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This page was generated on 2025-10-02 11:42 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4612
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4584
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 1976/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.38.0  (landing page)
Phil Webster
Snapshot Date: 2025-09-29 13:40 -0400 (Mon, 29 Sep 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)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for sevenbridges on kunpeng2

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.

raw results


Summary

Package: sevenbridges
Version: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2025-09-30 14:36:10 -0000 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 14:39:37 -0000 (Tue, 30 Sep 2025)
EllapsedTime: 206.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sevenbridges.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* 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 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        65.606  0.387  66.285
Tool-class  17.846  0.010  17.886
link_what   11.067  0.004  11.101
link         9.320  0.000   9.351
convert_app  7.379  0.038   7.430
* 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-3.21-bioc/meat/sevenbridges.Rcheck/00check.log’
for details.


Installation output

sevenbridges.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL sevenbridges
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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)

Tests output

sevenbridges.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 
  3.085   0.128   3.207 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class000
Auth-class0.0090.0000.009
Binding0.0140.0000.014
CCBList0.0190.0000.019
CWL0.0020.0000.001
CommandInputParameter-class0.0280.0000.029
CommandInputSchema-class0.0330.0000.034
CommandLineBinding-class0.0090.0000.009
CommandLineTool0.020.000.02
CommandOutputBinding-class0.010.000.01
CommandOutputParameter-class0.0220.0080.029
CommandOutputSchema-class0.0190.0000.020
DSCList0.0280.0000.029
Enum0.0560.0080.064
Expression-class0.0110.0000.011
ExpressionTool-class0.030.000.03
File-class0.0980.0000.098
Files-class0.0110.0000.011
Flow65.606 0.38766.285
Metadata0.1150.0000.115
Parameter0.0400.0040.044
Process0.0730.0000.073
ProcessRequirement0.0660.0000.066
Schema0.020.000.02
TaskHook0.0000.0020.002
Tool-class17.846 0.01017.886
Workflow0.0360.0000.036
WorkflowStep0.0070.0000.006
addIdNum000
api000
as-methods0.0890.0000.088
batch0.0010.0000.000
cli_list_projects000
cli_list_tags0.0000.0000.001
cli_upload000
convert_app7.3790.0387.430
cwl-utils0.1230.0000.125
delete-methods000
download-methods000
get_token000
get_uploader0.0000.0000.001
input_output_matrix0.1110.0000.110
link9.3200.0009.351
link_what11.067 0.00411.101
project_details000
project_members000
requirements0.1020.0000.102
response-methods000
sbg_get_env0.0000.0000.001
sbg_set_env0.0010.0000.000
set_test_env000
shorthand-cwl0.0310.0000.032
tag-methods000
test_tool_bunny000
test_tool_cwlrun000
test_tool_rabix000
upload_complete_all000
upload_complete_part000
upload_delete000
upload_info000
upload_info_part000
upload_init000