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CHECK report for graphite on tokay2

This page was generated on 2020-10-17 11:56:46 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE graphite PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 774/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.34.0
Gabriele Sales
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/graphite
Branch: RELEASE_3_11
Last Commit: 35c24be
Last Changed Date: 2020-04-27 14:26:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: graphite
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graphite.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings graphite_1.34.0.tar.gz
StartedAt: 2020-10-17 04:42:39 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:52:08 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 568.6 seconds
RetCode: 0
Status:  OK  
CheckDir: graphite.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graphite.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings graphite_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/graphite.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'graphite/DESCRIPTION' ... OK
* this is package 'graphite' version '1.34.0'
* 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 'graphite' 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
runClipper         14.00   0.90   70.44
runSPIA             5.69   1.64   45.14
convertIdentifiers  6.32   0.19   20.14
runTopologyGSA      2.12   0.01   20.71
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
runClipper     12.00   0.44   15.77
runSPIA         5.95   0.92   12.99
runTopologyGSA  1.48   0.03    5.47
* 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

graphite.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/graphite_1.34.0.tar.gz && rm -rf graphite.buildbin-libdir && mkdir graphite.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=graphite.buildbin-libdir graphite_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL graphite_1.34.0.zip && rm graphite_1.34.0.tar.gz graphite_1.34.0.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  457k  100  457k    0     0  6628k      0 --:--:-- --:--:-- --:--:-- 7371k

install for i386

* installing *source* package 'graphite' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'graphite'
    finding HTML links ... done
    Pathway-class                           html  
    PathwayList-class                       html  
    Pathways-class                          html  
    as.list.PathwayList                     html  
    buildPathway                            html  
    convertIdentifiers                      html  
    cytoscapePlot                           html  
    finding level-2 HTML links ... done

    pathwayDatabases                        html  
    pathwayGraph                            html  
    pathways                                html  
    prepareSPIA                             html  
    runClipper                              html  
    runSPIA                                 html  
    runTopologyGSA                          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 'graphite' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'graphite' as graphite_1.34.0.zip
* DONE (graphite)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'graphite' successfully unpacked and MD5 sums checked

Tests output

graphite.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(graphite)
> 
> test_check("graphite")
== testthat results  ===========================================================
[ OK: 95 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  35.73    2.84  102.51 

graphite.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(graphite)
> 
> test_check("graphite")
== testthat results  ===========================================================
[ OK: 95 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  42.14    2.45  102.23 

Example timings

graphite.Rcheck/examples_i386/graphite-Ex.timings

nameusersystemelapsed
as.list.PathwayList0.640.060.71
buildPathway0.010.000.01
convertIdentifiers 6.32 0.1920.14
cytoscapePlot000
pathwayDatabases000
pathwayGraph4.620.174.80
pathways3.830.013.84
runClipper14.00 0.9070.44
runSPIA 5.69 1.6445.14
runTopologyGSA 2.12 0.0120.71

graphite.Rcheck/examples_x64/graphite-Ex.timings

nameusersystemelapsed
as.list.PathwayList0.580.030.61
buildPathway0.010.000.01
convertIdentifiers4.420.134.55
cytoscapePlot000
pathwayDatabases000
pathwayGraph2.990.033.02
pathways3.260.003.26
runClipper12.00 0.4415.77
runSPIA 5.95 0.9212.99
runTopologyGSA1.480.035.47