BioC 3.4: CHECK report for MultiDataSet on zin1

Package: MultiDataSet

Version: 1.1.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MultiDataSet_1.1.2.tar.gz

StartedAt: 2016-09-20 09:44:43 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:48:16 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 213.3 seconds

RetCode: 0

Status:  OK

CheckDir: MultiDataSet.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MultiDataSet_1.1.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MultiDataSet.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.1.2’
* 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
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 ... 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
add_methy 15.072  1.296  17.493
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-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	0.000	0.000	0.001
MultiDataSet-class	0.000	0.000	0.001
add_eset	0.084	0.008	0.093
add_genexp	0.096	0.004	0.100
add_methy	15.072	1.296	17.493
add_rnaseq-methods	0.048	0.000	0.049
add_rse	0.128	0.004	0.129
add_snps	0.048	0.000	0.047
checkProbes-methods	2.156	0.028	2.182
checkSamples-methods	2.168	0.000	2.165
chrNumToChar	0	0	0
commonIds	0.120	0.000	0.117
commonSamples	0.180	0.000	0.181
getMs-methods	2.668	0.052	2.720
prepareMethylationSet	1.744	0.028	1.771