Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-03 11:42 -0400 (Thu, 03 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 1920/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sevenbridges 1.35.0 (landing page) Phil Webster
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
palomino8 | 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.35.0 |
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: 2024-10-03 01:19:16 -0400 (Thu, 03 Oct 2024) |
EndedAt: 2024-10-03 01:22:18 -0400 (Thu, 03 Oct 2024) |
EllapsedTime: 182.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: sevenbridges.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sevenbridges.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘1.35.0’ * 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 41.024 0.348 41.375 Tool-class 11.859 0.070 11.930 link_what 6.817 0.001 6.818 link 6.045 0.001 6.046 * 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 Warning in file("", "w+b") : cannot open file '/tmp/RtmpiZiyW1/Rf2abe4f2d202fdc': No space left on device Quitting from lines 810-829 [unnamed-chunk-26] (apps.Rmd) Error: processing vignette 'apps.Rmd' failed with diagnostics: cannot open the connection --- failed re-building ‘apps.Rmd’ Warning in gzfile(file, mode) : cannot open compressed file '/tmp/RtmpoL6CZv/file2ab6782d791f54.rds', probable reason 'No space left on device' Error in gzfile(file, mode) : cannot open the connection Calls: <Anonymous> -> saveRDS -> gzfile Execution halted * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without index ... ERROR Re-running with no redirection of stdout/stderr. Fatal error: cannot create 'R_TempDir' * DONE Status: 2 ERRORs, 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/sevenbridges.Rcheck/00check.log’ for details.
sevenbridges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
sevenbridges.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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 2.137 0.187 2.312
sevenbridges.Rcheck/sevenbridges-Ex.timings
name | user | system | elapsed | |
App-class | 0 | 0 | 0 | |
Auth-class | 0.006 | 0.001 | 0.007 | |
Binding | 0.010 | 0.000 | 0.011 | |
CCBList | 0.014 | 0.000 | 0.013 | |
CWL | 0.002 | 0.000 | 0.001 | |
CommandInputParameter-class | 0.02 | 0.00 | 0.02 | |
CommandInputSchema-class | 0.025 | 0.000 | 0.026 | |
CommandLineBinding-class | 0.006 | 0.000 | 0.006 | |
CommandLineTool | 0.014 | 0.000 | 0.013 | |
CommandOutputBinding-class | 0.007 | 0.000 | 0.007 | |
CommandOutputParameter-class | 0.012 | 0.000 | 0.013 | |
CommandOutputSchema-class | 0.011 | 0.000 | 0.012 | |
DSCList | 0.017 | 0.000 | 0.017 | |
Enum | 0.042 | 0.000 | 0.042 | |
Expression-class | 0.008 | 0.000 | 0.007 | |
ExpressionTool-class | 0.019 | 0.000 | 0.019 | |
File-class | 0.062 | 0.000 | 0.062 | |
Files-class | 0.007 | 0.000 | 0.008 | |
Flow | 41.024 | 0.348 | 41.375 | |
Metadata | 0.078 | 0.002 | 0.080 | |
Parameter | 0.029 | 0.000 | 0.029 | |
Process | 0.039 | 0.000 | 0.039 | |
ProcessRequirement | 0.046 | 0.000 | 0.046 | |
Schema | 0.015 | 0.000 | 0.014 | |
TaskHook | 0.001 | 0.001 | 0.001 | |
Tool-class | 11.859 | 0.070 | 11.930 | |
Workflow | 0.023 | 0.000 | 0.024 | |
WorkflowStep | 0.004 | 0.000 | 0.004 | |
addIdNum | 0 | 0 | 0 | |
api | 0 | 0 | 0 | |
as-methods | 0.058 | 0.002 | 0.059 | |
batch | 0 | 0 | 0 | |
cli_list_projects | 0 | 0 | 0 | |
cli_list_tags | 0 | 0 | 0 | |
cli_upload | 0 | 0 | 0 | |
convert_app | 4.617 | 0.000 | 4.617 | |
cwl-utils | 0.084 | 0.001 | 0.086 | |
delete-methods | 0 | 0 | 0 | |
download-methods | 0 | 0 | 0 | |
get_token | 0 | 0 | 0 | |
get_uploader | 0.001 | 0.000 | 0.000 | |
input_output_matrix | 0.069 | 0.001 | 0.070 | |
link | 6.045 | 0.001 | 6.046 | |
link_what | 6.817 | 0.001 | 6.818 | |
project_details | 0 | 0 | 0 | |
project_members | 0 | 0 | 0 | |
requirements | 0.045 | 0.000 | 0.046 | |
response-methods | 0.000 | 0.000 | 0.001 | |
sbg_get_env | 0.001 | 0.000 | 0.000 | |
sbg_set_env | 0 | 0 | 0 | |
set_test_env | 0 | 0 | 0 | |
shorthand-cwl | 0.020 | 0.000 | 0.021 | |
tag-methods | 0 | 0 | 0 | |
test_tool_bunny | 0 | 0 | 0 | |
test_tool_cwlrun | 0 | 0 | 0 | |
test_tool_rabix | 0.000 | 0.000 | 0.001 | |
upload_complete_all | 0.001 | 0.000 | 0.000 | |
upload_complete_part | 0 | 0 | 0 | |
upload_delete | 0 | 0 | 0 | |
upload_info | 0 | 0 | 0 | |
upload_info_part | 0.000 | 0.000 | 0.001 | |
upload_init | 0.001 | 0.000 | 0.000 | |