Phil Webster
| Snapshot Date: 2025-08-22 13:45 -0400 (Fri, 22 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/sevenbridges |
| git_branch: devel |
| git_last_commit: f4f2f96 |
| git_last_commit_date: 2025-04-15 10:53:08 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-23 12:08 -0400 (Sat, 23 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4599 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
| 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 1960/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sevenbridges 1.39.0 (landing page) Phil Webster
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: sevenbridges |
| Version: 1.39.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sevenbridges_1.39.0.tar.gz |
| StartedAt: 2025-08-22 12:21:09 -0000 (Fri, 22 Aug 2025) |
| EndedAt: 2025-08-22 12:24:33 -0000 (Fri, 22 Aug 2025) |
| EllapsedTime: 204.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sevenbridges.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sevenbridges_1.39.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sevenbridges.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sevenbridges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sevenbridges’ version ‘1.39.0’
* 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 loading without being on the library search path ... 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 65.046 0.519 65.768
Tool-class 18.605 0.072 18.731
link_what 11.482 0.036 11.555
link 9.676 0.000 9.697
convert_app 7.882 0.004 8.001
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/sevenbridges.Rcheck/00check.log’
for details.
sevenbridges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL sevenbridges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘sevenbridges’ ... ** this is package ‘sevenbridges’ version ‘1.39.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
2.945 0.177 3.116
sevenbridges.Rcheck/sevenbridges-Ex.timings
| name | user | system | elapsed | |
| App-class | 0 | 0 | 0 | |
| Auth-class | 0.009 | 0.000 | 0.009 | |
| Binding | 0.015 | 0.000 | 0.014 | |
| CCBList | 0.019 | 0.000 | 0.019 | |
| CWL | 0.001 | 0.000 | 0.002 | |
| CommandInputParameter-class | 0.023 | 0.000 | 0.023 | |
| CommandInputSchema-class | 0.030 | 0.004 | 0.033 | |
| CommandLineBinding-class | 0.009 | 0.000 | 0.009 | |
| CommandLineTool | 0.02 | 0.00 | 0.02 | |
| CommandOutputBinding-class | 0.009 | 0.000 | 0.009 | |
| CommandOutputParameter-class | 0.018 | 0.000 | 0.018 | |
| CommandOutputSchema-class | 0.016 | 0.000 | 0.016 | |
| DSCList | 0.024 | 0.000 | 0.024 | |
| Enum | 0.046 | 0.000 | 0.047 | |
| Expression-class | 0.010 | 0.000 | 0.011 | |
| ExpressionTool-class | 0.029 | 0.000 | 0.029 | |
| File-class | 0.095 | 0.019 | 0.114 | |
| Files-class | 0.011 | 0.051 | 0.064 | |
| Flow | 65.046 | 0.519 | 65.768 | |
| Metadata | 0.110 | 0.008 | 0.118 | |
| Parameter | 0.045 | 0.000 | 0.045 | |
| Process | 0.061 | 0.000 | 0.061 | |
| ProcessRequirement | 0.073 | 0.000 | 0.074 | |
| Schema | 0.033 | 0.000 | 0.033 | |
| TaskHook | 0.003 | 0.000 | 0.003 | |
| Tool-class | 18.605 | 0.072 | 18.731 | |
| Workflow | 0.038 | 0.000 | 0.039 | |
| WorkflowStep | 0.007 | 0.000 | 0.007 | |
| addIdNum | 0.001 | 0.000 | 0.000 | |
| api | 0 | 0 | 0 | |
| as-methods | 0.088 | 0.000 | 0.089 | |
| batch | 0.000 | 0.000 | 0.001 | |
| cli_list_projects | 0.000 | 0.000 | 0.001 | |
| cli_list_tags | 0.001 | 0.000 | 0.000 | |
| cli_upload | 0 | 0 | 0 | |
| convert_app | 7.882 | 0.004 | 8.001 | |
| cwl-utils | 0.124 | 0.000 | 0.126 | |
| delete-methods | 0.000 | 0.000 | 0.001 | |
| download-methods | 0 | 0 | 0 | |
| get_token | 0 | 0 | 0 | |
| get_uploader | 0.001 | 0.000 | 0.000 | |
| input_output_matrix | 0.103 | 0.004 | 0.107 | |
| link | 9.676 | 0.000 | 9.697 | |
| link_what | 11.482 | 0.036 | 11.555 | |
| project_details | 0 | 0 | 0 | |
| project_members | 0 | 0 | 0 | |
| requirements | 0.067 | 0.004 | 0.070 | |
| response-methods | 0 | 0 | 0 | |
| sbg_get_env | 0.000 | 0.000 | 0.001 | |
| sbg_set_env | 0 | 0 | 0 | |
| set_test_env | 0.000 | 0.000 | 0.001 | |
| shorthand-cwl | 0.033 | 0.000 | 0.033 | |
| tag-methods | 0 | 0 | 0 | |
| test_tool_bunny | 0 | 0 | 0 | |
| test_tool_cwlrun | 0 | 0 | 0 | |
| test_tool_rabix | 0 | 0 | 0 | |
| upload_complete_all | 0 | 0 | 0 | |
| upload_complete_part | 0 | 0 | 0 | |
| upload_delete | 0 | 0 | 0 | |
| upload_info | 0 | 0 | 0 | |
| upload_info_part | 0 | 0 | 0 | |
| upload_init | 0.001 | 0.000 | 0.000 | |