BioC 3.3: CHECK report for MultiDataSet on morelia

Package: MultiDataSet

Version: 0.99.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiDataSet_0.99.9.tar.gz

StartedAt: 2016-04-18 04:42:08 -0700 (Mon, 18 Apr 2016)

EndedAt: 2016-04-18 04:46:59 -0700 (Mon, 18 Apr 2016)

EllapsedTime: 290.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MultiDataSet.Rcheck

Warnings: 1

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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_0.99.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MultiDataSet.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘0.99.9’
* 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 ... [21s/21s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'MultiDataSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [43s/46s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
add_methy 16.976  1.431  20.901
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [35s/42s]
 [35s/42s] 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/MultiDataSet.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
MethylationSet-class	0.003	0.000	0.002
MultiDataSet-class	0.001	0.000	0.001
add_eset	0.078	0.000	0.078
add_genexp	0.048	0.001	0.048
add_methy	16.976	1.431	20.901
add_rnaseq-methods	0.052	0.000	0.052
add_rse	0.232	0.008	0.241
add_snps	0.040	0.004	0.044
checkProbes-methods	3.293	0.043	3.339
checkSamples-methods	3.484	0.019	3.508
chrNumToChar	0.001	0.001	0.001
commonIds	0.091	0.000	0.091
commonSamples	0.138	0.001	0.139
getMs-methods	3.690	0.139	3.834
prepareMethylationSet	2.839	0.121	2.964