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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BiocAzul.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BiocAzul_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BiocAzul.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-30 01:54:07 UTC
* checking for file ‘BiocAzul/DESCRIPTION’ ... OK
* this is package ‘BiocAzul’ version ‘1.0.1’
* 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 ‘BiocAzul’ 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 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 ... ERROR
Running examples in ‘BiocAzul-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Azul-utils
> ### Title: Obtain a list of projects and their IDs from the specified
> ###   catalog
> ### Aliases: Azul-utils projectTable listCatalogs availableFacets
> ###   facetTable
> 
> ### ** Examples
> 
> hca <- Azul(provider = "hca")
> 
> listCatalogs(hca)
[1] "dcp59"    "dcp59-it" "lm10"     "lm10-it" 
> projectTable(hca, catalog = "dcp58")
Error in projectTable(hca, catalog = "dcp58") : 
  Invalid catalog specified. Use 'listCatalogs()' for all catalogs.
Calls: projectTable -> stopifnot
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.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 ‘BiocAzul.Rmd’ using rmarkdown

Quitting from BiocAzul.Rmd:93-96 [project-table]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `projectTable()`:
! Invalid catalog specified. Use 'listCatalogs()' for all catalogs.
---
Backtrace:
    ▆
 1. └─BiocAzul::projectTable(hca, catalog = "dcp58")
 2.   └─base::stopifnot(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'BiocAzul.Rmd' failed with diagnostics:
Invalid catalog specified. Use 'listCatalogs()' for all catalogs.
--- failed re-building ‘BiocAzul.Rmd’

SUMMARY: processing the following file failed:
  ‘BiocAzul.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/BiocAzul.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BiocAzul
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BiocAzul’ ...
** this is package ‘BiocAzul’ version ‘1.0.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (BiocAzul)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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.

> if (requireNamespace("tinytest", quietly = TRUE))
+     tinytest::test_package("BiocAzul")
Loading required package: AnVIL
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: AnVILBase

test_makeFilter.R.............    1 tests OK 
test_makeFilter.R.............    2 tests OK 
test_makeFilter.R.............    3 tests OK 
test_makeFilter.R.............    4 tests OK 
test_makeFilter.R.............    5 tests OK 
test_makeFilter.R.............    6 tests OK 
test_makeFilter.R.............    7 tests OK 
test_makeFilter.R.............    8 tests OK 
test_makeFilter.R.............    9 tests OK 
test_makeFilter.R.............   10 tests OK 
test_makeFilter.R.............   11 tests OK 
test_makeFilter.R.............   12 tests OK 
test_makeFilter.R.............   13 tests OK 
test_makeFilter.R.............   14 tests OK 
test_makeFilter.R.............   15 tests OK 
test_makeFilter.R.............   16 tests OK 
test_makeFilter.R.............   17 tests OK 
test_makeFilter.R.............   18 tests OK 61ms
All ok, 18 results (63ms)
> 
> proc.time()
   user  system elapsed 
  1.099   0.098   1.184