Phil Webster
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/sevenbridges |
| git_branch: RELEASE_3_21 |
| git_last_commit: 7e22d1c |
| git_last_commit_date: 2025-04-15 10:53:08 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1976/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sevenbridges 1.38.0 (landing page) Phil Webster
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: sevenbridges |
| Version: 1.38.0 |
| 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_1.38.0.tar.gz |
| StartedAt: 2025-10-14 10:22:22 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 10:28:44 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 382.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sevenbridges.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/sevenbridges.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sevenbridges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sevenbridges’ version ‘1.38.0’
* 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 code 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 whether 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 ... NOTE
checkRd: (-1) CommandLineBinding-class.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineBinding-class.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineBinding-class.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineBinding-class.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineBinding-class.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineBinding-class.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineBinding-class.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineTool.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineTool.Rd:80-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineTool.Rd:86-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineTool.Rd:92-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineTool.Rd:95-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CommandLineTool.Rd:99-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Tool-class.Rd:12: Lost braces
12 | code{Tool} class extends \code{CommandLineTool}
| ^
checkRd: (-1) WorkflowStep.Rd:168-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WorkflowStep.Rd:172-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WorkflowStep.Rd:178-182: Lost braces in \itemize; meant \describe ?
* 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 110.114 0.463 114.600
Tool-class 31.476 0.184 32.599
link_what 18.411 0.048 18.492
link 16.498 0.047 16.935
convert_app 13.512 0.040 13.862
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/sevenbridges.Rcheck/00check.log’
for details.
sevenbridges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sevenbridges ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘sevenbridges’ ... ** this is package ‘sevenbridges’ version ‘1.38.0’ ** 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)
sevenbridges.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
4.461 0.322 4.756
sevenbridges.Rcheck/sevenbridges-Ex.timings
| name | user | system | elapsed | |
| App-class | 0.000 | 0.001 | 0.001 | |
| Auth-class | 0.015 | 0.001 | 0.018 | |
| Binding | 0.022 | 0.001 | 0.025 | |
| CCBList | 0.031 | 0.002 | 0.033 | |
| CWL | 0.002 | 0.000 | 0.003 | |
| CommandInputParameter-class | 0.038 | 0.002 | 0.042 | |
| CommandInputSchema-class | 0.047 | 0.001 | 0.051 | |
| CommandLineBinding-class | 0.014 | 0.001 | 0.016 | |
| CommandLineTool | 0.035 | 0.002 | 0.039 | |
| CommandOutputBinding-class | 0.014 | 0.001 | 0.016 | |
| CommandOutputParameter-class | 0.029 | 0.000 | 0.030 | |
| CommandOutputSchema-class | 0.027 | 0.000 | 0.027 | |
| DSCList | 0.037 | 0.001 | 0.039 | |
| Enum | 0.074 | 0.002 | 0.080 | |
| Expression-class | 0.015 | 0.000 | 0.016 | |
| ExpressionTool-class | 0.045 | 0.001 | 0.046 | |
| File-class | 0.130 | 0.004 | 0.135 | |
| Files-class | 0.023 | 0.001 | 0.024 | |
| Flow | 110.114 | 0.463 | 114.600 | |
| Metadata | 0.203 | 0.004 | 0.211 | |
| Parameter | 0.078 | 0.002 | 0.086 | |
| Process | 0.100 | 0.001 | 0.108 | |
| ProcessRequirement | 0.108 | 0.002 | 0.113 | |
| Schema | 0.036 | 0.000 | 0.036 | |
| TaskHook | 0.004 | 0.001 | 0.004 | |
| Tool-class | 31.476 | 0.184 | 32.599 | |
| Workflow | 0.062 | 0.002 | 0.071 | |
| WorkflowStep | 0.011 | 0.001 | 0.012 | |
| addIdNum | 0.001 | 0.001 | 0.001 | |
| api | 0.000 | 0.001 | 0.001 | |
| as-methods | 0.136 | 0.004 | 0.144 | |
| batch | 0.001 | 0.001 | 0.003 | |
| cli_list_projects | 0.001 | 0.001 | 0.001 | |
| cli_list_tags | 0.000 | 0.001 | 0.001 | |
| cli_upload | 0.000 | 0.001 | 0.001 | |
| convert_app | 13.512 | 0.040 | 13.862 | |
| cwl-utils | 0.218 | 0.006 | 0.285 | |
| delete-methods | 0.000 | 0.000 | 0.001 | |
| download-methods | 0.000 | 0.001 | 0.000 | |
| get_token | 0.000 | 0.000 | 0.001 | |
| get_uploader | 0.000 | 0.001 | 0.001 | |
| input_output_matrix | 0.172 | 0.010 | 0.208 | |
| link | 16.498 | 0.047 | 16.935 | |
| link_what | 18.411 | 0.048 | 18.492 | |
| project_details | 0 | 0 | 0 | |
| project_members | 0.000 | 0.001 | 0.001 | |
| requirements | 0.115 | 0.002 | 0.117 | |
| response-methods | 0 | 0 | 0 | |
| sbg_get_env | 0.000 | 0.000 | 0.001 | |
| sbg_set_env | 0.000 | 0.001 | 0.001 | |
| set_test_env | 0.000 | 0.001 | 0.001 | |
| shorthand-cwl | 0.054 | 0.002 | 0.056 | |
| tag-methods | 0.001 | 0.001 | 0.001 | |
| test_tool_bunny | 0.000 | 0.001 | 0.001 | |
| test_tool_cwlrun | 0.000 | 0.001 | 0.001 | |
| test_tool_rabix | 0.000 | 0.000 | 0.001 | |
| upload_complete_all | 0.000 | 0.001 | 0.001 | |
| upload_complete_part | 0.000 | 0.001 | 0.000 | |
| upload_delete | 0.000 | 0.001 | 0.001 | |
| upload_info | 0.000 | 0.001 | 0.000 | |
| upload_info_part | 0.000 | 0.001 | 0.001 | |
| upload_init | 0.000 | 0.000 | 0.001 | |