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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnVILWorkflow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnVILWorkflow_1.11.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/AnVILWorkflow.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-24 22:25:11 UTC
* using option ‘--no-vignettes’
* checking for file ‘AnVILWorkflow/DESCRIPTION’ ... OK
* this is package ‘AnVILWorkflow’ version ‘1.11.1’
* 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 ‘AnVILWorkflow’ 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 dependencies in R code ... WARNING
Missing or unexported object: ‘AnVIL::gsutil_cat’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.avSampleData: no visible binding for global variable ‘.’
.tableToString: no visible binding for global variable ‘.’
AnVILBrowse: no visible binding for global variable ‘workspace_key’
getAllWorkspaces: no visible binding for global variable
  ‘workspace.workspaceId’
getAllWorkspaces: no visible binding for global variable ‘public’
getAllWorkspaces: no visible binding for global variable
  ‘workspace.attributes.library:indication’
getAllWorkspaces: no visible binding for global variable
  ‘workspace.attributes.library:studyDesign’
getAllWorkspaces: no visible binding for global variable
  ‘workspace.attributes.library:numSubjects’
getAllWorkspaces: no visible binding for global variable
  ‘workspace.attributes.library:primaryDiseaseSite’
getAllWorkspaces: no visible binding for global variable
  ‘workspace.attributes.library:cohortCountry’
getAllWorkspaces: no visible binding for global variable
  ‘workspace.attributes.library:projectName’
getAllWorkspaces: no visible binding for global variable
  ‘workspace.attributes.library:reference’
getData: no visible binding for global variable ‘.’
getOutput: no visible binding for global variable ‘gsutil_cp’
getWorkspaces: no visible binding for global variable ‘cloudPlatform’
getWorkspaces: no visible binding for global variable ‘namespace’
getWorkspaces: no visible binding for global variable ‘name’
getWorkspaces: no visible binding for global variable ‘accessLevel’
getWorkspaces: no visible binding for global variable ‘public’
getWorkspaces: no visible binding for global variable ‘isLocked’
getWorkspaces: no visible binding for global variable
  ‘workspace_namespace’
getWorkspaces: no visible binding for global variable ‘workspace_name’
getWorkspaces: no visible binding for global variable ‘datatype’
getWorkspaces: no visible binding for global variable ‘itemsType’
getWorkspaces: no visible binding for global variable ‘items’
setCloudEnv: no visible global function definition for ‘gcloud_exists’
updateInput: no visible binding for global variable ‘ws_namespace’
updateInput: no visible binding for global variable ‘ws_name’
updateInput: no visible binding for global variable ‘ws_fullname’
updateInput: no visible binding for global variable ‘wf_fullname’
Undefined global functions or variables:
  . accessLevel cloudPlatform datatype gcloud_exists gsutil_cp isLocked
  items itemsType name namespace public wf_fullname
  workspace.attributes.library:cohortCountry
  workspace.attributes.library:indication
  workspace.attributes.library:numSubjects
  workspace.attributes.library:primaryDiseaseSite
  workspace.attributes.library:projectName
  workspace.attributes.library:reference
  workspace.attributes.library:studyDesign workspace.workspaceId
  workspace_key workspace_name workspace_namespace ws_fullname ws_name
  ws_namespace
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'dot-nonMetadataOutputs.Rd':
  ‘[AnVIL]{avworkflow_files}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ‘AnVILWorkflow-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: setCloudEnv
> ### Title: Setup Google Cloud Account and Project
> ### Aliases: setCloudEnv
> 
> ### ** Examples
> 
> if (gcloud_exists()) {
+ setCloudEnv()
+ }
Error in gcloud_exists() : could not find function "gcloud_exists"
Execution halted
* 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, 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/AnVILWorkflow.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AnVILWorkflow
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘AnVILWorkflow’ ...
** this is package ‘AnVILWorkflow’ version ‘1.11.1’
** 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 (AnVILWorkflow)