############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gaggle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gaggle_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/gaggle.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * 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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gaggle/DESCRIPTION’ ... OK * this is package ‘gaggle’ version ‘1.68.0’ * 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 ‘gaggle’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Non-standard license specification: GPL version 2 or newer Standardizable: TRUE Standardized license specification: GPL (>= 2) * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 startup messages can be suppressed ... NOTE onLoad -- libname: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library pkgname: gaggle path to jar: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gaggle/jars/gaggleRShell.jar script: gaggle.R $Revision: 4499 $ $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $ os version: Mac OS X jvm version: 18.0.1.1 You are using the wrong version of Java. Please see http://gaggle.systemsbiology.org/docs/html/java It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘RUnit’ ‘rJava’ Please remove these calls from your code. Packages in Depends field not imported from: ‘RUnit’ ‘rJava’ 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 File ‘gaggle/R/gaggle.R’: .onLoad calls: require("rJava") cat(paste("\nonLoad -- libname:", libname, "pkgname:", pkgname, "\n")) cat("path to jar:", fullPathToGaggleJar, "\n") cat(" script: ", .scriptVersion(), "\n") cat(" os version: ", .jcall("java/lang/System", "S", "getProperty", "os.name"), "\n") cat(" jvm version: ", jvmVersion, "\n") cat("\n You are using the wrong version of Java.\n", " Please see http://gaggle.systemsbiology.org/docs/html/java\n\n") Package startup functions should not change the search path. Package startup functions should use ‘packageStartupMessage’ to generate messages. See section ‘Good practice’ in '?.onAttach'. onLoad -- libname: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library pkgname: gaggle path to jar: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gaggle/jars/gaggleRShell.jar script: gaggle.R $Revision: 4499 $ $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $ os version: Mac OS X jvm version: 18.0.1.1 You are using the wrong version of Java. Please see http://gaggle.systemsbiology.org/docs/html/java .broadcastAssociativeArray: no visible binding for global variable ‘goose’ .broadcastEnvironment: no visible binding for global variable ‘goose’ .broadcastGraph: no visible binding for global variable ‘goose’ .pkgVersion: no visible global function definition for ‘sessionInfo’ broadcast: no visible binding for global variable ‘goose’ connectToGaggle: no visible binding for global variable ‘goose’ disconnectFromGaggle: no visible binding for global variable ‘goose’ gaggleInit: no visible binding for '<<-' assignment to ‘goose’ gaggleInit: no visible binding for '<<-' assignment to ‘targetGoose’ gaggleInit: no visible binding for global variable ‘goose’ geese: no visible binding for global variable ‘goose’ getCluster: no visible binding for global variable ‘goose’ getMatrix: no visible binding for global variable ‘goose’ getNameList: no visible binding for global variable ‘goose’ getNetwork: no visible binding for global variable ‘goose’ getSpecies: no visible binding for global variable ‘goose’ getTargetGoose: no visible binding for global variable ‘goose’ getTuple: no visible binding for global variable ‘goose’ getTupleAsList: no visible binding for global variable ‘goose’ hideGoose: no visible binding for global variable ‘goose’ setSpecies: no visible binding for global variable ‘goose’ setTargetGoose: no visible binding for '<<-' assignment to ‘targetGoose’ setTargetGoose: no visible binding for global variable ‘goose’ showGoose: no visible binding for global variable ‘goose’ testGagglePackage: no visible global function definition for ‘test.gaggle’ Undefined global functions or variables: goose sessionInfo test.gaggle Consider adding importFrom("utils", "sessionInfo") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: connectToGaggle.Rd:9-10: Dropping empty section \arguments prepare_Rd: disconnectFromGaggle.Rd:8-9: Dropping empty section \arguments prepare_Rd: getCluster.Rd:8-9: Dropping empty section \arguments prepare_Rd: getNameList.Rd:8-9: Dropping empty section \arguments prepare_Rd: getTuple.Rd:6-7: Dropping empty section \arguments * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/gaggle.Rcheck/00check.log’ for details.