Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:28:07 -0400 (Thu, 12 Apr 2018).
Package 412/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
EGAD 1.6.0 Sara Ballouz
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: EGAD |
Version: 1.6.0 |
Command: rm -rf EGAD.buildbin-libdir EGAD.Rcheck && mkdir EGAD.buildbin-libdir EGAD.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EGAD.buildbin-libdir EGAD_1.6.0.tar.gz >EGAD.Rcheck\00install.out 2>&1 && cp EGAD.Rcheck\00install.out EGAD-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=EGAD.buildbin-libdir --install="check:EGAD-install.out" --force-multiarch --no-vignettes --timings EGAD_1.6.0.tar.gz |
StartedAt: 2018-04-11 23:43:36 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 23:48:56 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 319.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EGAD.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf EGAD.buildbin-libdir EGAD.Rcheck && mkdir EGAD.buildbin-libdir EGAD.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EGAD.buildbin-libdir EGAD_1.6.0.tar.gz >EGAD.Rcheck\00install.out 2>&1 && cp EGAD.Rcheck\00install.out EGAD-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=EGAD.buildbin-libdir --install="check:EGAD-install.out" --force-multiarch --no-vignettes --timings EGAD_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/EGAD.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'EGAD/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'EGAD' version '1.6.0' * 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 whether package 'EGAD' can be installed ... OK * checking installed package size ... NOTE installed size is 42.5Mb sub-directories of 1Mb or more: data 41.1Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * 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 * loading checks for arch 'i386' ** 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 loading without being on the library search path ... OK * loading checks for arch 'x64' ** 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'affy' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE assortativity: no visible global function definition for 'cor' build_coexp_network: no visible global function definition for 'cor' conv_smoother: no visible global function definition for 'convolve' conv_smoother: no visible global function definition for 'plot' conv_smoother: no visible global function definition for 'polygon' conv_smoother: no visible global function definition for 'points' conv_smoother: no visible global function definition for 'rgb' conv_smoother: no visible global function definition for 'lines' get_biogrid: no visible global function definition for 'download.file' get_biogrid: no visible global function definition for 'unzip' get_biogrid: no visible global function definition for 'read.table' get_expression_data_gemma: no visible global function definition for 'read.table' get_expression_matrix_from_GEO: no visible global function definition for 'median' get_expression_matrix_from_GEO: no visible global function definition for 'aggregate' get_expression_matrix_from_GEO: no visible binding for global variable 'median' get_phenocarta: no visible global function definition for 'read.table' make_transparent: no visible global function definition for 'col2rgb' make_transparent : <anonymous>: no visible global function definition for 'rgb' plot_densities: no visible global function definition for 'plot' plot_densities : <anonymous>: no visible global function definition for 'polygon' plot_densities : <anonymous>: no visible global function definition for 'lines' plot_density_compare: no visible global function definition for 'density' plot_density_compare: no visible global function definition for 'plot' plot_density_compare: no visible global function definition for 'polygon' plot_density_compare: no visible global function definition for 'lines' plot_distribution: no visible global function definition for 'hist' plot_distribution: no visible global function definition for 'boxplot' plot_distribution: no visible global function definition for 'plot' plot_distribution: no visible global function definition for 'polygon' plot_distribution: no visible global function definition for 'lines' plot_distribution: no visible global function definition for 'abline' plot_prc: no visible global function definition for 'plot' plot_prc: no visible global function definition for 'abline' plot_roc: no visible global function definition for 'plot' plot_roc_overlay: no visible global function definition for 'axis' plot_roc_overlay: no visible global function definition for 'lines' plot_value_compare: no visible global function definition for 'plot' plot_value_compare: no visible global function definition for 'abline' Undefined global functions or variables: abline aggregate axis boxplot col2rgb convolve cor density download.file hist lines median plot points polygon read.table rgb unzip Consider adding importFrom("grDevices", "col2rgb", "rgb") importFrom("graphics", "abline", "axis", "boxplot", "hist", "lines", "plot", "points", "polygon") importFrom("stats", "aggregate", "convolve", "cor", "density", "median") importFrom("utils", "download.file", "read.table", "unzip") 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/EGAD.Rcheck/00check.log' for details.
EGAD.Rcheck/00install.out
install for i386 * installing *source* package 'EGAD' ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'EGAD' finding HTML links ... done GO.human html GO.mouse html GO.voc html assortativity html atrr.human html attr.mouse html auc_multifunc html auprc html auroc_analytic html biogrid html build_binary_network html build_coexp_GEOID html build_coexp_expressionSet html build_coexp_network html build_semantic_similarity_network html build_weighted_network html calculate_multifunc html conv_smoother html example_annotations html example_binary_network html example_coexpression html example_neighbor_voting html extend_network html filter_network html filter_network_cols html filter_network_rows html filter_orthologs html fmeasure html genes html get_auc html get_biogrid html get_counts html get_density html get_expression_data_gemma html get_expression_matrix_from_GEO html get_phenocarta html get_prc html get_roc html make_annotations html make_gene_network html make_genelist html make_transparent html neighbor_voting html node_degree html ortho html pheno html plot_densities html plot_density_compare html plot_distribution html plot_network_heatmap html plot_prc html plot_roc html plot_roc_overlay html plot_value_compare html predictions html repmat html run_GBA html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'EGAD' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'EGAD' as EGAD_1.6.0.zip * DONE (EGAD) In R CMD INSTALL In R CMD INSTALL
EGAD.Rcheck/tests_i386/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(EGAD) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > test_check("EGAD") == testthat results =========================================================== OK: 9 SKIPPED: 2 FAILED: 0 > > proc.time() user system elapsed 6.57 0.20 6.87 |
EGAD.Rcheck/tests_x64/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(EGAD) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > test_check("EGAD") == testthat results =========================================================== OK: 9 SKIPPED: 2 FAILED: 0 > > proc.time() user system elapsed 7.90 0.23 8.25 |
EGAD.Rcheck/examples_i386/EGAD-Ex.timings
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EGAD.Rcheck/examples_x64/EGAD-Ex.timings
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