Phil Webster
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/sevenbridges |
| git_branch: RELEASE_3_18 |
| git_last_commit: bd309cc |
| git_last_commit_date: 2023-10-24 10:45:02 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:23 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1936/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sevenbridges 1.32.0 (landing page) Phil Webster
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.32.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sevenbridges_1.32.0.tar.gz |
| StartedAt: 2024-04-16 03:52:20 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 03:56:50 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 269.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: sevenbridges.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sevenbridges.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sevenbridges_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sevenbridges.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘1.32.0’
* 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 R 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 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 ... OK
* 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 41.254 0.284 41.539
Tool-class 11.634 0.072 11.707
link_what 7.066 0.008 7.074
link 6.606 0.036 6.642
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘api.Rmd’ using ‘UTF-8’... failed
‘apps.Rmd’ using ‘UTF-8’... OK
‘bioc-workflow.Rmd’ using ‘UTF-8’... failed
‘cgc-datasets.Rmd’ using ‘UTF-8’... failed
‘docker.Rmd’ using ‘UTF-8’... OK
‘rstudio.Rmd’ using ‘UTF-8’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘api.Rmd’
...
> library("sevenbridges")
> a <- Auth(token = "your_token", platform = "aws-us")
Using platform: aws-us
> a$api(path = "projects", method = "GET")
When sourcing ‘api.R’:
Error: HTTP Status 401: Unauthorized
Execution halted
when running code in ‘bioc-workflow.Rmd’
...
> library("sevenbridges")
> if (!require("devtools", quietly = TRUE)) install.packages("devtools")
Installing package into ‘/tmp/RtmphB0n94/RLIBS_2628f43e2b38c1’
(as ‘lib’ is unspecified)
When sourcing ‘bioc-workflow.R’:
Error: trying to use CRAN without setting a mirror
Execution halted
when running code in ‘cgc-datasets.Rmd’
...
> library("sevenbridges")
> a <- Auth(url = "https://cgc-datasets-api.sbgenomics.com/",
+ token = "your_cgc_token")
> a$api(path = "datasets")
When sourcing ‘cgc-datasets.R’:
Error: $ operator is invalid for atomic vectors
Execution halted
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.18-bioc/meat/sevenbridges.Rcheck/00check.log’
for details.
sevenbridges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL sevenbridges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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
2.211 0.089 2.288
sevenbridges.Rcheck/sevenbridges-Ex.timings
| name | user | system | elapsed | |
| App-class | 0 | 0 | 0 | |
| Auth-class | 0.007 | 0.000 | 0.007 | |
| Binding | 0.011 | 0.000 | 0.011 | |
| CCBList | 0.014 | 0.000 | 0.014 | |
| CWL | 0.002 | 0.000 | 0.002 | |
| CommandInputParameter-class | 0.02 | 0.00 | 0.02 | |
| CommandInputSchema-class | 0.025 | 0.000 | 0.025 | |
| CommandLineBinding-class | 0.006 | 0.000 | 0.006 | |
| CommandLineTool | 0.010 | 0.004 | 0.014 | |
| CommandOutputBinding-class | 0.007 | 0.000 | 0.007 | |
| CommandOutputParameter-class | 0.012 | 0.000 | 0.012 | |
| CommandOutputSchema-class | 0.01 | 0.00 | 0.01 | |
| DSCList | 0.016 | 0.000 | 0.016 | |
| Enum | 0.036 | 0.000 | 0.036 | |
| Expression-class | 0.007 | 0.000 | 0.007 | |
| ExpressionTool-class | 0.018 | 0.000 | 0.018 | |
| File-class | 0.061 | 0.000 | 0.061 | |
| Files-class | 0.007 | 0.000 | 0.007 | |
| Flow | 41.254 | 0.284 | 41.539 | |
| Metadata | 0.074 | 0.000 | 0.075 | |
| Parameter | 0.028 | 0.000 | 0.028 | |
| Process | 0.039 | 0.000 | 0.039 | |
| ProcessRequirement | 0.057 | 0.000 | 0.057 | |
| Schema | 0.015 | 0.000 | 0.014 | |
| TaskHook | 0.002 | 0.000 | 0.002 | |
| Tool-class | 11.634 | 0.072 | 11.707 | |
| Workflow | 0.024 | 0.000 | 0.024 | |
| WorkflowStep | 0.004 | 0.000 | 0.004 | |
| addIdNum | 0 | 0 | 0 | |
| api | 0 | 0 | 0 | |
| as-methods | 0.061 | 0.000 | 0.061 | |
| batch | 0 | 0 | 0 | |
| cli_list_projects | 0 | 0 | 0 | |
| cli_list_tags | 0 | 0 | 0 | |
| cli_upload | 0 | 0 | 0 | |
| convert_app | 4.761 | 0.000 | 4.761 | |
| cwl-utils | 0.087 | 0.000 | 0.088 | |
| delete-methods | 0 | 0 | 0 | |
| download-methods | 0 | 0 | 0 | |
| get_token | 0 | 0 | 0 | |
| get_uploader | 0 | 0 | 0 | |
| input_output_matrix | 0.084 | 0.000 | 0.084 | |
| link | 6.606 | 0.036 | 6.642 | |
| link_what | 7.066 | 0.008 | 7.074 | |
| project_details | 0 | 0 | 0 | |
| project_members | 0 | 0 | 0 | |
| requirements | 0.042 | 0.000 | 0.043 | |
| response-methods | 0.000 | 0.000 | 0.001 | |
| sbg_get_env | 0 | 0 | 0 | |
| sbg_set_env | 0 | 0 | 0 | |
| set_test_env | 0 | 0 | 0 | |
| shorthand-cwl | 0.017 | 0.003 | 0.020 | |
| tag-methods | 0.001 | 0.000 | 0.000 | |
| test_tool_bunny | 0 | 0 | 0 | |
| test_tool_cwlrun | 0 | 0 | 0 | |
| test_tool_rabix | 0 | 0 | 0 | |
| upload_complete_all | 0 | 0 | 0 | |
| upload_complete_part | 0 | 0 | 0 | |
| upload_delete | 0.000 | 0.000 | 0.001 | |
| upload_info | 0 | 0 | 0 | |
| upload_info_part | 0 | 0 | 0 | |
| upload_init | 0 | 0 | 0 | |