Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:47 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for sevenbridges on machv2


To the developers/maintainers of the sevenbridges package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/sevenbridges.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1777/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.24.0  (landing page)
Soner Koc
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/sevenbridges
git_branch: RELEASE_3_14
git_last_commit: 9e0d83f
git_last_commit_date: 2021-10-26 12:22:17 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: sevenbridges
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sevenbridges_1.24.0.tar.gz
StartedAt: 2022-04-12 18:29:05 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:33:18 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 253.6 seconds
RetCode: 0
Status:   OK  
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sevenbridges_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/sevenbridges.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.24.0’
* 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        81.556  0.170  82.013
Tool-class  22.839  0.101  23.101
link_what   13.622  0.028  13.716
link        11.477  0.023  11.512
convert_app  9.496  0.018   9.610
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sevenbridges
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  3.330   0.230   3.538 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class0.0000.0010.001
Auth-class0.0110.0010.014
Binding0.0570.0070.064
CCBList0.0440.0010.045
CWL0.0010.0000.001
CommandInputParameter-class0.0410.0010.042
CommandInputSchema-class0.0270.0000.027
CommandLineBinding-class0.0090.0000.009
CommandLineTool0.020.000.02
CommandOutputBinding-class0.0130.0000.014
CommandOutputParameter-class0.0230.0000.024
CommandOutputSchema-class0.0150.0000.016
DSCList0.0330.0010.033
Enum0.0500.0010.052
Expression-class0.0130.0000.014
ExpressionTool-class0.0280.0010.028
File-class0.0760.0030.079
Files-class0.0120.0010.012
Flow81.556 0.17082.013
Metadata0.1550.0020.158
Parameter0.0680.0010.071
Process0.0890.0010.090
ProcessRequirement0.0900.0010.092
Schema0.0280.0000.029
TaskHook0.0030.0000.003
Tool-class22.839 0.10123.101
Workflow0.0410.0010.041
WorkflowStep0.0080.0000.009
addIdNum0.0000.0010.001
api0.0000.0010.001
as-methods0.1030.0020.105
batch0.0010.0000.001
cli_list_projects0.0010.0000.000
cli_list_tags0.0000.0010.001
cli_upload000
convert_app9.4960.0189.610
cwl-utils0.1460.0030.149
delete-methods0.0000.0010.001
download-methods0.0000.0010.000
get_token000
get_uploader000
input_output_matrix0.1500.0060.156
link11.477 0.02311.512
link_what13.622 0.02813.716
project_details0.0010.0010.001
project_members0.0010.0010.000
requirements0.0950.0010.096
response-methods0.0000.0010.000
sbg_get_env0.0000.0010.001
sbg_set_env0.0000.0010.000
set_test_env000
shorthand-cwl0.0270.0010.028
tag-methods0.0000.0010.001
test_tool_bunny000
test_tool_cwlrun000
test_tool_rabix000
upload_complete_all0.0000.0000.001
upload_complete_part0.0000.0000.001
upload_delete0.0010.0010.001
upload_info0.0000.0010.000
upload_info_part0.0010.0000.001
upload_init0.0010.0010.000