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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnVIL.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AnVIL_1.17.4.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/AnVIL.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AnVIL/DESCRIPTION' ... OK
* this is package 'AnVIL' version '1.17.4'
* 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 whether package 'AnVIL' 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 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 ... 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'AnVIL-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Services
> ### Title: RESTful services useful for AnVIL developers
> ### Aliases: Services .DollarNames.Service operations,Service-method
> ###   schemas,Service-method show,Service-method Service-class empty_object
> ###   operations schemas tags $,Service-method Leonardo Leonardo-class
> ###   operations,Leonardo-method Terra Terra-class operations,Terra-method
> ###   schemas,Terra-method Rawls Rawls-class operations,Rawls-method
> ###   schemas,Rawls-method Dockstore Dockstore-class
> ###   operations,Dockstore-method TDR TDR-class operations,TDR-method
> ### Keywords: datasets
> 
> ### ** Examples
> 
> empty_object
named list()
> 
> if (gcloud_exists()) {
+     ## Arguments to be used as the 'body' (`.__body__=`) of a REST query
+     Terra()$createBillingProjectFull       # 6 arguments...
+     args(Terra()$createBillingProjectFull) # ... passed as `.__body__ = list(...)`
+ }
> if (gcloud_exists())
+     Leonardo()
> 
> if (gcloud_exists()) {
+     tags(Terra())
+     tags(Terra(), "Billing")
+ }
> 
> if (gcloud_exists()) {
+     tags(Rawls())
+     tags(Rawls(), "billing")
+ }
> 
> Dockstore()
service: dockstore
tags(); use dockstore$<tab completion>:
# A tibble: 245 × 3
   tag             operation               summary                              
   <chr>           <chr>                   <chr>                                
 1 Cloud Instances deleteCloudInstance     Delete a public cloud instance, admi…
 2 Cloud Instances getCloudInstances       Get all known public cloud instances 
 3 Cloud Instances postCloudInstance       Add a new public cloud instance, adm…
 4 GA4GHV1         descriptorGetV1         Get the tool descriptor (CWL/WDL) fo…
 5 GA4GHV1         dockerfileGetV1         Get the dockerfile for the specified…
 6 GA4GHV1         relativeDescriptorGetV1 Get additional tool descriptor files…
 7 GA4GHV1         testsGetV1              Get an array of test JSONs suitable …
 8 GA4GHV1         toolsGetV1              List all tools                       
 9 GA4GHV1         toolsIdGetV1            List one specific tool, acts as an a…
10 GA4GHV1         toolsIdVersionGetV1     List versions of a tool              
# ℹ 235 more rows
tag values:
  Cloud Instances, GA4GHV1, GA4GHV20, GA4GHV20BETA, aliases,
  categories, containers, containertags, curation, entries, events,
  extendedGA4GH, hosted, lambdaEvents, metadata, organizations, tokens,
  toolTester, users, workflows
schemas():
  AggregatedExecution, Alias, AppTool, Author, BioWorkflow
  # ... with 115 more elements
> 
> TDR()
Error: failed to find 'gcloud' binary; set option or environment variable 'GCLOUD_SDK_PATH'?
Execution halted
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  'F:/biocbuild/bbs-3.20-bioc/meat/AnVIL.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL AnVIL
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'AnVIL' ...
** 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 (AnVIL)

R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(AnVIL)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> test_check("AnVIL")
[ FAIL 0 | WARN 7 | SKIP 4 | PASS 48 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• !gcloud_exists() is TRUE (4): 'test_Services.R:2:5', 'test_api.R:2:5',
  'test_api.R:38:5', 'test_gcloud_sdk.R:17:5'

[ FAIL 0 | WARN 7 | SKIP 4 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
   4.21    1.87    6.56