Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-03-29 11:38:15 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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

Package 1936/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.32.0  (landing page)
Phil Webster
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/sevenbridges
git_branch: RELEASE_3_18
git_last_commit: bd309cc
git_last_commit_date: 2023-10-24 10:45:02 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for sevenbridges on merida1


To the developers/maintainers of the sevenbridges package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sevenbridges.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: sevenbridges
Version: 1.32.0
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_1.32.0.tar.gz
StartedAt: 2024-03-28 08:52:19 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 08:58:35 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 375.9 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_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/sevenbridges.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sevenbridges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sevenbridges’ version ‘1.32.0’
* 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 startup messages can be suppressed ... 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        109.028  0.849 122.405
Tool-class   28.576  0.395  32.554
link_what    17.938  0.089  19.473
link         16.137  0.078  18.069
convert_app  12.659  0.072  14.475
* 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/4.3-x86_64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
  4.465   0.364   5.196 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class0.0010.0010.002
Auth-class0.0150.0010.018
Binding0.0220.0000.026
CCBList0.0270.0010.031
CWL0.0030.0000.003
CommandInputParameter-class0.0450.0010.050
CommandInputSchema-class0.0440.0000.051
CommandLineBinding-class0.0140.0010.016
CommandLineTool0.0310.0010.039
CommandOutputBinding-class0.0140.0000.016
CommandOutputParameter-class0.0280.0000.030
CommandOutputSchema-class0.0230.0010.027
DSCList0.0360.0010.040
Enum0.0750.0020.085
Expression-class0.0140.0000.019
ExpressionTool-class0.0400.0000.045
File-class0.1310.0050.149
Files-class0.0210.0010.026
Flow109.028 0.849122.405
Metadata0.1790.0070.225
Parameter0.0670.0020.069
Process0.0850.0030.093
ProcessRequirement0.1170.0040.130
Schema0.0330.0010.035
TaskHook0.0030.0010.008
Tool-class28.576 0.39532.554
Workflow0.0610.0010.071
WorkflowStep0.0100.0000.012
addIdNum0.0010.0000.001
api0.0000.0000.001
as-methods0.1490.0030.187
batch0.0010.0010.002
cli_list_projects000
cli_list_tags0.0000.0010.001
cli_upload0.0010.0010.001
convert_app12.659 0.07214.475
cwl-utils0.2090.0060.260
delete-methods0.0010.0010.004
download-methods0.0000.0010.001
get_token0.0000.0010.001
get_uploader0.0000.0010.001
input_output_matrix0.1710.0110.219
link16.137 0.07818.069
link_what17.938 0.08919.473
project_details0.0010.0010.000
project_members0.0010.0010.000
requirements0.1070.0020.119
response-methods000
sbg_get_env0.0000.0010.001
sbg_set_env0.0010.0010.001
set_test_env0.0000.0010.001
shorthand-cwl0.0540.0020.062
tag-methods0.0000.0010.001
test_tool_bunny0.0000.0000.001
test_tool_cwlrun0.0000.0010.001
test_tool_rabix0.0000.0010.001
upload_complete_all0.0000.0010.001
upload_complete_part0.0000.0000.001
upload_delete0.0010.0010.001
upload_info0.0010.0000.001
upload_info_part0.0010.0010.001
upload_init0.0010.0010.001