BioC 3.4: CHECK report for MEAL on tokay1

Package: MEAL

Version: 1.4.2

Command: rm -rf MEAL.buildbin-libdir MEAL.Rcheck && mkdir MEAL.buildbin-libdir MEAL.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.4.2.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.4.2.tar.gz

StartedAt: 2017-04-14 23:21:49 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:39:25 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 1055.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MEAL.Rcheck

Warnings: 1

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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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.4.2.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.4.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/MEAL.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.4.2'
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'multiCorrMethExprs'
All user-level objects in a package 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotRDA-methods    36.61   0.73   37.34
plotRegion-methods 33.56   0.58   34.16
topRDAhits-methods 32.82   0.50   33.33
DAPipeline         16.61   1.23   17.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
topRDAhits-methods 49.89   0.57   50.45
plotRDA-methods    41.45   0.61   42.08
plotRegion-methods 40.97   0.64   41.61
DAPipeline         18.50   0.82   19.32
RDAset              5.91   0.08    5.98
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.4-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_1.4.2.zip
* DONE (MEAL)

name	user	system	elapsed
AnalysisRegionResults-class	0.00	0.02	0.01
AnalysisResults-class	0	0	0
DAPipeline	16.61	1.23	17.85
DAProbe	0.51	0.08	0.59
DARegion	3.66	0.26	3.92
DARegionAnalysis	3.75	0.66	4.41
RDAset	2.67	0.11	2.78
calculateRelevantSNPs	0	0	0
createRanges	0.02	0.00	0.02
explainedVariance	0.01	0.00	0.01
exportResults-methods	2.68	0.05	2.78
filterSet-methods	1.73	0.01	1.75
getGeneVals-methods	2.48	0.05	2.53
normalSNP	0	0	0
plotBestFeatures	2.20	0.03	2.24
plotEWAS-methods	2.90	0.08	3.00
plotFeature	2.14	0.08	2.22
plotLM	0.16	0.01	0.18
plotQQ-methods	3.42	0.10	3.51
plotRDA-methods	36.61	0.73	37.34
plotRegion-methods	33.56	0.58	34.16
plotVolcano-methods	3.72	0.17	3.89
preparePhenotype	0	0	0
topRDAhits-methods	32.82	0.50	33.33

name	user	system	elapsed
AnalysisRegionResults-class	0.02	0.00	0.02
AnalysisResults-class	0	0	0
DAPipeline	18.50	0.82	19.32
DAProbe	0.51	0.02	0.53
DARegion	4.2	0.2	4.4
DARegionAnalysis	4.53	0.28	4.82
RDAset	5.91	0.08	5.98
calculateRelevantSNPs	0	0	0
createRanges	0.02	0.00	0.01
explainedVariance	0.01	0.00	0.02
exportResults-methods	4.35	0.03	4.43
filterSet-methods	2.06	0.00	2.07
getGeneVals-methods	3.72	0.05	3.76
normalSNP	0	0	0
plotBestFeatures	2.82	0.06	2.87
plotEWAS-methods	4.65	0.06	4.72
plotFeature	2.63	0.07	2.69
plotLM	0.2	0.0	0.2
plotQQ-methods	4.24	0.11	4.34
plotRDA-methods	41.45	0.61	42.08
plotRegion-methods	40.97	0.64	41.61
plotVolcano-methods	4.80	0.15	4.95
preparePhenotype	0.02	0.00	0.02
topRDAhits-methods	49.89	0.57	50.45