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CHECK report for strandCheckR on tokay2

This page was generated on 2019-10-16 12:41:59 -0400 (Wed, 16 Oct 2019).

Package 1599/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
strandCheckR 1.2.0
Thu-Hien To
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/strandCheckR
Branch: RELEASE_3_9
Last Commit: daa606f
Last Changed Date: 2019-05-02 11:54:12 -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: strandCheckR
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:strandCheckR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings strandCheckR_1.2.0.tar.gz
StartedAt: 2019-10-16 07:24:28 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:29:58 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 330.1 seconds
RetCode: 0
Status:  OK  
CheckDir: strandCheckR.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:strandCheckR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings strandCheckR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/strandCheckR.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 'strandCheckR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'strandCheckR' version '1.2.0'
* 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 'strandCheckR' 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
Examples with CPU or elapsed time > 5s
                     user system elapsed
intersectWithFeature 5.03   0.33    5.36
** 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

strandCheckR.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/strandCheckR_1.2.0.tar.gz && rm -rf strandCheckR.buildbin-libdir && mkdir strandCheckR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=strandCheckR.buildbin-libdir strandCheckR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL strandCheckR_1.2.0.zip && rm strandCheckR_1.2.0.tar.gz strandCheckR_1.2.0.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  486k  100  486k    0     0  8100k      0 --:--:-- --:--:-- --:--:-- 9178k

install for i386

* installing *source* package 'strandCheckR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'strandCheckR'
    finding HTML links ... done
    calculateStrandCoverage                 html  
    calculateStrandNbReads                  html  
    checkPairedEnd                          html  
    concatenateAlignments                   html  
    filterDNA                               html  
    getWinFromBamFile                       html  
    getWinFromGranges                       html  
    getWinFromIRanges                       html  
    finding level-2 HTML links ... done

    getWinFromReadInfo                      html  
    getWinOfAlignments                      html  
    intersectWithFeature                    html  
    keptProbaWin                            html  
    keptReadFragment                        html  
    plotHist                                html  
    plotWin                                 html  
    strandCheckR-package                    html  
    summarizeHist                           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 'strandCheckR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'strandCheckR' as strandCheckR_1.2.0.zip
* DONE (strandCheckR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'strandCheckR' successfully unpacked and MD5 sums checked

Tests output

strandCheckR.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.

> library(testthat)
> library(strandCheckR)
> 
> test_check("strandCheckR")
== testthat results  ===========================================================
[ OK: 28 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.03    1.29   14.37 

strandCheckR.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.

> library(testthat)
> library(strandCheckR)
> 
> test_check("strandCheckR")
== testthat results  ===========================================================
[ OK: 28 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  15.06    0.53   15.57 

Example timings

strandCheckR.Rcheck/examples_i386/strandCheckR-Ex.timings

nameusersystemelapsed
checkPairedEnd0.040.010.19
filterDNA0.630.130.92
getWinFromBamFile0.550.040.60
intersectWithFeature5.030.335.36
plotHist0.560.030.59
plotWin2.940.022.95
strandCheckR-package2.110.062.17

strandCheckR.Rcheck/examples_x64/strandCheckR-Ex.timings

nameusersystemelapsed
checkPairedEnd0.030.010.05
filterDNA0.750.090.85
getWinFromBamFile0.590.020.61
intersectWithFeature4.440.114.55
plotHist0.80.00.8
plotWin2.670.022.70
strandCheckR-package3.270.033.30