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CHECK report for ReactomePA on tokay1

This page was generated on 2019-04-13 11:22:05 -0400 (Sat, 13 Apr 2019).

Package 1275/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomePA 1.26.0
Guangchuang Yu
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/ReactomePA
Branch: RELEASE_3_8
Last Commit: cc07e54
Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ReactomePA
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomePA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ReactomePA_1.26.0.tar.gz
StartedAt: 2019-04-13 04:55:29 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:59:28 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 238.5 seconds
RetCode: 0
Status:  OK  
CheckDir: ReactomePA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomePA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ReactomePA_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ReactomePA.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 'ReactomePA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ReactomePA' version '1.26.0'
* 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 'ReactomePA' 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
enrichPathway 9.92   0.26   10.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
enrichPathway 10.67   1.29   11.97
* 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

ReactomePA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ReactomePA_1.26.0.tar.gz && rm -rf ReactomePA.buildbin-libdir && mkdir ReactomePA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReactomePA.buildbin-libdir ReactomePA_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ReactomePA_1.26.0.zip && rm ReactomePA_1.26.0.tar.gz ReactomePA_1.26.0.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 1713k  100 1713k    0     0  28.2M      0 --:--:-- --:--:-- --:--:-- 29.8M

install for i386

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

    enrichPathway                           html  
    getALLEG                                html  
    getDb                                   html  
    gsePathway                              html  
    reexports                               html  
    viewPathway                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ReactomePA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReactomePA' as ReactomePA_1.26.0.zip
* DONE (ReactomePA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ReactomePA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

ReactomePA.Rcheck/tests_i386/testthat.Rout


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(ReactomePA)

ReactomePA v1.26.0  For help: https://guangchuangyu.github.io/ReactomePA

If you use ReactomePA in published research, please cite:
Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479
> 
> test_check("ReactomePA")
== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
   4.51    0.39    4.90 

ReactomePA.Rcheck/tests_x64/testthat.Rout


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(ReactomePA)

ReactomePA v1.26.0  For help: https://guangchuangyu.github.io/ReactomePA

If you use ReactomePA in published research, please cite:
Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479
> 
> test_check("ReactomePA")
== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
   4.82    0.29    5.11 

Example timings

ReactomePA.Rcheck/examples_i386/ReactomePA-Ex.timings

nameusersystemelapsed
enrichPathway 9.92 0.2610.19

ReactomePA.Rcheck/examples_x64/ReactomePA-Ex.timings

nameusersystemelapsed
enrichPathway10.67 1.2911.97