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CHECK report for DMRcate on tokay1

This page was generated on 2018-04-12 13:23:51 -0400 (Thu, 12 Apr 2018).

Package 376/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcate 1.14.0
Tim Peters
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/DMRcate
Branch: RELEASE_3_6
Last Commit: 3fe507a
Last Changed Date: 2017-10-30 12:40:12 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DMRcate
Version: 1.14.0
Command: rm -rf DMRcate.buildbin-libdir DMRcate.Rcheck && mkdir DMRcate.buildbin-libdir DMRcate.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRcate.buildbin-libdir DMRcate_1.14.0.tar.gz >DMRcate.Rcheck\00install.out 2>&1 && cp DMRcate.Rcheck\00install.out DMRcate-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DMRcate.buildbin-libdir --install="check:DMRcate-install.out" --force-multiarch --no-vignettes --timings DMRcate_1.14.0.tar.gz
StartedAt: 2018-04-11 23:34:16 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:51:15 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 1018.5 seconds
RetCode: 0
Status:  OK  
CheckDir: DMRcate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DMRcate.buildbin-libdir DMRcate.Rcheck && mkdir DMRcate.buildbin-libdir DMRcate.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRcate.buildbin-libdir DMRcate_1.14.0.tar.gz >DMRcate.Rcheck\00install.out 2>&1 && cp DMRcate.Rcheck\00install.out DMRcate-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DMRcate.buildbin-libdir --install="check:DMRcate-install.out" --force-multiarch --no-vignettes --timings DMRcate_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DMRcate.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DMRcate/DESCRIPTION' ... OK
* this is package 'DMRcate' version '1.14.0'
* 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 'DMRcate' 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
* 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 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 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
DMRcate-package 114.31   9.19  163.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
DMRcate-package 140.2   5.24  169.99
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: OK

Installation output

DMRcate.Rcheck/00install.out


install for i386

* installing *source* package 'DMRcate' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DMRcate'
    finding HTML links ... done
    DMR.plot                                html  
    DMRcate-internal                        html  
    DMRcate-package                         html  
    cpg.annotate                            html  
    dmrcate                                 html  
    extractRanges                           html  
    rmSNPandCH                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DMRcate' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRcate' as DMRcate_1.14.0.zip
* DONE (DMRcate)
In R CMD INSTALL
In R CMD INSTALL

Tests output

DMRcate.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("DMRcate")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply


Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'bsseq'

The following object is masked from 'package:minfi':

    getMeth



Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Fitting chr20...
Consecutive mode specified, lambda is now set at -1 consecutive CpGs.
Fitting chr20...
Demarcating regions...
Done!
Fitting chr20...
Demarcating regions...
Done!


RUNIT TEST PROTOCOL -- Wed Apr 11 23:49:00 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DMRcate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> 
> 
>   
> 
> proc.time()
   user  system elapsed 
 105.68    4.79  110.78

DMRcate.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("DMRcate")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply


Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit

locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'bsseq'

The following object is masked from 'package:minfi':

    getMeth



Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Your contrast returned 6091 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Fitting chr20...
Consecutive mode specified, lambda is now set at -1 consecutive CpGs.
Fitting chr20...
Demarcating regions...
Done!
Fitting chr20...
Demarcating regions...
Done!


RUNIT TEST PROTOCOL -- Wed Apr 11 23:51:10 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DMRcate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> 
> 
>   
> 
> proc.time()
   user  system elapsed 
 126.01    3.28  129.37

Example timings

DMRcate.Rcheck/examples_i386/DMRcate-Ex.timings

nameusersystemelapsed
DMR.plot000
DMRcate-package114.31 9.19163.47
cpg.annotate000
dmrcate000
extractRanges000
rmSNPandCH000

DMRcate.Rcheck/examples_x64/DMRcate-Ex.timings

nameusersystemelapsed
DMR.plot000
DMRcate-package140.20 5.24169.99
cpg.annotate000
dmrcate000
extractRanges000
rmSNPandCH0.010.000.02