Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 | |||||||||
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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CEMiTool_1.30.0.tar.gz |
StartedAt: 2024-12-19 21:15:03 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 21:23:12 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 489.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CEMiTool.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CEMiTool_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CEMiTool.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 8.369 0.257 8.627 plot_interactions 8.347 0.137 8.485 * 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 re-building of vignette outputs ... OK * 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/bbs-3.20-bioc/R/bin/R CMD INSTALL CEMiTool ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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 24.031 0.754 24.735
CEMiTool.Rcheck/CEMiTool-Ex.timings
name | user | system | elapsed | |
CEMiTool-class | 0.011 | 0.000 | 0.012 | |
adj_data | 0.250 | 0.005 | 0.254 | |
cem | 0.488 | 0.001 | 0.489 | |
cemitool | 8.369 | 0.257 | 8.627 | |
expr0 | 0.000 | 0.000 | 0.001 | |
expr_data | 0.091 | 0.001 | 0.092 | |
filter_expr | 0.139 | 0.000 | 0.139 | |
find_modules | 1.593 | 0.002 | 1.596 | |
fit_data | 1.574 | 0.000 | 1.574 | |
generate_report | 0 | 0 | 0 | |
get_adj | 0.084 | 0.001 | 0.086 | |
get_beta_data | 0.690 | 0.002 | 0.692 | |
get_cemitool_r2_beta | 1.573 | 0.001 | 1.574 | |
get_connectivity | 1.564 | 0.000 | 1.564 | |
get_hubs | 0.012 | 0.001 | 0.013 | |
get_merged_mods | 0.838 | 0.000 | 0.839 | |
get_mods | 0.701 | 0.001 | 0.702 | |
get_phi | 1.540 | 0.002 | 1.543 | |
gsea_data | 3.527 | 0.003 | 3.532 | |
interactions_data | 0.195 | 0.012 | 0.207 | |
mod_colors | 0.026 | 0.002 | 0.027 | |
mod_gene_num | 0.057 | 0.002 | 0.058 | |
mod_gsea | 1.540 | 0.001 | 1.542 | |
mod_names | 0.012 | 0.000 | 0.013 | |
mod_ora | 1.843 | 0.021 | 1.866 | |
mod_summary | 0.119 | 0.002 | 0.113 | |
module_genes | 0.015 | 0.001 | 0.018 | |
new_cem | 0.010 | 0.001 | 0.011 | |
nmodules | 0.024 | 0.003 | 0.026 | |
ora_data | 1.868 | 0.002 | 1.869 | |
plot_beta_r2 | 0.14 | 0.00 | 0.14 | |
plot_gsea | 1.620 | 0.002 | 1.624 | |
plot_hist | 0.288 | 0.003 | 0.289 | |
plot_interactions | 8.347 | 0.137 | 8.485 | |
plot_mean_k | 0.145 | 0.007 | 0.152 | |
plot_mean_var | 0.311 | 0.018 | 0.330 | |
plot_ora | 2.686 | 0.079 | 2.765 | |
plot_profile | 1.335 | 0.006 | 1.341 | |
plot_qq | 0.363 | 0.004 | 0.367 | |
plot_sample_tree | 0.555 | 0.008 | 0.563 | |
read_gmt | 0.444 | 0.005 | 0.449 | |
sample_annot | 0.002 | 0.000 | 0.001 | |
sample_annotation | 0.011 | 0.001 | 0.012 | |
save_plots | 0.022 | 0.002 | 0.024 | |
select_genes | 0.146 | 0.001 | 0.147 | |
show_plot | 0.116 | 0.001 | 0.118 | |
write_files | 0.363 | 0.003 | 0.350 | |