Multiple platform build/check report for BioC 3.8 - CHECK report for roar on tokay1

Package: roar

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:roar.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings roar_1.18.0.tar.gz

StartedAt: 2019-04-13 05:09:10 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:14:17 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 306.9 seconds

RetCode: 0

Status: OK

CheckDir: roar.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:roar.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings roar_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/roar.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'roar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'roar' version '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'roar' 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 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/roar_1.18.0.tar.gz && rm -rf roar.buildbin-libdir && mkdir roar.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=roar.buildbin-libdir roar_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL roar_1.18.0.zip && rm roar_1.18.0.tar.gz roar_1.18.0.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  528k  100  528k    0     0  11.9M      0 --:--:-- --:--:-- --:--:-- 13.2M

install for i386

* installing *source* package 'roar' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'roar'
    finding HTML links ... done
    RoarDataset-class                       html  
    finding level-2 HTML links ... done

    RoarDataset-constructor                 html  
    RoarDatasetFromFiles-constructor        html  
    RoarDatasetMultipleAPA-class            html  
    RoarDatasetMultipleAPA-constructor      html  
    RoarDatasetMultipleAPAFromFiles-constructor
                                            html  
    checkStep-method                        html  
    combineFisherMethod-method              html  
    computePairedPvals-method               html  
    computePvals-method                     html  
    computeRoars-method                     html  
    cores-method                            html  
    countPrePost-method                     html  
    countResults-method                     html  
    fpkmResults-method                      html  
    getFisher-method                        html  
    meanAcrossAssays-method                 html  
    pvalueCorrectFilter-method              html  
    pvalueFilter-method                     html  
    roar-package                            html  
    standardFilter-method                   html  
    totalResults-method                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'roar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'roar' as roar_1.18.0.zip
* DONE (roar)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'roar' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> library(testthat)
> library(roar)
> 
> test_check("roar")
== testthat results  ===========================================================
OK: 137 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  17.18    0.54   17.75


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> library(testthat)
> library(roar)
> 
> test_check("roar")
== testthat results  ===========================================================
OK: 137 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  19.31    0.23   19.53

name	user	system	elapsed
RoarDataset-class	0	0	0
RoarDataset-constructor	0.33	0.09	0.42
RoarDatasetFromFiles-constructor	0	0	0
RoarDatasetMultipleAPA-class	0	0	0
RoarDatasetMultipleAPA-constructor	0.36	0.01	0.38
RoarDatasetMultipleAPAFromFiles-constructor	0	0	0
computePairedPvals-method	1.03	0.00	1.03
computePvals-method	0.51	0.02	0.53
computeRoars-method	0.53	0.03	0.56
countPrePost-method	0.47	0.03	0.50
countResults-method	0.53	0.02	0.55
fpkmResults-method	0.59	0.01	0.61
pvalueCorrectFilter-method	0.92	0.04	0.95
pvalueFilter-method	0.91	0.03	0.94
standardFilter-method	0.82	0.01	0.85
totalResults-method	0.50	0.03	0.53

name	user	system	elapsed
RoarDataset-class	0	0	0
RoarDataset-constructor	0.34	0.04	0.39
RoarDatasetFromFiles-constructor	0	0	0
RoarDatasetMultipleAPA-class	0	0	0
RoarDatasetMultipleAPA-constructor	0.33	0.08	0.40
RoarDatasetMultipleAPAFromFiles-constructor	0	0	0
computePairedPvals-method	1.23	0.05	1.29
computePvals-method	0.62	0.03	0.66
computeRoars-method	0.92	0.03	0.96
countPrePost-method	0.77	0.02	0.78
countResults-method	0.73	0.04	0.78
fpkmResults-method	0.55	0.07	0.61
pvalueCorrectFilter-method	0.60	0.03	0.63
pvalueFilter-method	0.61	0.03	0.64
standardFilter-method	0.60	0.02	0.63
totalResults-method	0.86	0.07	0.93

CHECK report for roar on tokay1

Summary

Command output

Installation output

Tests output

Example timings