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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 87/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnVILWorkflow 1.6.0  (landing page)
Sehyun Oh
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/AnVILWorkflow
git_branch: RELEASE_3_20
git_last_commit: 073e380
git_last_commit_date: 2024-10-29 11:17:51 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for AnVILWorkflow on palomino8

To the developers/maintainers of the AnVILWorkflow package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnVILWorkflow.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: AnVILWorkflow
Version: 1.6.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnVILWorkflow.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AnVILWorkflow_1.6.0.tar.gz
StartedAt: 2024-12-19 22:56:10 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 22:57:01 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 51.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: AnVILWorkflow.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnVILWorkflow.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AnVILWorkflow_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/AnVILWorkflow.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 ... 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 '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 'F:/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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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


Installation output

AnVILWorkflow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL AnVILWorkflow
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)

Tests output


Example timings

AnVILWorkflow.Rcheck/AnVILWorkflow-Ex.timings

nameusersystemelapsed
AnVILBrowse4.600.074.72
availableAnalysis000
cloneWorkspace000
currentInput0.000.010.01
dot-biobakery_currentInput000
dot-get_workspace_fullname000
findInputName0.000.020.02
getAllDataTables000
getAllWorkflows000
getAllWorkspaces000
getDashboard000
getOutput0.000.010.02
getWorkflowConfig000
monitorWorkflow000
runWorkflow000
setCloudEnv000
stopWorkflow000
updateInput0.020.000.01