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CHECK report for MIRA on tokay2

This page was generated on 2019-10-16 12:39:32 -0400 (Wed, 16 Oct 2019).

Package 1006/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIRA 1.6.0
John Lawson
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MIRA
Branch: RELEASE_3_9
Last Commit: e4c8897
Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MIRA
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MIRA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MIRA_1.6.0.tar.gz
StartedAt: 2019-10-16 05:14:49 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:20:42 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 352.9 seconds
RetCode: 0
Status:  OK  
CheckDir: MIRA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MIRA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MIRA_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MIRA.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MIRA/DESCRIPTION' ... OK
* this is package 'MIRA' version '1.6.0'
* 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 'MIRA' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: OK


Installation output

MIRA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MIRA_1.6.0.tar.gz && rm -rf MIRA.buildbin-libdir && mkdir MIRA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MIRA.buildbin-libdir MIRA_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MIRA_1.6.0.zip && rm MIRA_1.6.0.tar.gz MIRA_1.6.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1220k  100 1220k    0     0  13.1M      0 --:--:-- --:--:-- --:--:-- 14.3M

install for i386

* installing *source* package 'MIRA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MIRA'
    finding HTML links ... done
    BSBinAggregate                          html  
    BSreadBiSeq                             html  
    MIRA                                    html  
    SummarizedExperimentToDataTable         html  
    addMethPropCol                          html  
    aggregateMethyl                         html  
    bigBinDT1                               html  
    bigBinDT2                               html  
    binRegion                               html  
    bsseqToDataTable                        html  
    calcMIRAScore                           html  
    exampleAnnoDT1                          html  
    exampleAnnoDT2                          html  
    exampleBSDT                             html  
    exampleBSseqObj                         html  
    exampleBins                             html  
    exampleRegionSet                        html  
    plotMIRAProfiles                        html  
    plotMIRAScores                          html  
    rbindNamedList                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MIRA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MIRA' as MIRA_1.6.0.zip
* DONE (MIRA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MIRA' successfully unpacked and MD5 sums checked

Tests output

MIRA.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(MIRA)
> 
> test_check("MIRA")
== testthat results  ===========================================================
[ OK: 60 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.48    2.45   16.59 

MIRA.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(MIRA)
> 
> test_check("MIRA")
== testthat results  ===========================================================
[ OK: 60 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  17.68    0.90   18.50 

Example timings

MIRA.Rcheck/examples_i386/MIRA-Ex.timings

nameusersystemelapsed
BSBinAggregate1.270.061.32
BSreadBiSeq0.030.000.03
SummarizedExperimentToDataTable0.370.020.39
addMethPropCol0.020.010.03
aggregateMethyl0.340.170.50
binRegion0.030.000.03
bsseqToDataTable0.420.020.44
calcMIRAScore0.020.020.03
plotMIRAProfiles0.060.000.06
plotMIRAScores0.210.010.22
rbindNamedList0.430.000.45

MIRA.Rcheck/examples_x64/MIRA-Ex.timings

nameusersystemelapsed
BSBinAggregate0.470.050.51
BSreadBiSeq0.010.000.02
SummarizedExperimentToDataTable0.470.010.49
addMethPropCol0.120.000.12
aggregateMethyl0.440.030.42
binRegion0.020.000.02
bsseqToDataTable0.310.020.33
calcMIRAScore0.920.000.84
plotMIRAProfiles0.060.000.06
plotMIRAScores0.250.010.27
rbindNamedList0.320.020.33