Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:25:45 -0400 (Tue, 09 Apr 2019).
Package 497/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ENVISIONQuery 1.31.0 Alex Lisovich
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: ENVISIONQuery |
Version: 1.31.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ENVISIONQuery.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ENVISIONQuery_1.31.0.tar.gz |
StartedAt: 2019-04-09 00:43:21 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 00:44:01 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 40.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ENVISIONQuery.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ENVISIONQuery.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ENVISIONQuery_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ENVISIONQuery.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ENVISIONQuery/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ENVISIONQuery’ version ‘1.31.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ENVISIONQuery’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 Packages in Depends field not imported from: ‘XML’ ‘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 NB: .First.lib is obsolete and will not be used in R >= 3.0.0 File ‘ENVISIONQuery/R/zzz.R’: .onAttach calls: cat("This is ", pkgname, " ", desc$Version, " ", desc$Date, "\n") Package startup functions should use ‘packageStartupMessage’ to generate messages. See section ‘Good practice’ in '?.onAttach'. .First.lib: no visible global function definition for ‘data’ .onAttach : getJavaVersion: no visible global function definition for ‘.jcall’ .onAttach : jpackage: no visible binding for global variable ‘.jniInitialized’ .onAttach : jpackage: no visible global function definition for ‘.jinit’ .onAttach : jpackage: no visible global function definition for ‘.jaddClassPath’ .onAttach : jpackage: no visible global function definition for ‘.jaddLibrary’ .onAttach: no visible global function definition for ‘packageDescription’ ENVISIONQuery.chunk: no visible global function definition for ‘.jarray’ formatIdMap: no visible global function definition for ‘xmlTreeParse’ formatIdMap: no visible global function definition for ‘xmlRoot’ formatIdMap: no visible global function definition for ‘xmlChildren’ formatIntact: no visible global function definition for ‘xmlTreeParse’ formatIntact: no visible global function definition for ‘xmlRoot’ formatIntact: no visible global function definition for ‘xmlChildren’ formatPicr: no visible global function definition for ‘xmlTreeParse’ formatPicr: no visible global function definition for ‘xmlRoot’ formatPicr: no visible global function definition for ‘xmlChildren’ formatReactome: no visible global function definition for ‘xmlTreeParse’ formatReactome: no visible global function definition for ‘xmlRoot’ formatReactome: no visible global function definition for ‘xmlChildren’ getIdEntries: no visible global function definition for ‘xmlChildren’ getIdEntries : <anonymous>: no visible global function definition for ‘xmlAttrs’ getIdMatchInfo: no visible global function definition for ‘xmlChildren’ getIdMatchInfo : <anonymous>: no visible global function definition for ‘xmlAttrs’ getIdMatchInfo : <anonymous>: no visible global function definition for ‘xmlValue’ getIdMatchInfo : <anonymous>: no visible global function definition for ‘xmlChildren’ getInputIdEntries: no visible global function definition for ‘xmlChildren’ getInputIdEntries : <anonymous>: no visible global function definition for ‘xmlAttrs’ getIntactMatchInfo: no visible global function definition for ‘xmlChildren’ getIntactMatchInfo : <anonymous>: no visible global function definition for ‘xmlAttrs’ getIntactMatchInfo: no visible global function definition for ‘xmlAttrs’ getPicrMatchInfo: no visible global function definition for ‘xmlChildren’ getPicrMatchInfo : <anonymous>: no visible global function definition for ‘xmlAttrs’ getPicrMatchInfo: no visible global function definition for ‘xmlAttrs’ getPositiveResultSetIDs: no visible global function definition for ‘xmlChildren’ getPositiveResultSetIDs: no visible global function definition for ‘xmlAttrs’ getPositiveResultSetIDs : <anonymous>: no visible global function definition for ‘xmlAttrs’ getReactomeMatchInfo: no visible global function definition for ‘xmlChildren’ getReactomeMatchInfo : <anonymous>: no visible global function definition for ‘xmlAttrs’ getReactomeMatchInfo: no visible global function definition for ‘xmlValue’ getReactomeMatchInfo: no visible global function definition for ‘xmlAttrs’ getService: no visible global function definition for ‘menu’ getServices: no visible global function definition for ‘assignInNamespace’ getTool: no visible global function definition for ‘menu’ progressMsg: no visible global function definition for ‘flush.console’ registerServices: no visible global function definition for ‘new’ registerServices: no visible global function definition for ‘J’ Undefined global functions or variables: .jaddClassPath .jaddLibrary .jarray .jcall .jinit .jniInitialized J assignInNamespace data flush.console menu new packageDescription xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue Consider adding importFrom("methods", "new") importFrom("utils", "assignInNamespace", "data", "flush.console", "menu", "packageDescription") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 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-3.9-bioc/meat/ENVISIONQuery.Rcheck/00check.log’ for details.
ENVISIONQuery.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ENVISIONQuery ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘ENVISIONQuery’ ... ** 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 This is ENVISIONQuery 1.31.0 2013-08-20 * DONE (ENVISIONQuery)
ENVISIONQuery.Rcheck/ENVISIONQuery-Ex.timings
name | user | system | elapsed | |
ENVISIONQuery | 1.945 | 0.238 | 2.122 | |
getInputTypes | 0 | 0 | 0 | |
getService | 0.000 | 0.000 | 0.001 | |
getServiceClient | 0.000 | 0.000 | 0.001 | |
getServiceNames | 0 | 0 | 0 | |
getServiceOptions | 0.031 | 0.005 | 0.037 | |
getServices | 0 | 0 | 0 | |
getTool | 0.001 | 0.001 | 0.001 | |
getToolNames | 0 | 0 | 0 | |