Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:23:19 -0400 (Tue, 09 Apr 2019).
Package 337/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
copa 1.51.0 James W. MacDonald
| 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: copa |
Version: 1.51.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:copa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings copa_1.51.0.tar.gz |
StartedAt: 2019-04-09 00:08:05 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 00:08:36 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 31.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: copa.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:copa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings copa_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/copa.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 ‘copa/DESCRIPTION’ ... OK * this is package ‘copa’ version ‘1.51.0’ * 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 ‘copa’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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: ‘Biobase’ ‘methods’ 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 copa: warning in matrix(1:dim(mat)[1], nc = dim(mat)[1], nr = dim(mat)[1]): partial argument match of 'nr' to 'nrow' copa: warning in matrix(1:dim(mat)[1], nc = dim(mat)[1], nr = dim(mat)[1]): partial argument match of 'nc' to 'ncol' pSum: warning in matrix(out, nc = length(a), nr = length(a)): partial argument match of 'nr' to 'nrow' pSum: warning in matrix(out, nc = length(a), nr = length(a)): partial argument match of 'nc' to 'ncol' plotCopa: warning in matrix(1:2, nc = 1): partial argument match of 'nc' to 'ncol' copa: no visible binding for global variable ‘quantile’ do.copaFilter: no visible binding for global variable ‘median’ do.copaFilter: no visible binding for global variable ‘mad’ do.copaFilter: no visible global function definition for ‘quantile’ pSum: no visible binding for global variable ‘mat’ plotCopa: no visible global function definition for ‘par’ plotCopa: no visible global function definition for ‘layout’ plotCopa: no visible global function definition for ‘barplot’ scatterPlotCopa: no visible global function definition for ‘plot’ copaFilter,ExpressionSet: no visible global function definition for ‘exprs’ Undefined global functions or variables: barplot exprs layout mad mat median par plot quantile Consider adding importFrom("graphics", "barplot", "layout", "par", "plot") importFrom("stats", "mad", "median", "quantile") 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 * 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/copa.Rcheck/00check.log’ for details.
copa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL copa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘copa’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c copa.c -o copa.o clang -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 copa.so copa.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/copa/libs ** 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 * DONE (copa)
copa.Rcheck/copa-Ex.timings
name | user | system | elapsed | |
copa | 0.215 | 0.019 | 0.235 | |
copaTable | 0.173 | 0.006 | 0.178 | |
plotCopa | 0.001 | 0.000 | 0.002 | |
scatterPlotCopa | 0.001 | 0.000 | 0.001 | |
summaryCopa | 0.001 | 0.000 | 0.001 | |