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### Running command:
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###   /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
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* 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.