BioC 3.5: CHECK report for DMRScan on tokay2

Package: DMRScan

Version: 1.0.0

Command: rm -rf DMRScan.buildbin-libdir DMRScan.Rcheck && mkdir DMRScan.buildbin-libdir DMRScan.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRScan.buildbin-libdir DMRScan_1.0.0.tar.gz >DMRScan.Rcheck\00install.out 2>&1 && cp DMRScan.Rcheck\00install.out DMRScan-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=DMRScan.buildbin-libdir --install="check:DMRScan-install.out" --force-multiarch --no-vignettes --timings DMRScan_1.0.0.tar.gz

StartedAt: 2017-10-17 23:22:25 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:32:37 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 612.4 seconds

RetCode: 0

Status:  OK

CheckDir: DMRScan.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf DMRScan.buildbin-libdir DMRScan.Rcheck && mkdir DMRScan.buildbin-libdir DMRScan.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRScan.buildbin-libdir DMRScan_1.0.0.tar.gz >DMRScan.Rcheck\00install.out 2>&1 && cp DMRScan.Rcheck\00install.out DMRScan-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=DMRScan.buildbin-libdir --install="check:DMRScan-install.out" --force-multiarch --no-vignettes --timings DMRScan_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/DMRScan.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 'DMRScan/DESCRIPTION' ... OK
* this is package 'DMRScan' version '1.0.0'
* 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 'DMRScan' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
makeCpGregions        57.28   0.05   57.33
DMRScan_slidingWindow 55.53   0.06   55.59
DMRScan_package       53.75   0.05   53.80
makeCpGgenes          49.81   0.05   49.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
DMRScan_slidingWindow 79.60   0.03   79.63
DMRScan_package       79.28   0.10   79.37
makeCpGregions        63.88   0.05   63.92
makeCpGgenes          63.84   0.03   63.88
* 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/DMRScan.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'DMRScan' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'DMRScan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRScan' as DMRScan_1.0.0.zip
* DONE (DMRScan)

name	user	system	elapsed
DMRScan.methylationData	0.40	0.04	0.46
DMRScan.phenotypes	0	0	0
DMRScan_package	53.75	0.05	53.80
DMRScan_slidingWindow	55.53	0.06	55.59
Region-class_init	0	0	0
RegionList-class_init	0	0	0
Rt-methods	0	0	0
St-methods	0	0	0
estimateThreshold	0.05	0.00	0.05
getRegions	0	0	0
makeCpGgenes	49.81	0.05	49.86
makeCpGregions	57.28	0.05	57.33
nCpG	0	0	0
pVal	0	0	0
pos	0	0	0
setRegion	0	0	0
tVal	0	0	0

name	user	system	elapsed
DMRScan.methylationData	0.78	0.03	0.81
DMRScan.phenotypes	0	0	0
DMRScan_package	79.28	0.10	79.37
DMRScan_slidingWindow	79.60	0.03	79.63
Region-class_init	0	0	0
RegionList-class_init	0	0	0
Rt-methods	0	0	0
St-methods	0	0	0
estimateThreshold	0.06	0.00	0.06
getRegions	0	0	0
makeCpGgenes	63.84	0.03	63.88
makeCpGregions	63.88	0.05	63.92
nCpG	0	0	0
pVal	0	0	0
pos	0	0	0
setRegion	0	0	0
tVal	0	0	0