioSet: no visible global function definition
  for ‘rowData’
Undefined global functions or variables:
  rowData
* 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 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        11.893  1.502  13.778
checkProbes-methods  10.825  1.345  12.500
add_methy             8.183  0.924   9.353
checkSamples-methods  5.444  1.080   6.771
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘limma’
'library' or 'require' call not declared from: ‘limma’
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MultiDataSet.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
MethylationSet-class	0.001	0.000	0.002
MultiDataSet-class	0.001	0.001	0.002
add_eset	0.187	0.014	0.206
add_genexp	0.568	0.016	0.591
add_methy	8.183	0.924	9.353
add_rnaseq-methods	0.088	0.001	0.088
add_rse	0.238	0.017	0.256
add_se	0.211	0.013	0.227
add_snps	0.056	0.000	0.057
add_table	0.008	0.000	0.009
checkProbes-methods	10.825	1.345	12.500
checkSamples-methods	5.444	1.080	6.771
chrNumToChar	0.001	0.000	0.000
commonIds	0.121	0.001	0.124
commonSamples	0.164	0.003	0.167
getMs-methods	11.893	1.502	13.778
rowRangesElements	0.107	0.001	0.108