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This page was generated on 2019-04-09 13:25:11 -0400 (Tue, 09 Apr 2019).
Package 523/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ExpressionView 1.35.0 Gabor Csardi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | 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: ExpressionView |
Version: 1.35.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExpressionView.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExpressionView_1.35.0.tar.gz |
StartedAt: 2019-04-09 00:49:14 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 00:51:42 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 147.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ExpressionView.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExpressionView.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExpressionView_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ExpressionView.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 ‘ExpressionView/DESCRIPTION’ ... OK * this is package ‘ExpressionView’ version ‘1.35.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'caTools', 'bitops', 'isa2', 'eisa', 'GO.db', 'KEGG.db', 'AnnotationDbi' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘ExpressionView’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘isa2’ ‘eisa’ ‘GO.db’ ‘KEGG.db’ ‘AnnotationDbi’ A package should be listed in only one of these fields. * 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: ‘AnnotationDbi’ ‘GO.db’ ‘KEGG.db’ Please remove these calls from your code. 'library' or 'require' call to ‘affy’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘bitops’ ‘caTools’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Missing or unexported object: ‘isa2::.onUnload’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE NB: .Last.lib will not be used unless it is exported ExportEV.Biclust: no visible global function definition for ‘annotation’ ExportEV.ISAModules: no visible global function definition for ‘annotation’ ExportEV.ISAModules: no visible global function definition for ‘featureNames’ ExportEV.ISAModules: no visible global function definition for ‘sampleNames’ ExportEV.ISAModules: no visible global function definition for ‘phenoData’ ExportEV.ISAModules: no visible global function definition for ‘base64encode’ ExportEV.list: no visible global function definition for ‘base64encode’ LaunchEV: no visible global function definition for ‘URLencode’ LaunchEV: no visible global function definition for ‘browseURL’ OrderEV.list: no visible global function definition for ‘flush.console’ normalize: no visible global function definition for ‘hist’ ExportEV,Biclust: no visible global function definition for ‘annotation’ ExportEV,ISAModules: no visible global function definition for ‘annotation’ ExportEV,ISAModules: no visible global function definition for ‘featureNames’ ExportEV,ISAModules: no visible global function definition for ‘sampleNames’ ExportEV,ISAModules: no visible global function definition for ‘phenoData’ ExportEV,ISAModules: no visible global function definition for ‘base64encode’ ExportEV,list: no visible global function definition for ‘base64encode’ OrderEV,list: no visible global function definition for ‘flush.console’ Undefined global functions or variables: URLencode annotation base64encode browseURL featureNames flush.console hist phenoData sampleNames Consider adding importFrom("graphics", "hist") importFrom("utils", "URLencode", "browseURL", "flush.console") to your NAMESPACE file. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ExpressionView/libs/ExpressionView.so’: Found ‘_rand’, possibly from ‘rand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed ExportEV 8.967 0.805 9.862 * 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-3.9-bioc/meat/ExpressionView.Rcheck/00check.log’ for details.
ExpressionView.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ExpressionView ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘ExpressionView’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c order.cpp -o order.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c orderclusters.cpp -o orderclusters.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ExpressionView.so order.o orderclusters.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ExpressionView/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘ExportEV’ with signature ‘biclusters="Biclust"’: no definition for class “Biclust” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ExpressionView)
ExpressionView.Rcheck/ExpressionView-Ex.timings
name | user | system | elapsed | |
ExportEV | 8.967 | 0.805 | 9.862 | |
LaunchEV | 0 | 0 | 0 | |
OrderEV | 3.669 | 0.434 | 4.123 | |