Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the CEMiTool package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CEMiTool.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 271/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CEMiTool 1.16.0 (landing page) Helder Nakaya
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: CEMiTool |
Version: 1.16.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CEMiTool_1.16.0.tar.gz |
StartedAt: 2021-10-14 20:52:07 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:58:53 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 406.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CEMiTool.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CEMiTool_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CEMiTool.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'CEMiTool/DESCRIPTION' ... OK * this is package 'CEMiTool' version '1.16.0' * package encoding: UTF-8 * 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 'CEMiTool' can be installed ... OK * checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: data 3.1Mb extdata 2.8Mb * 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 * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE flip_vector: no visible global function definition for 'setNames' select_genes: no visible global function definition for 'var' get_hubs,CEMiTool : <anonymous>: no visible global function definition for 'head' get_merged_mods,CEMiTool: no visible global function definition for 'as.dist' get_mods,CEMiTool: no visible global function definition for 'as.dist' get_phi,CEMiTool: no visible global function definition for 'tail' get_phi,CEMiTool: no visible global function definition for 'head' mod_gene_num,CEMiTool: no visible binding for global variable 'modules' mod_gene_num,CEMiTool: no visible binding for global variable 'num_genes' mod_summary,CEMiTool: no visible global function definition for ':=' plot_gsea,CEMiTool: no visible global function definition for 'dist' plot_mean_var,CEMiTool: no visible binding for global variable 'var' plot_mean_var,CEMiTool: no visible binding for global variable 'Mean' plot_mean_var,CEMiTool: no visible binding for global variable 'Variance' plot_mean_var,CEMiTool: no visible binding for global variable '..eq.label..' plot_mean_var,CEMiTool: no visible binding for global variable '..rr.label..' plot_ora,CEMiTool : <anonymous>: no visible global function definition for 'head' plot_qq,CEMiTool: no visible binding for global variable 'data' plot_sample_tree,CEMiTool: no visible global function definition for 'dist' plot_sample_tree,CEMiTool: no visible global function definition for 'dev.off' save_plots,CEMiTool : <anonymous>: no visible global function definition for 'dev.off' save_plots,CEMiTool: no visible global function definition for 'dev.off' Undefined global functions or variables: ..eq.label.. ..rr.label.. := Mean Variance as.dist data dev.off dist head modules num_genes setNames tail var Consider adding importFrom("grDevices", "dev.off") importFrom("stats", "as.dist", "dist", "setNames", "var") importFrom("utils", "data", "head", "tail") 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cemitool 7.69 0.30 8.0 plot_interactions 6.82 0.25 7.1 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cemitool 9.47 0.08 9.55 plot_interactions 5.72 0.16 5.87 * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CEMiTool.Rcheck/00check.log' for details.
CEMiTool.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CEMiTool_1.16.0.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.16.0.zip && rm CEMiTool_1.16.0.tar.gz CEMiTool_1.16.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 43 4048k 43 1749k 0 0 2240k 0 0:00:01 --:--:-- 0:00:01 2240k 100 4048k 100 4048k 0 0 2826k 0 0:00:01 0:00:01 --:--:-- 2827k install for i386 * installing *source* package 'CEMiTool' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** exec ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CEMiTool' finding HTML links ... done CEMiTool-class html adj_data html cem html cemitool html diagnostic_report html expr0 html expr_data html expr_pct_filter html filter_expr html find_modules html fit_data html generate_report html get_adj html get_beta_data html get_cemitool_r2_beta html get_connectivity html get_hubs html get_merged_mods html get_mods html get_phi html gsea_data html interactions_data html mod_colors html mod_gene_num html mod_gsea html mod_names html mod_ora html mod_summary html module_genes html module_to_gmt html new_cem html nmodules html ora_data html plot_beta_r2 html plot_gsea html plot_hist html plot_interactions html plot_mean_k html plot_mean_var html plot_ora html plot_ora_single html plot_profile html plot_qq html plot_sample_tree html read_gmt html sample_annot html sample_annotation html save_plots html select_genes html show-CEMiTool-method html show_plot html vst html write_files html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'CEMiTool' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'CEMiTool' as CEMiTool_1.16.0.zip * DONE (CEMiTool) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'CEMiTool' successfully unpacked and MD5 sums checked
CEMiTool.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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(CEMiTool) > test_check('CEMiTool') [ FAIL 0 | WARN 16 | SKIP 0 | PASS 105 ] > > proc.time() user system elapsed 25.89 1.14 27.00 |
CEMiTool.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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(CEMiTool) > test_check('CEMiTool') [ FAIL 0 | WARN 16 | SKIP 0 | PASS 105 ] > > proc.time() user system elapsed 26.32 0.96 27.28 |
CEMiTool.Rcheck/examples_i386/CEMiTool-Ex.timings
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CEMiTool.Rcheck/examples_x64/CEMiTool-Ex.timings
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