Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-17 15:06:07 -0400 (Fri, 17 Sep 2021).

CHECK results for graphite on tokay2

To the developers/maintainers of the graphite package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graphite.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 808/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.38.0  (landing page)
Gabriele Sales
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/graphite
git_branch: RELEASE_3_13
git_last_commit: 7517460
git_last_commit_date: 2021-05-19 11:49:41 -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: graphite
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graphite.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings graphite_1.38.0.tar.gz
StartedAt: 2021-09-17 00:07:13 -0400 (Fri, 17 Sep 2021)
EndedAt: 2021-09-17 00:13:50 -0400 (Fri, 17 Sep 2021)
EllapsedTime: 397.1 seconds
RetCode: 0
Status:   OK  
CheckDir: graphite.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graphite.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings graphite_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/graphite.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.38.0'
* 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         10.24   0.53   10.76
runSPIA             5.49   1.22    9.72
convertIdentifiers  5.33   0.27    5.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
runClipper         10.03   0.45   10.48
convertIdentifiers  5.22   0.06    5.28
runSPIA             4.72   0.53    5.25
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/graphite_1.38.0.tar.gz && rm -rf graphite.buildbin-libdir && mkdir graphite.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=graphite.buildbin-libdir graphite_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL graphite_1.38.0.zip && rm graphite_1.38.0.tar.gz graphite_1.38.0.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
 35  459k   35  163k    0     0   656k      0 --:--:-- --:--:-- --:--:--  655k
100  459k  100  459k    0     0  1266k      0 --:--:-- --:--:-- --:--:-- 1265k

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_1.38.0.zip
* DONE (graphite)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'graphite' successfully unpacked and MD5 sums checked

Tests output

graphite.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(graphite)
> 
> test_check("graphite")
== Skipped tests ===============================================================
* On Bioconductor (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 95 ]
> 
> proc.time()
   user  system elapsed 
  41.54    2.70   83.89 

graphite.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(graphite)
> 
> test_check("graphite")
== Skipped tests ===============================================================
* On Bioconductor (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 95 ]
> 
> proc.time()
   user  system elapsed 
  45.39    2.18   97.28 

Example timings

graphite.Rcheck/examples_i386/graphite-Ex.timings

nameusersystemelapsed
as.list.PathwayList1.050.021.07
buildPathway0.010.000.01
convertIdentifiers5.330.275.59
cytoscapePlot000
pathwayDatabases0.020.000.02
pathwayGraph3.890.124.02
pathways3.870.023.89
runClipper10.24 0.5310.76
runSPIA5.491.229.72
runTopologyGSA2.530.063.65

graphite.Rcheck/examples_x64/graphite-Ex.timings

nameusersystemelapsed
as.list.PathwayList1.110.001.11
buildPathway0.020.000.01
convertIdentifiers5.220.065.28
cytoscapePlot000
pathwayDatabases0.020.000.02
pathwayGraph3.450.023.46
pathways3.090.033.13
runClipper10.03 0.4510.48
runSPIA4.720.535.25
runTopologyGSA1.860.061.95