BioC 3.5: CHECK report for MEAL on tokay2

Package: MEAL

Version: 1.6.0

Command: rm -rf MEAL.buildbin-libdir MEAL.Rcheck && mkdir MEAL.buildbin-libdir MEAL.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.6.0.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.6.0.tar.gz

StartedAt: 2017-10-18 01:06:37 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:27:21 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 1244.0 seconds

RetCode: 0

Status:  OK

CheckDir: MEAL.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MEAL.buildbin-libdir MEAL.Rcheck && mkdir MEAL.buildbin-libdir MEAL.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.6.0.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.6.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEAL/DESCRIPTION' ... OK
* this is package 'MEAL' version '1.6.0'
* package encoding: UTF-8
* 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 'MEAL' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
correlationMethSNPs: no visible binding for global variable 'num_cores'
prepareMethylationSet: no visible global function definition for
  'colData'
Undefined global functions or variables:
  colData num_cores
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotRDA-methods    53.16   0.97   54.12
topRDAhits-methods 48.35   0.87   49.23
plotRegion-methods 43.33   0.89   44.22
DAPipeline         22.53   2.23   26.28
DARegion            6.31   0.41    6.75
DARegionAnalysis    5.60   0.81    6.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
topRDAhits-methods 65.07   0.93   66.04
plotRDA-methods    55.31   0.87   56.19
plotRegion-methods 54.99   0.96   55.94
DAPipeline         20.37   0.98   21.36
DARegion            6.50   0.30    6.80
plotQQ-methods      5.67   0.33    6.00
DARegionAnalysis    5.09   0.48    5.58
plotEWAS-methods    5.23   0.33    5.56
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MEAL' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MEAL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEAL' as MEAL_1.6.0.zip
* DONE (MEAL)

name	user	system	elapsed
AnalysisRegionResults-class	0.00	0.02	0.02
AnalysisResults-class	0	0	0
DAPipeline	22.53	2.23	26.28
DAProbe	1.13	0.06	1.19
DARegion	6.31	0.41	6.75
DARegionAnalysis	5.60	0.81	6.41
RDAset	2.55	0.14	2.69
calculateRelevantSNPs	0	0	0
createRanges	0.01	0.00	0.01
explainedVariance	0.03	0.00	0.03
exportResults-methods	3.00	0.33	3.33
filterSet-methods	1.00	0.06	1.06
getGeneVals-methods	2.83	0.20	3.07
normalSNP	0	0	0
plotBestFeatures	3.0	0.2	3.2
plotEWAS-methods	3.09	0.33	3.42
plotFeature	1.37	0.11	1.48
plotLM	0.27	0.00	0.27
plotQQ-methods	2.81	0.25	3.06
plotRDA-methods	53.16	0.97	54.12
plotRegion-methods	43.33	0.89	44.22
plotVolcano-methods	2.57	0.33	2.91
prepareMethylationSet	1.28	0.08	1.36
preparePhenotype	0	0	0
topRDAhits-methods	48.35	0.87	49.23

name	user	system	elapsed
AnalysisRegionResults-class	0	0	0
AnalysisResults-class	0	0	0
DAPipeline	20.37	0.98	21.36
DAProbe	0.92	0.11	1.03
DARegion	6.5	0.3	6.8
DARegionAnalysis	5.09	0.48	5.58
RDAset	1.72	0.14	1.85
calculateRelevantSNPs	0	0	0
createRanges	0.03	0.00	0.04
explainedVariance	0.03	0.00	0.03
exportResults-methods	3.16	0.33	3.50
filterSet-methods	1.10	0.03	1.14
getGeneVals-methods	3.27	0.31	3.58
normalSNP	0	0	0
plotBestFeatures	3.36	0.16	3.52
plotEWAS-methods	5.23	0.33	5.56
plotFeature	1.53	0.23	1.77
plotLM	0.33	0.00	0.32
plotQQ-methods	5.67	0.33	6.00
plotRDA-methods	55.31	0.87	56.19
plotRegion-methods	54.99	0.96	55.94
plotVolcano-methods	3.16	0.28	3.44
prepareMethylationSet	1.39	0.16	1.55
preparePhenotype	0.02	0.00	0.01
topRDAhits-methods	65.07	0.93	66.04