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This page was generated on 2021-07-23 15:06:17 -0400 (Fri, 23 Jul 2021).

CHECK results for ReactomePA on tokay2

To the developers/maintainers of the ReactomePA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReactomePA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1535/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomePA 1.36.0  (landing page)
Guangchuang Yu
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/ReactomePA
Branch: RELEASE_3_13
Last Commit: 78eb2e3
Last Changed Date: 2021-05-19 11:51:50 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ReactomePA
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomePA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ReactomePA_1.36.0.tar.gz
StartedAt: 2021-07-23 04:35:39 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 04:39:38 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 238.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomePA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReactomePA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ReactomePA_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ReactomePA.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.36.0'
* 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 '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 (user + system) or elapsed time > 5s
              user system elapsed
enrichPathway 8.67   0.36    9.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
enrichPathway 10.26   0.95   11.22
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ReactomePA_1.36.0.tar.gz && rm -rf ReactomePA.buildbin-libdir && mkdir ReactomePA.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReactomePA.buildbin-libdir ReactomePA_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ReactomePA_1.36.0.zip && rm ReactomePA_1.36.0.tar.gz ReactomePA_1.36.0.zip
###
##############################################################################
##############################################################################


  % 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 15202  100 15202    0     0   192k      0 --:--:-- --:--:-- --:--:--  195k

install for i386

* installing *source* package 'ReactomePA' ...
** using staged installation
** 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 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 'ReactomePA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReactomePA' as ReactomePA_1.36.0.zip
* DONE (ReactomePA)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ReactomePA' successfully unpacked and MD5 sums checked

Tests output

ReactomePA.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 v1.36.0  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/reactomepa.html

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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> 
> proc.time()
   user  system elapsed 
   7.06    0.62    7.67 

ReactomePA.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 v1.36.0  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/reactomepa.html

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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> 
> proc.time()
   user  system elapsed 
   8.35    0.45    8.79 

Example timings

ReactomePA.Rcheck/examples_i386/ReactomePA-Ex.timings

nameusersystemelapsed
enrichPathway8.670.369.59

ReactomePA.Rcheck/examples_x64/ReactomePA-Ex.timings

nameusersystemelapsed
enrichPathway10.26 0.9511.22