Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1940/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sevenbridges 1.36.0  (landing page)
Phil Webster
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/sevenbridges
git_branch: RELEASE_3_20
git_last_commit: 7d65500
git_last_commit_date: 2024-10-29 10:03:29 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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


CHECK results for sevenbridges on palomino8

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: 1.36.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sevenbridges.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings sevenbridges_1.36.0.tar.gz
StartedAt: 2024-12-20 05:57:48 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:01:28 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 220.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sevenbridges.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sevenbridges.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings sevenbridges_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/sevenbridges.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sevenbridges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sevenbridges' version '1.36.0'
* 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 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        54.09   0.72   54.92
Tool-class  18.94   0.16   20.17
link_what   11.64   0.14   13.23
link        10.05   0.08   10.53
convert_app  7.62   0.01    8.75
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/sevenbridges.Rcheck/00check.log'
for details.


Installation output

sevenbridges.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL sevenbridges
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   2.96    0.43    6.68 

Example timings

sevenbridges.Rcheck/sevenbridges-Ex.timings

nameusersystemelapsed
App-class000
Auth-class0.010.000.02
Binding0.020.000.02
CCBList0.010.000.02
CWL0.020.000.01
CommandInputParameter-class0.010.000.02
CommandInputSchema-class0.050.000.04
CommandLineBinding-class000
CommandLineTool0.010.000.02
CommandOutputBinding-class000
CommandOutputParameter-class0.020.000.01
CommandOutputSchema-class0.020.000.02
DSCList0.010.000.02
Enum0.030.000.03
Expression-class000
ExpressionTool-class0.010.000.02
File-class0.070.000.06
Files-class000
Flow54.09 0.7254.92
Metadata0.130.000.14
Parameter0.040.000.05
Process0.060.000.06
ProcessRequirement0.080.000.08
Schema0.000.000.37
TaskHook0.000.000.13
Tool-class18.94 0.1620.17
Workflow0.030.000.03
WorkflowStep0.020.000.02
addIdNum000
api000
as-methods0.090.000.09
batch000
cli_list_projects000
cli_list_tags000
cli_upload000
convert_app7.620.018.75
cwl-utils0.140.000.15
delete-methods000
download-methods000
get_token000
get_uploader000
input_output_matrix0.140.020.38
link10.05 0.0810.53
link_what11.64 0.1413.23
project_details000
project_members000
requirements0.050.010.06
response-methods000
sbg_get_env000
sbg_set_env000
set_test_env000
shorthand-cwl0.030.000.04
tag-methods000
test_tool_bunny000
test_tool_cwlrun000
test_tool_rabix000
upload_complete_all000
upload_complete_part000
upload_delete000
upload_info0.000.020.00
upload_info_part000
upload_init000