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

EndedAt: 2017-08-16 01:21:22 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 1208.5 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 3.4.1 (2017-06-30)
* 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    38.58   0.89   39.46
topRDAhits-methods 38.13   0.72   38.86
plotRegion-methods 37.01   0.66   37.67
DAPipeline         21.40   1.95   28.98
DARegion            4.98   0.47    5.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotRDA-methods    56.96   0.85   57.81
plotRegion-methods 54.69   0.90   55.59
topRDAhits-methods 51.38   0.86   52.23
DAPipeline         22.72   1.19   23.91
DARegion            6.86   0.38    7.23
plotEWAS-methods    5.19   0.20    5.39
* 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	0	0
AnalysisResults-class	0	0	0
DAPipeline	21.40	1.95	28.98
DAProbe	0.80	0.14	0.94
DARegion	4.98	0.47	5.54
DARegionAnalysis	3.86	0.67	4.53
RDAset	1.42	0.10	1.52
calculateRelevantSNPs	0	0	0
createRanges	0.01	0.00	0.01
explainedVariance	0.02	0.01	0.03
exportResults-methods	2.59	0.27	2.92
filterSet-methods	1.02	0.01	1.04
getGeneVals-methods	3.91	0.19	4.09
normalSNP	0	0	0
plotBestFeatures	3.01	0.27	3.28
plotEWAS-methods	2.28	0.23	2.52
plotFeature	1.45	0.14	1.60
plotLM	0.24	0.02	0.25
plotQQ-methods	3.03	0.20	3.23
plotRDA-methods	38.58	0.89	39.46
plotRegion-methods	37.01	0.66	37.67
plotVolcano-methods	3.48	0.25	3.73
prepareMethylationSet	0.94	0.09	1.03
preparePhenotype	0	0	0
topRDAhits-methods	38.13	0.72	38.86

name	user	system	elapsed
AnalysisRegionResults-class	0	0	0
AnalysisResults-class	0	0	0
DAPipeline	22.72	1.19	23.91
DAProbe	1.45	0.09	1.54
DARegion	6.86	0.38	7.23
DARegionAnalysis	3.95	0.34	4.30
RDAset	1.80	0.09	1.89
calculateRelevantSNPs	0	0	0
createRanges	0.03	0.00	0.03
explainedVariance	0.03	0.00	0.03
exportResults-methods	2.92	0.28	3.20
filterSet-methods	1.23	0.01	1.25
getGeneVals-methods	3.03	0.27	3.30
normalSNP	0	0	0
plotBestFeatures	3.78	0.16	3.93
plotEWAS-methods	5.19	0.20	5.39
plotFeature	1.79	0.15	1.97
plotLM	0.33	0.00	0.32
plotQQ-methods	3.89	0.19	4.08
plotRDA-methods	56.96	0.85	57.81
plotRegion-methods	54.69	0.90	55.59
plotVolcano-methods	3.40	0.24	3.64
prepareMethylationSet	1.88	0.12	2.00
preparePhenotype	0	0	0
topRDAhits-methods	51.38	0.86	52.23