Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: CEMiTool |
Version: 1.30.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CEMiTool_1.30.0.tar.gz |
StartedAt: 2024-11-20 06:05:14 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 06:10:43 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 328.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CEMiTool.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CEMiTool_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CEMiTool.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 loading without being on the library search path ... 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 14.703 0.259 13.785 plot_interactions 13.078 0.119 13.216 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/CEMiTool.Rcheck/00check.log’ for details.
CEMiTool.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CEMiTool ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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 33.846 0.835 34.179
CEMiTool.Rcheck/CEMiTool-Ex.timings
name | user | system | elapsed | |
CEMiTool-class | 0.016 | 0.004 | 0.020 | |
adj_data | 1.086 | 0.004 | 1.007 | |
cem | 0.026 | 0.000 | 0.026 | |
cemitool | 14.703 | 0.259 | 13.785 | |
expr0 | 0.000 | 0.000 | 0.001 | |
expr_data | 0.182 | 0.000 | 0.182 | |
filter_expr | 0.245 | 0.004 | 0.250 | |
find_modules | 2.695 | 0.016 | 2.380 | |
fit_data | 2.753 | 0.004 | 2.361 | |
generate_report | 0.001 | 0.000 | 0.000 | |
get_adj | 0.247 | 0.000 | 0.181 | |
get_beta_data | 1.163 | 0.044 | 1.043 | |
get_cemitool_r2_beta | 2.649 | 0.004 | 2.332 | |
get_connectivity | 2.756 | 0.040 | 2.405 | |
get_hubs | 0.045 | 0.004 | 0.025 | |
get_merged_mods | 1.541 | 0.000 | 1.254 | |
get_mods | 1.274 | 0.008 | 1.037 | |
get_phi | 2.696 | 0.000 | 2.371 | |
gsea_data | 4.513 | 0.024 | 4.476 | |
interactions_data | 0.296 | 0.024 | 0.321 | |
mod_colors | 0.024 | 0.000 | 0.024 | |
mod_gene_num | 0.086 | 0.004 | 0.089 | |
mod_gsea | 1.735 | 0.008 | 1.745 | |
mod_names | 0.046 | 0.000 | 0.046 | |
mod_ora | 2.908 | 0.028 | 2.947 | |
mod_summary | 0.212 | 0.000 | 0.209 | |
module_genes | 0.063 | 0.004 | 0.067 | |
new_cem | 0.019 | 0.000 | 0.020 | |
nmodules | 0.023 | 0.000 | 0.024 | |
ora_data | 3.605 | 0.044 | 3.655 | |
plot_beta_r2 | 0.199 | 0.004 | 0.202 | |
plot_gsea | 1.875 | 0.020 | 1.898 | |
plot_hist | 0.437 | 0.032 | 0.469 | |
plot_interactions | 13.078 | 0.119 | 13.216 | |
plot_mean_k | 0.234 | 0.004 | 0.238 | |
plot_mean_var | 0.548 | 0.012 | 0.566 | |
plot_ora | 4.155 | 0.048 | 4.215 | |
plot_profile | 2.212 | 0.016 | 2.233 | |
plot_qq | 0.522 | 0.008 | 0.531 | |
plot_sample_tree | 0.779 | 0.008 | 0.789 | |
read_gmt | 0.754 | 0.008 | 0.764 | |
sample_annot | 0.002 | 0.000 | 0.003 | |
sample_annotation | 0.021 | 0.000 | 0.021 | |
save_plots | 0.041 | 0.000 | 0.040 | |
select_genes | 0.272 | 0.000 | 0.272 | |
show_plot | 0.233 | 0.000 | 0.234 | |
write_files | 0.619 | 0.004 | 0.592 | |