Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
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 310/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CEMiTool 1.28.0 (landing page) Helder Nakaya
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | 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: 1.28.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CEMiTool_1.28.0.tar.gz |
StartedAt: 2024-06-12 21:28:16 -0400 (Wed, 12 Jun 2024) |
EndedAt: 2024-06-12 21:33:22 -0400 (Wed, 12 Jun 2024) |
EllapsedTime: 305.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CEMiTool.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CEMiTool_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CEMiTool.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘CEMiTool/DESCRIPTION’ ... OK * this is package ‘CEMiTool’ version ‘1.28.0’ * 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 5.2Mb sub-directories of 1Mb or more: data 3.1Mb extdata 1.6Mb * 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 8.683 0.371 9.055 plot_interactions 8.648 0.120 8.768 * 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-3.19-bioc/meat/CEMiTool.Rcheck/00check.log’ for details.
CEMiTool.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CEMiTool ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup" 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 28.194 1.296 29.442
CEMiTool.Rcheck/CEMiTool-Ex.timings
name | user | system | elapsed | |
CEMiTool-class | 0.012 | 0.004 | 0.017 | |
adj_data | 0.825 | 0.079 | 0.904 | |
cem | 0.020 | 0.001 | 0.021 | |
cemitool | 8.683 | 0.371 | 9.055 | |
expr0 | 0.001 | 0.000 | 0.001 | |
expr_data | 0.108 | 0.000 | 0.107 | |
filter_expr | 0.691 | 0.005 | 0.696 | |
find_modules | 1.666 | 0.029 | 1.697 | |
fit_data | 1.668 | 0.041 | 1.708 | |
generate_report | 0 | 0 | 0 | |
get_adj | 0.106 | 0.000 | 0.105 | |
get_beta_data | 0.687 | 0.040 | 0.726 | |
get_cemitool_r2_beta | 1.580 | 0.019 | 1.599 | |
get_connectivity | 1.586 | 0.003 | 1.588 | |
get_hubs | 0.017 | 0.001 | 0.017 | |
get_merged_mods | 0.857 | 0.048 | 0.905 | |
get_mods | 0.751 | 0.000 | 0.751 | |
get_phi | 1.624 | 0.052 | 1.676 | |
gsea_data | 3.788 | 0.016 | 3.805 | |
interactions_data | 0.227 | 0.011 | 0.240 | |
mod_colors | 0.018 | 0.001 | 0.019 | |
mod_gene_num | 0.069 | 0.004 | 0.073 | |
mod_gsea | 1.649 | 0.011 | 1.660 | |
mod_names | 0.039 | 0.004 | 0.043 | |
mod_ora | 2.131 | 0.029 | 2.161 | |
mod_summary | 0.143 | 0.004 | 0.137 | |
module_genes | 0.022 | 0.004 | 0.026 | |
new_cem | 0.031 | 0.004 | 0.035 | |
nmodules | 0.016 | 0.000 | 0.016 | |
ora_data | 2.474 | 0.108 | 2.582 | |
plot_beta_r2 | 0.144 | 0.000 | 0.145 | |
plot_gsea | 1.716 | 0.028 | 1.744 | |
plot_hist | 0.262 | 0.004 | 0.266 | |
plot_interactions | 8.648 | 0.120 | 8.768 | |
plot_mean_k | 0.148 | 0.004 | 0.152 | |
plot_mean_var | 0.341 | 0.036 | 0.378 | |
plot_ora | 2.847 | 0.031 | 2.881 | |
plot_profile | 1.396 | 0.001 | 1.395 | |
plot_qq | 0.392 | 0.000 | 0.392 | |
plot_sample_tree | 0.568 | 0.004 | 0.573 | |
read_gmt | 0.434 | 0.000 | 0.433 | |
sample_annot | 0.002 | 0.000 | 0.002 | |
sample_annotation | 0.011 | 0.003 | 0.014 | |
save_plots | 0.629 | 0.055 | 0.685 | |
select_genes | 0.128 | 0.001 | 0.128 | |
show_plot | 0.122 | 0.003 | 0.126 | |
write_files | 0.362 | 0.000 | 0.340 | |