BioC 3.6: CHECK report for MultiDataSet on tokay1

Package: MultiDataSet

Version: 1.5.4

Command: rm -rf MultiDataSet.buildbin-libdir MultiDataSet.Rcheck && mkdir MultiDataSet.buildbin-libdir MultiDataSet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MultiDataSet.buildbin-libdir MultiDataSet_1.5.4.tar.gz >MultiDataSet.Rcheck\00install.out 2>&1 && cp MultiDataSet.Rcheck\00install.out MultiDataSet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MultiDataSet.buildbin-libdir --install="check:MultiDataSet-install.out" --force-multiarch --no-vignettes --timings MultiDataSet_1.5.4.tar.gz

StartedAt: 2017-08-16 01:06:23 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:12:13 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 350.2 seconds

RetCode: 0

Status:  OK

CheckDir: MultiDataSet.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MultiDataSet.buildbin-libdir MultiDataSet.Rcheck && mkdir MultiDataSet.buildbin-libdir MultiDataSet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MultiDataSet.buildbin-libdir MultiDataSet_1.5.4.tar.gz >MultiDataSet.Rcheck\00install.out 2>&1 && cp MultiDataSet.Rcheck\00install.out MultiDataSet-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MultiDataSet.buildbin-libdir --install="check:MultiDataSet-install.out" --force-multiarch --no-vignettes --timings MultiDataSet_1.5.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MultiDataSet.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getMs-methods 14.55   1.59   16.14
add_methy      8.05   0.84   11.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getMs-methods 13.74   1.16   14.89
add_methy      9.28   0.70    9.99
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/MultiDataSet.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'MultiDataSet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MultiDataSet' as MultiDataSet_1.5.4.zip
* DONE (MultiDataSet)

name	user	system	elapsed
MethylationSet-class	0	0	0
MultiDataSet-class	0	0	0
ResultSet-class	0	0	0
add_eset	0.09	0.06	0.15
add_genexp	0.39	0.00	0.39
add_methy	8.05	0.84	11.64
add_rnaseq-methods	0.06	0.00	0.07
add_rse	0.14	0.05	0.18
add_se	0.19	0.00	0.19
add_snps	0.05	0.00	0.04
add_table	0	0	0
chrNumToChar	0	0	0
commonIds	0.09	0.00	0.10
commonSamples	0.2	0.0	0.2
getAssociation-methods	0.05	0.00	0.05
getMs-methods	14.55	1.59	16.14
lambdaClayton	0	0	0
opt-methods	0	0	0
qq_plot	2.11	0.23	2.40
rowRangesElements	0.07	0.00	0.08
volcano_plot	0.43	0.07	0.49

name	user	system	elapsed
MethylationSet-class	0	0	0
MultiDataSet-class	0	0	0
ResultSet-class	0	0	0
add_eset	0.17	0.00	0.17
add_genexp	0.55	0.00	0.55
add_methy	9.28	0.70	9.99
add_rnaseq-methods	0.08	0.00	0.08
add_rse	0.20	0.02	0.21
add_se	0.22	0.00	0.22
add_snps	0.03	0.00	0.03
add_table	0	0	0
chrNumToChar	0	0	0
commonIds	0.11	0.00	0.11
commonSamples	0.30	0.00	0.29
getAssociation-methods	0.04	0.00	0.05
getMs-methods	13.74	1.16	14.89
lambdaClayton	0	0	0
opt-methods	0.00	0.01	0.02
qq_plot	1.83	0.11	2.03
rowRangesElements	0.21	0.00	0.22
volcano_plot	0.61	0.02	0.79