BioC 3.2: CHECK report for MEAL on windows1.bioconductor.org

Package: MEAL

Version: 1.0.1

Command: rm -rf MEAL.buildbin-libdir MEAL.Rcheck && mkdir MEAL.buildbin-libdir MEAL.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.0.1.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.0.1.tar.gz

StartedAt: 2015-10-27 03:17:51 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:27:34 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 583.5 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:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.0.1.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.0.1.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/MEAL.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.0.1'
* 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 ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::selectSome'
  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
plotVolcano,AnalysisResults: no visible binding for global variable
  'adj.p'
* 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' ... [74s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
DAPipeline         13.35   1.01   14.36
plotRDA-methods     7.69   0.67    8.36
plotRegion-methods  7.00   0.43    7.44
add.methy-methods   6.16   0.89    7.05
DARegionAnalysis    5.34   0.33    5.67
** running examples for arch 'x64' ... [88s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
DAPipeline         13.97   0.64   14.61
plotRegion-methods  9.69   0.38   10.06
plotRDA-methods     8.34   0.42    8.76
add.methy-methods   8.01   0.56    8.58
DARegionAnalysis    7.22   0.19    7.40
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [52s]
 [53s] OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [62s]
 [63s] 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:/biocbld/bbs-3.2-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_1.0.1.zip
* DONE (MEAL)

name	user	system	elapsed
AnalysisRegionResults-class	0	0	0
AnalysisResults-class	0	0	0
DAPipeline	13.35	1.01	14.36
DAProbe	0.61	0.07	0.67
DARegion	1.53	0.09	1.62
DARegionAnalysis	5.34	0.33	5.67
MethylationSet-class	0	0	0
RDAset	1.08	0.04	1.13
add.genexp-methods	0.05	0.00	0.04
add.methy-methods	6.16	0.89	7.05
add.set-methods	0.03	0.00	0.04
calculateRelevantSNPs	0	0	0
checkProbes-methods	1.16	0.05	1.20
checkSamples-methods	1.46	0.06	1.52
chrNumToChar	0	0	0
createRanges	0.02	0.00	0.01
explainedVariance	0.01	0.00	0.02
exportResults-methods	1.04	0.05	1.08
filterSet-methods	1.26	0.06	1.32
getGeneVals-methods	1.01	0.07	1.08
getMs-methods	1.25	0.07	1.33
normalSNP	0	0	0
plotBestFeatures	1.44	0.02	1.45
plotEWAS-methods	1.82	0.09	1.93
plotFeature	1.81	0.08	1.89
plotQQ-methods	1.78	0.10	1.88
plotRDA-methods	7.69	0.67	8.36
plotRegion-methods	7.00	0.43	7.44
plotVolcano-methods	1.70	0.14	1.84
prepareMethylationSet	1.03	0.05	1.08
preparePhenotype	0.02	0.00	0.01

name	user	system	elapsed
AnalysisRegionResults-class	0	0	0
AnalysisResults-class	0.02	0.00	0.02
DAPipeline	13.97	0.64	14.61
DAProbe	0.54	0.05	0.58
DARegion	2.05	0.12	2.17
DARegionAnalysis	7.22	0.19	7.40
MethylationSet-class	0	0	0
RDAset	1.32	0.10	1.41
add.genexp-methods	0.05	0.00	0.05
add.methy-methods	8.01	0.56	8.58
add.set-methods	0.05	0.00	0.04
calculateRelevantSNPs	0	0	0
checkProbes-methods	1.23	0.01	1.25
checkSamples-methods	1.28	0.00	1.28
chrNumToChar	0	0	0
createRanges	0.02	0.00	0.02
explainedVariance	0.03	0.00	0.03
exportResults-methods	1.83	0.08	2.08
filterSet-methods	1.13	0.03	1.16
getGeneVals-methods	2.60	0.14	2.74
getMs-methods	0.99	0.02	1.00
normalSNP	0	0	0
plotBestFeatures	1.72	0.06	1.78
plotEWAS-methods	2.26	0.17	2.43
plotFeature	1.98	0.10	2.08
plotQQ-methods	2.18	0.14	2.31
plotRDA-methods	8.34	0.42	8.76
plotRegion-methods	9.69	0.38	10.06
plotVolcano-methods	2.16	0.07	2.24
prepareMethylationSet	1.34	0.03	1.38
preparePhenotype	0	0	0