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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AnVILWorkflow.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AnVILWorkflow_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AnVILWorkflow.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘AnVILWorkflow/DESCRIPTION’ ... OK
* this is package ‘AnVILWorkflow’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  Note: possible error in 'avworkflows(namespace = unlist(strsplit(ws_fullname, ': unused argument (platform = "gcp") 
See ‘/home/biocbuild/bbs-3.20-bioc/meat/AnVILWorkflow.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... NOTE
Package in Depends field not imported from: ‘AnVILBase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ‘.’
.get_workflow_fullname: possible error in avworkflows(namespace =
  unlist(strsplit(ws_fullname, split = "/"))[1], name =
  unlist(strsplit(ws_fullname, split = "/"))[2], platform = "gcp"):
  unused argument (platform = "gcp")
.tableToString: no visible binding for global variable ‘.’
AnVILBrowse: no visible binding for global variable ‘workspace_key’
getAllWorkflows: no visible global function definition for ‘flatten’
getAllWorkspaces: no visible global function definition for ‘flatten’
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’
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 flatten 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 ... 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/AnVILWorkflow.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL AnVILWorkflow
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘AnVILWorkflow’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'avworkflows(namespace = unlist(strsplit(ws_fullname, ': unused argument (platform = "gcp") 
** 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)