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CHECK report for sevenbridges on machv2

This page was generated on 2020-10-17 11:59:35 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE sevenbridges PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1640/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.18.1
Nan Xiao
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/sevenbridges
Branch: RELEASE_3_11
Last Commit: 5983145
Last Changed Date: 2020-06-03 06:20:57 -0400 (Wed, 03 Jun 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  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: sevenbridges
Version: 1.18.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sevenbridges_1.18.1.tar.gz
StartedAt: 2020-10-17 05:16:15 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:20:33 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 257.9 seconds
RetCode: 0
Status:  OK 
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sevenbridges_1.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/sevenbridges.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sevenbridges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sevenbridges’ version ‘1.18.1’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘sevenbridges’ 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
Flow        84.731  0.175  84.986
Tool-class  23.363  0.085  23.473
link_what   14.330  0.026  14.369
link        11.815  0.021  11.846
convert_app  9.738  0.023   9.768
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

sevenbridges.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sevenbridges
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘sevenbridges’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (sevenbridges)

Tests output

sevenbridges.Rcheck/tests/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-apple-darwin17.0 (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("sevenbridges")
> test_check("sevenbridges")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  4.430   0.221   4.630 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class0.0010.0010.001
Auth-class0.0100.0020.013
Binding0.0720.0070.079
CCBList0.0230.0030.026
CWL0.0030.0010.003
CommandInputParameter-class0.0580.0030.061
CommandInputSchema-class0.0260.0000.026
CommandLineBinding-class0.0120.0000.012
CommandLineTool0.0310.0000.031
CommandOutputBinding-class0.0120.0000.012
CommandOutputParameter-class0.0230.0000.024
CommandOutputSchema-class0.0200.0000.021
DSCList0.0210.0010.021
Enum0.0310.0020.032
Expression-class0.0120.0000.012
ExpressionTool-class0.0360.0000.037
File-class0.1060.0030.109
Files-class0.0130.0000.013
Flow84.731 0.17584.986
Metadata0.1430.0020.145
Parameter0.0530.0000.053
Process0.0870.0010.089
ProcessRequirement0.0870.0010.087
Schema0.0280.0000.029
TaskHook0.0030.0000.004
Tool-class23.363 0.08523.473
Workflow0.0450.0000.046
WorkflowStep0.0100.0010.010
addIdNum0.0000.0000.001
api0.0000.0000.001
as-methods0.1230.0020.125
batch0.0010.0010.001
cli_list_projects0.0000.0000.001
cli_list_tags0.0000.0000.001
cli_upload0.0010.0000.001
convert_app9.7380.0239.768
cwl-utils0.1850.0030.189
delete-methods0.0000.0000.001
download-methods0.0000.0000.001
get_token0.0000.0000.001
get_uploader0.0010.0000.001
input_output_matrix0.1470.0070.154
link11.815 0.02111.846
link_what14.330 0.02614.369
project_details0.0000.0000.001
project_members0.0000.0010.001
requirements0.0850.0020.086
response-methods0.0010.0010.000
sbg_get_env0.0010.0010.001
sbg_set_env0.0010.0010.001
set_test_env000
shorthand-cwl0.0430.0010.044
tag-methods0.0010.0000.001
test_tool_bunny0.0000.0010.001
test_tool_cwlrun0.0000.0010.001
test_tool_rabix0.0010.0000.001
upload_complete_all000
upload_complete_part0.0010.0010.001
upload_delete0.0000.0010.001
upload_info0.0000.0010.001
upload_info_part0.0010.0010.000
upload_init0.0000.0000.001