Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1954/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sevenbridges 1.34.0 (landing page) Phil Webster
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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. |
Package: sevenbridges |
Version: 1.34.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sevenbridges_1.34.0.tar.gz |
StartedAt: 2024-06-06 03:29:47 -0400 (Thu, 06 Jun 2024) |
EndedAt: 2024-06-06 03:33:50 -0400 (Thu, 06 Jun 2024) |
EllapsedTime: 243.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: sevenbridges.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sevenbridges_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sevenbridges.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.34.0’ * 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 43.027 0.348 43.377 Tool-class 11.756 0.092 11.848 link_what 7.262 0.016 7.278 link 6.411 0.040 6.451 * 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 ... ERROR Error(s) in re-building vignettes: --- re-building ‘api.Rmd’ using rmarkdown --- finished re-building ‘api.Rmd’ --- re-building ‘apps.Rmd’ using rmarkdown --- finished re-building ‘apps.Rmd’ --- re-building ‘bioc-workflow.Rmd’ using rmarkdown Could not fetch https://i.imgur.com/OkgB2tl.png HttpExceptionRequest Request { host = "i.imgur.com" port = 443 secure = True requestHeaders = [] path = "/OkgB2tl.png" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 } ConnectionTimeout Error: processing vignette 'bioc-workflow.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘bioc-workflow.Rmd’ --- re-building ‘cgc-datasets.Rmd’ using rmarkdown --- finished re-building ‘cgc-datasets.Rmd’ --- re-building ‘docker.Rmd’ using rmarkdown --- finished re-building ‘docker.Rmd’ --- re-building ‘rstudio.Rmd’ using rmarkdown --- finished re-building ‘rstudio.Rmd’ SUMMARY: processing the following file failed: ‘bioc-workflow.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/sevenbridges.Rcheck/00check.log’ for details.
sevenbridges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL sevenbridges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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)
sevenbridges.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "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 2.297 0.175 2.460
sevenbridges.Rcheck/sevenbridges-Ex.timings
name | user | system | elapsed | |
App-class | 0 | 0 | 0 | |
Auth-class | 0.008 | 0.000 | 0.008 | |
Binding | 0.011 | 0.000 | 0.011 | |
CCBList | 0.015 | 0.000 | 0.015 | |
CWL | 0.002 | 0.000 | 0.002 | |
CommandInputParameter-class | 0.024 | 0.000 | 0.024 | |
CommandInputSchema-class | 0.032 | 0.000 | 0.032 | |
CommandLineBinding-class | 0.007 | 0.000 | 0.007 | |
CommandLineTool | 0.015 | 0.000 | 0.015 | |
CommandOutputBinding-class | 0.007 | 0.000 | 0.007 | |
CommandOutputParameter-class | 0.010 | 0.003 | 0.014 | |
CommandOutputSchema-class | 0.012 | 0.000 | 0.012 | |
DSCList | 0.019 | 0.000 | 0.019 | |
Enum | 0.039 | 0.000 | 0.039 | |
Expression-class | 0.007 | 0.000 | 0.007 | |
ExpressionTool-class | 0.018 | 0.000 | 0.018 | |
File-class | 0.065 | 0.004 | 0.069 | |
Files-class | 0.008 | 0.000 | 0.008 | |
Flow | 43.027 | 0.348 | 43.377 | |
Metadata | 0.082 | 0.008 | 0.090 | |
Parameter | 0.026 | 0.003 | 0.029 | |
Process | 0.039 | 0.000 | 0.038 | |
ProcessRequirement | 0.044 | 0.004 | 0.048 | |
Schema | 0.014 | 0.000 | 0.014 | |
TaskHook | 0.001 | 0.000 | 0.002 | |
Tool-class | 11.756 | 0.092 | 11.848 | |
Workflow | 0.025 | 0.000 | 0.025 | |
WorkflowStep | 0.004 | 0.000 | 0.004 | |
addIdNum | 0.000 | 0.000 | 0.001 | |
api | 0 | 0 | 0 | |
as-methods | 0.058 | 0.006 | 0.065 | |
batch | 0.001 | 0.000 | 0.001 | |
cli_list_projects | 0.001 | 0.000 | 0.000 | |
cli_list_tags | 0.000 | 0.000 | 0.001 | |
cli_upload | 0 | 0 | 0 | |
convert_app | 4.728 | 0.000 | 4.728 | |
cwl-utils | 0.1 | 0.0 | 0.1 | |
delete-methods | 0.000 | 0.000 | 0.001 | |
download-methods | 0 | 0 | 0 | |
get_token | 0 | 0 | 0 | |
get_uploader | 0 | 0 | 0 | |
input_output_matrix | 0.071 | 0.004 | 0.076 | |
link | 6.411 | 0.040 | 6.451 | |
link_what | 7.262 | 0.016 | 7.278 | |
project_details | 0 | 0 | 0 | |
project_members | 0.001 | 0.000 | 0.001 | |
requirements | 0.046 | 0.004 | 0.050 | |
response-methods | 0.001 | 0.000 | 0.000 | |
sbg_get_env | 0 | 0 | 0 | |
sbg_set_env | 0 | 0 | 0 | |
set_test_env | 0.001 | 0.000 | 0.001 | |
shorthand-cwl | 0.02 | 0.00 | 0.02 | |
tag-methods | 0 | 0 | 0 | |
test_tool_bunny | 0 | 0 | 0 | |
test_tool_cwlrun | 0.001 | 0.000 | 0.001 | |
test_tool_rabix | 0.000 | 0.001 | 0.000 | |
upload_complete_all | 0 | 0 | 0 | |
upload_complete_part | 0.000 | 0.000 | 0.001 | |
upload_delete | 0.000 | 0.001 | 0.000 | |
upload_info | 0 | 0 | 0 | |
upload_info_part | 0 | 0 | 0 | |
upload_init | 0.000 | 0.001 | 0.000 | |