Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:31 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE gaggle PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 650/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
gaggle 1.56.0 Christopher Bare
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
Package: gaggle |
Version: 1.56.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gaggle.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gaggle_1.56.0.tar.gz |
StartedAt: 2020-10-17 01:18:16 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 01:19:11 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 55.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gaggle.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gaggle.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gaggle_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/gaggle.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gaggle/DESCRIPTION’ ... OK * this is package ‘gaggle’ version ‘1.56.0’ * 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 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/4.0/Resources/library pkgname: gaggle path to jar: /Library/Frameworks/R.framework/Versions/4.0/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: 14 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.11-bioc/meat/gaggle.Rcheck/00check.log’ for details.
gaggle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gaggle ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘gaggle’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location onLoad -- libname: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-gaggle/00new pkgname: gaggle path to jar: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-gaggle/00new/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: 14 You are using the wrong version of Java. Please see http://gaggle.systemsbiology.org/docs/html/java ** testing if installed package can be loaded from final location onLoad -- libname: /Library/Frameworks/R.framework/Versions/4.0/Resources/library pkgname: gaggle path to jar: /Library/Frameworks/R.framework/Versions/4.0/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: 14 You are using the wrong version of Java. Please see http://gaggle.systemsbiology.org/docs/html/java ** testing if installed package keeps a record of temporary installation path * DONE (gaggle)
gaggle.Rcheck/gaggle-Ex.timings
name | user | system | elapsed | |
newTuple | 0.021 | 0.003 | 0.021 | |