BioC 3.3: CHECK report for MEAL on windows2.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-3.3-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-3.3-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 03:52:44 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:02:11 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 567.3 seconds

RetCode: 0

Status:  OK

CheckDir: MEAL.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MEAL.buildbin-libdir MEAL.Rcheck && mkdir MEAL.buildbin-libdir MEAL.Rcheck && c:\biocbld\bbs-3.3-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-3.3-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
###
##############################################################################
##############################################################################


* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/MEAL.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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'
Undefined global functions or variables:
  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' ... [77s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
DAPipeline         13.25   1.17   14.42
plotRegion-methods  9.17   0.52    9.69
plotRDA-methods     7.54   0.65    8.20
add.methy-methods   5.75   0.72    6.47
DARegionAnalysis    5.75   0.31    6.07
** running examples for arch 'x64' ... [88s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
DAPipeline         15.14   0.77   15.90
plotRegion-methods 10.18   0.51   10.70
plotRDA-methods     8.50   0.52    9.01
add.methy-methods   8.06   0.41    8.47
DARegionAnalysis    8.21   0.21    8.43
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [58s]
 [58s] 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-3.3-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	13.25	1.17	14.42
DAProbe	0.46	0.08	0.53
DARegion	1.55	0.20	1.75
DARegionAnalysis	5.75	0.31	6.07
MethylationSet-class	0	0	0
RDAset	0.97	0.08	1.05
add.genexp-methods	0.04	0.00	0.05
add.methy-methods	5.75	0.72	6.47
add.set-methods	0.03	0.00	0.04
calculateRelevantSNPs	0	0	0
checkProbes-methods	1.31	0.03	1.36
checkSamples-methods	0.99	0.02	1.00
chrNumToChar	0	0	0
createRanges	0.02	0.00	0.02
explainedVariance	0.01	0.00	0.01
exportResults-methods	1.64	0.11	1.75
filterSet-methods	1.1	0.0	1.1
getGeneVals-methods	1.55	0.09	1.64
getMs-methods	0.86	0.02	0.88
normalSNP	0	0	0
plotBestFeatures	1.97	0.14	2.11
plotEWAS-methods	2.29	0.11	2.39
plotFeature	1.44	0.03	1.47
plotQQ-methods	2.14	0.19	2.33
plotRDA-methods	7.54	0.65	8.20
plotRegion-methods	9.17	0.52	9.69
plotVolcano-methods	2.17	0.33	2.50
prepareMethylationSet	1.28	0.09	1.37
preparePhenotype	0	0	0

name	user	system	elapsed
AnalysisRegionResults-class	0.02	0.00	0.02
AnalysisResults-class	0	0	0
DAPipeline	15.14	0.77	15.90
DAProbe	0.39	0.02	0.41
DARegion	2.08	0.11	2.19
DARegionAnalysis	8.21	0.21	8.43
MethylationSet-class	0	0	0
RDAset	1.42	0.11	1.53
add.genexp-methods	0.09	0.00	0.10
add.methy-methods	8.06	0.41	8.47
add.set-methods	0.05	0.00	0.04
calculateRelevantSNPs	0	0	0
checkProbes-methods	1.3	0.0	1.3
checkSamples-methods	1.89	0.05	1.93
chrNumToChar	0	0	0
createRanges	0.03	0.00	0.03
explainedVariance	0.03	0.01	0.05
exportResults-methods	1.80	0.11	1.90
filterSet-methods	1.33	0.02	1.34
getGeneVals-methods	2.93	0.20	3.14
getMs-methods	1.12	0.00	1.13
normalSNP	0	0	0
plotBestFeatures	1.58	0.06	1.64
plotEWAS-methods	1.72	0.11	1.83
plotFeature	1.36	0.06	1.42
plotQQ-methods	1.32	0.08	1.39
plotRDA-methods	8.50	0.52	9.01
plotRegion-methods	10.18	0.51	10.70
plotVolcano-methods	1.23	0.16	1.39
prepareMethylationSet	1.52	0.14	1.65
preparePhenotype	0	0	0