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This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1899/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.30.0  (landing page)
Phil Webster
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/sevenbridges
git_branch: RELEASE_3_17
git_last_commit: d00e91c
git_last_commit_date: 2023-04-25 10:41:13 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for sevenbridges on kjohnson2


To the developers/maintainers of the sevenbridges package:
- 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: 1.30.0
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_1.30.0.tar.gz
StartedAt: 2023-10-19 00:35:12 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 00:40:43 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 330.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/sevenbridges.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sevenbridges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sevenbridges’ version ‘1.30.0’
* 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        54.033  0.538  95.355
Tool-class  15.247  0.173  27.429
link_what    9.688  0.094  17.448
link         8.316  0.074  14.970
convert_app  6.304  0.056  11.251
* 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-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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 
  2.621   0.202   5.083 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class0.0000.0000.001
Auth-class0.0080.0010.017
Binding0.0130.0010.022
CCBList0.0170.0000.028
CWL0.0010.0000.006
CommandInputParameter-class0.0250.0010.043
CommandInputSchema-class0.0300.0010.054
CommandLineBinding-class0.0070.0000.013
CommandLineTool0.0180.0010.035
CommandOutputBinding-class0.0090.0000.016
CommandOutputParameter-class0.0160.0010.032
CommandOutputSchema-class0.0140.0010.027
DSCList0.0210.0010.037
Enum0.0450.0020.081
Expression-class0.0080.0000.013
ExpressionTool-class0.0230.0000.041
File-class0.0800.0030.146
Files-class0.0160.0000.028
Flow54.033 0.53895.355
Metadata0.0980.0030.179
Parameter0.0400.0010.073
Process0.0540.0020.098
ProcessRequirement0.0610.0020.114
Schema0.0350.0010.064
TaskHook0.0030.0000.008
Tool-class15.247 0.17327.429
Workflow0.0320.0000.056
WorkflowStep0.0060.0000.009
addIdNum0.0000.0000.001
api0.0000.0000.001
as-methods0.0790.0020.150
batch0.0000.0000.001
cli_list_projects000
cli_list_tags0.0000.0000.003
cli_upload000
convert_app 6.304 0.05611.251
cwl-utils0.0980.0040.181
delete-methods000
download-methods0.0000.0010.000
get_token000
get_uploader0.0000.0000.001
input_output_matrix0.0810.0060.157
link 8.316 0.07414.970
link_what 9.688 0.09417.448
project_details0.0000.0010.001
project_members0.0000.0000.001
requirements0.0560.0010.103
response-methods0.0000.0000.001
sbg_get_env000
sbg_set_env000
set_test_env0.0000.0000.001
shorthand-cwl0.0260.0010.046
tag-methods0.0010.0000.000
test_tool_bunny0.0000.0010.000
test_tool_cwlrun000
test_tool_rabix0.0000.0000.001
upload_complete_all0.0000.0010.000
upload_complete_part000
upload_delete000
upload_info0.0000.0000.001
upload_info_part0.0000.0000.001
upload_init000