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This page was generated on 2024-06-14 12:02 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1900/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.35.0  (landing page)
Phil Webster
Snapshot Date: 2024-06-13 14:00 -0400 (Thu, 13 Jun 2024)
git_url: https://git.bioconductor.org/packages/sevenbridges
git_branch: devel
git_last_commit: 842f68a
git_last_commit_date: 2024-04-30 10:45:27 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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


CHECK results for sevenbridges on nebbiolo2

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: 1.35.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sevenbridges_1.35.0.tar.gz
StartedAt: 2024-06-14 04:08:30 -0400 (Fri, 14 Jun 2024)
EndedAt: 2024-06-14 04:11:53 -0400 (Fri, 14 Jun 2024)
EllapsedTime: 203.8 seconds
RetCode: 0
Status:   OK  
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sevenbridges_1.35.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sevenbridges.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘sevenbridges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sevenbridges’ version ‘1.35.0’
* 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       39.632  0.256  39.889
Tool-class 11.162  0.060  11.223
link_what   6.547  0.047   6.595
link        5.930  0.000   5.930
* 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-3.20-bioc/meat/sevenbridges.Rcheck/00check.log’
for details.


Installation output

sevenbridges.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL sevenbridges
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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 version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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 
  2.172   0.149   2.311 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class0.0010.0000.000
Auth-class0.0070.0010.007
Binding0.010.000.01
CCBList0.0130.0000.014
CWL0.0010.0000.001
CommandInputParameter-class0.0190.0000.019
CommandInputSchema-class0.0230.0000.023
CommandLineBinding-class0.0050.0000.005
CommandLineTool0.0090.0030.012
CommandOutputBinding-class0.0060.0010.007
CommandOutputParameter-class0.0110.0000.012
CommandOutputSchema-class0.0110.0000.011
DSCList0.0160.0000.017
Enum0.0360.0000.037
Expression-class0.0070.0000.007
ExpressionTool-class0.0170.0000.017
File-class0.0590.0000.059
Files-class0.0070.0000.008
Flow39.632 0.25639.889
Metadata0.0770.0040.081
Parameter0.0270.0000.027
Process0.0370.0000.037
ProcessRequirement0.0430.0000.042
Schema0.0140.0000.013
TaskHook0.0020.0000.002
Tool-class11.162 0.06011.223
Workflow0.0230.0000.023
WorkflowStep0.0000.0030.004
addIdNum000
api000
as-methods0.0600.0010.060
batch0.0000.0000.001
cli_list_projects000
cli_list_tags000
cli_upload000
convert_app4.4340.0044.439
cwl-utils0.0870.0000.087
delete-methods000
download-methods000
get_token000
get_uploader000
input_output_matrix0.0630.0000.062
link5.930.005.93
link_what6.5470.0476.595
project_details000
project_members000
requirements0.0430.0000.042
response-methods000
sbg_get_env000
sbg_set_env000
set_test_env000
shorthand-cwl0.0180.0000.018
tag-methods000
test_tool_bunny000
test_tool_cwlrun000
test_tool_rabix000
upload_complete_all0.0000.0000.001
upload_complete_part000
upload_delete000
upload_info000
upload_info_part000
upload_init000