Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-04-02 19:33 -0400 (Wed, 02 Apr 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 310/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CEMiTool 1.30.0 (landing page) Helder Nakaya
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the CEMiTool package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: CEMiTool |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CEMiTool_1.30.0.tar.gz |
StartedAt: 2025-04-01 13:38:04 -0400 (Tue, 01 Apr 2025) |
EndedAt: 2025-04-01 13:43:15 -0400 (Tue, 01 Apr 2025) |
EllapsedTime: 310.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CEMiTool.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CEMiTool_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CEMiTool.Rcheck’ * using R version 4.4.3 (2025-02-28) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CEMiTool/DESCRIPTION’ ... OK * this is package ‘CEMiTool’ version ‘1.30.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘CEMiTool’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.6Mb 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 code 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 ... 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cemitool 11.715 0.253 12.121 plot_interactions 10.462 0.200 10.764 gsea_data 5.598 0.040 5.665 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/CEMiTool.Rcheck/00check.log’ for details.
CEMiTool.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CEMiTool ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * 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 ** 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 * DONE (CEMiTool)
CEMiTool.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 13 | SKIP 0 | PASS 105 ] [ FAIL 0 | WARN 13 | SKIP 0 | PASS 105 ] > > proc.time() user system elapsed 36.011 1.324 37.054
CEMiTool.Rcheck/CEMiTool-Ex.timings
name | user | system | elapsed | |
CEMiTool-class | 0.016 | 0.003 | 0.019 | |
adj_data | 0.338 | 0.019 | 0.359 | |
cem | 0.773 | 0.007 | 0.782 | |
cemitool | 11.715 | 0.253 | 12.121 | |
expr0 | 0.001 | 0.001 | 0.002 | |
expr_data | 0.119 | 0.007 | 0.127 | |
filter_expr | 0.180 | 0.013 | 0.193 | |
find_modules | 2.329 | 0.037 | 2.408 | |
fit_data | 2.998 | 0.049 | 3.185 | |
generate_report | 0 | 0 | 0 | |
get_adj | 0.114 | 0.005 | 0.120 | |
get_beta_data | 1.023 | 0.018 | 1.047 | |
get_cemitool_r2_beta | 2.261 | 0.034 | 2.300 | |
get_connectivity | 2.260 | 0.038 | 2.303 | |
get_hubs | 0.020 | 0.004 | 0.023 | |
get_merged_mods | 1.224 | 0.025 | 1.251 | |
get_mods | 1.056 | 0.028 | 1.099 | |
get_phi | 2.265 | 0.048 | 2.423 | |
gsea_data | 5.598 | 0.040 | 5.665 | |
interactions_data | 0.289 | 0.023 | 0.314 | |
mod_colors | 0.041 | 0.007 | 0.049 | |
mod_gene_num | 0.087 | 0.006 | 0.093 | |
mod_gsea | 2.476 | 0.018 | 2.503 | |
mod_names | 0.021 | 0.005 | 0.026 | |
mod_ora | 2.405 | 0.118 | 2.532 | |
mod_summary | 0.144 | 0.008 | 0.141 | |
module_genes | 0.057 | 0.011 | 0.038 | |
new_cem | 0.032 | 0.006 | 0.020 | |
nmodules | 0.082 | 0.011 | 0.048 | |
ora_data | 2.486 | 0.117 | 2.547 | |
plot_beta_r2 | 0.157 | 0.006 | 0.164 | |
plot_gsea | 2.647 | 0.028 | 2.693 | |
plot_hist | 0.387 | 0.015 | 0.407 | |
plot_interactions | 10.462 | 0.200 | 10.764 | |
plot_mean_k | 0.165 | 0.007 | 0.180 | |
plot_mean_var | 0.370 | 0.021 | 0.410 | |
plot_ora | 3.219 | 0.146 | 3.397 | |
plot_profile | 1.586 | 0.032 | 1.632 | |
plot_qq | 0.532 | 0.032 | 0.568 | |
plot_sample_tree | 0.817 | 0.016 | 0.837 | |
read_gmt | 0.586 | 0.011 | 0.601 | |
sample_annot | 0.003 | 0.004 | 0.008 | |
sample_annotation | 0.020 | 0.006 | 0.028 | |
save_plots | 0.035 | 0.004 | 0.040 | |
select_genes | 0.197 | 0.013 | 0.209 | |
show_plot | 0.151 | 0.008 | 0.158 | |
write_files | 0.749 | 0.078 | 0.538 | |