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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1925/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.37.0  (landing page)
Phil Webster
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/sevenbridges
git_branch: devel
git_last_commit: 265369e
git_last_commit_date: 2024-10-29 10:03:29 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for sevenbridges on nebbiolo1

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: 1.37.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings sevenbridges_1.37.0.tar.gz
StartedAt: 2024-12-24 02:11:37 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 02:15:05 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 208.4 seconds
RetCode: 0
Status:   OK  
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings sevenbridges_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sevenbridges.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘sevenbridges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sevenbridges’ version ‘1.37.0’
* 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       40.776  0.725  41.510
Tool-class 11.679  0.106  11.786
link_what   7.165  0.053   7.219
link        6.248  0.002   6.251
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.21-bioc/R/bin/R CMD INSTALL sevenbridges
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
  2.094   0.146   2.227 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class0.0010.0000.001
Auth-class0.0070.0000.007
Binding0.010.000.01
CCBList0.0120.0000.013
CWL0.0010.0000.001
CommandInputParameter-class0.0190.0010.020
CommandInputSchema-class0.0240.0000.024
CommandLineBinding-class0.0050.0010.006
CommandLineTool0.0130.0000.013
CommandOutputBinding-class0.0060.0000.006
CommandOutputParameter-class0.0120.0000.011
CommandOutputSchema-class0.0110.0000.010
DSCList0.0160.0000.016
Enum0.0340.0010.035
Expression-class0.0070.0000.006
ExpressionTool-class0.0180.0000.017
File-class0.0550.0010.055
Files-class0.0130.0000.013
Flow40.776 0.72541.510
Metadata0.0800.0030.083
Parameter0.0290.0010.031
Process0.0400.0010.041
ProcessRequirement0.0450.0020.048
Schema0.0150.0010.016
TaskHook0.0020.0000.002
Tool-class11.679 0.10611.786
Workflow0.0230.0010.024
WorkflowStep0.0040.0000.005
addIdNum0.0000.0000.001
api000
as-methods0.0590.0040.062
batch0.0000.0000.001
cli_list_projects000
cli_list_tags0.0010.0000.000
cli_upload0.0000.0010.000
convert_app4.6580.0114.670
cwl-utils0.0750.0050.081
delete-methods000
download-methods000
get_token0.0010.0000.000
get_uploader000
input_output_matrix0.0660.0030.069
link6.2480.0026.251
link_what7.1650.0537.219
project_details0.0000.0000.001
project_members000
requirements0.0520.0020.054
response-methods000
sbg_get_env0.0010.0000.000
sbg_set_env0.0000.0010.000
set_test_env0.0000.0000.001
shorthand-cwl0.0220.0000.022
tag-methods0.0000.0000.001
test_tool_bunny000
test_tool_cwlrun000
test_tool_rabix000
upload_complete_all000
upload_complete_part0.0000.0010.000
upload_delete000
upload_info000
upload_info_part000
upload_init0.0000.0000.001