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CHECK report for sevenbridges on merida1

This page was generated on 2021-05-06 12:36:47 -0400 (Thu, 06 May 2021).

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 1691/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.20.1  (landing page)
Soner Koc
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/sevenbridges
Branch: RELEASE_3_12
Last Commit: 6d0ec68
Last Changed Date: 2021-03-24 06:17:51 -0400 (Wed, 24 Mar 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: sevenbridges
Version: 1.20.1
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_1.20.1.tar.gz
StartedAt: 2021-05-06 06:10:47 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:14:21 -0400 (Thu, 06 May 2021)
EllapsedTime: 213.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

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### Running 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_1.20.1.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/sevenbridges.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.20.1’
* 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        66.777  0.167  67.012
Tool-class  18.918  0.097  19.052
link_what   11.232  0.057  11.307
link         8.936  0.018   8.961
convert_app  7.146  0.020   7.175
* 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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sevenbridges
###
##############################################################################
##############################################################################


* 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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  2.975   0.197   3.159 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class0.0000.0000.001
Auth-class0.0080.0010.010
Binding0.0610.0070.068
CCBList0.0190.0020.020
CWL0.0010.0000.001
CommandInputParameter-class0.0530.0020.056
CommandInputSchema-class0.0270.0000.028
CommandLineBinding-class0.0120.0000.011
CommandLineTool0.0180.0010.019
CommandOutputBinding-class0.0080.0010.007
CommandOutputParameter-class0.0180.0000.018
CommandOutputSchema-class0.0200.0010.019
DSCList0.0210.0010.022
Enum0.0280.0010.029
Expression-class0.0080.0000.009
ExpressionTool-class0.0260.0010.026
File-class0.0780.0020.080
Files-class0.0110.0000.011
Flow66.777 0.16767.012
Metadata0.1200.0020.123
Parameter0.0420.0000.043
Process0.0600.0010.061
ProcessRequirement0.0800.0010.081
Schema0.0240.0000.024
TaskHook0.0030.0010.003
Tool-class18.918 0.09719.052
Workflow0.0400.0010.040
WorkflowStep0.0090.0010.010
addIdNum0.0010.0000.001
api000
as-methods0.1000.0020.102
batch0.0010.0010.002
cli_list_projects0.0010.0010.001
cli_list_tags0.0000.0010.001
cli_upload000
convert_app7.1460.0207.175
cwl-utils0.1370.0030.140
delete-methods000
download-methods000
get_token000
get_uploader000
input_output_matrix0.1030.0030.106
link8.9360.0188.961
link_what11.232 0.05711.307
project_details000
project_members0.0010.0000.001
requirements0.0670.0010.067
response-methods0.0000.0000.001
sbg_get_env0.0000.0000.001
sbg_set_env0.0000.0010.000
set_test_env000
shorthand-cwl0.0360.0000.038
tag-methods000
test_tool_bunny0.0000.0010.001
test_tool_cwlrun0.0010.0000.001
test_tool_rabix000
upload_complete_all0.0000.0000.001
upload_complete_part000
upload_delete000
upload_info0.0000.0010.000
upload_info_part000
upload_init0.0010.0000.001