Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (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 87/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AnVILWorkflow 1.6.0 (landing page) Sehyun Oh
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: AnVILWorkflow |
Version: 1.6.0 |
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 |
StartedAt: 2024-12-19 19:58:26 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 20:02:41 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 254.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: AnVILWorkflow.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AnVILWorkflow.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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.
AnVILWorkflow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL AnVILWorkflow ### ############################################################################## ############################################################################## * 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)
AnVILWorkflow.Rcheck/AnVILWorkflow-Ex.timings
name | user | system | elapsed | |
AnVILBrowse | 3.147 | 0.053 | 3.200 | |
availableAnalysis | 0.021 | 0.023 | 0.044 | |
cloneWorkspace | 0.018 | 0.020 | 0.038 | |
currentInput | 0.017 | 0.022 | 0.054 | |
dot-biobakery_currentInput | 0.022 | 0.020 | 0.039 | |
dot-get_workspace_fullname | 0.017 | 0.019 | 0.036 | |
findInputName | 0.027 | 0.011 | 0.038 | |
getAllDataTables | 0.020 | 0.016 | 0.037 | |
getAllWorkflows | 0.015 | 0.022 | 0.038 | |
getAllWorkspaces | 0.014 | 0.025 | 0.038 | |
getDashboard | 0.019 | 0.020 | 0.038 | |
getOutput | 0.016 | 0.023 | 0.038 | |
getWorkflowConfig | 0.018 | 0.020 | 0.039 | |
monitorWorkflow | 0.010 | 0.027 | 0.036 | |
runWorkflow | 0.021 | 0.019 | 0.039 | |
setCloudEnv | 0.022 | 0.014 | 0.036 | |
stopWorkflow | 0.018 | 0.021 | 0.038 | |
updateInput | 0.022 | 0.020 | 0.039 | |