############################################################################## ############################################################################## ### ### 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_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/AnVILWorkflow.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * 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 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 ‘/Users/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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed AnVILBrowse 11.744 0.111 11.981 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/AnVILWorkflow.Rcheck/00check.log’ for details.