Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-18 12:07 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 318/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.33.2  (landing page)
Helder Nakaya
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/CEMiTool
git_branch: devel
git_last_commit: 797a29e
git_last_commit_date: 2025-10-13 11:02:00 -0400 (Mon, 13 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CEMiTool on taishan

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.

raw results


Summary

Package: CEMiTool
Version: 1.33.2
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_1.33.2.tar.gz
StartedAt: 2025-10-17 07:07:40 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 07:13:18 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 338.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.33.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CEMiTool.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CEMiTool/DESCRIPTION’ ... OK
* this is package ‘CEMiTool’ version ‘1.33.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... INFO
  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’
get_args: no visible global function definition for ‘is’
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 is modules num_genes setNames tail var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "dist", "setNames", "var")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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          13.928  0.315  14.293
plot_interactions 13.861  0.044  13.939
plot_ora           5.328  0.024   5.371
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CEMiTool.Rcheck/00check.log’
for details.


Installation output

CEMiTool.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL CEMiTool
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘CEMiTool’ ...
** this is package ‘CEMiTool’ version ‘1.33.2’
** 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)

Tests output

CEMiTool.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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 
 34.362   1.529  35.975 

Example timings

CEMiTool.Rcheck/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.0140.0040.018
adj_data0.9220.0200.945
cem0.0380.0000.038
cemitool13.928 0.31514.293
expr00.0010.0000.001
expr_data0.1710.0000.172
filter_expr0.2200.0000.221
find_modules2.1300.0362.172
fit_data2.0610.0042.073
generate_report000
get_adj0.1510.0000.152
get_beta_data0.9040.0080.915
get_cemitool_r2_beta2.1100.0002.116
get_connectivity2.1520.0202.178
get_hubs0.0210.0000.020
get_merged_mods1.0970.0001.101
get_mods0.8710.0000.874
get_phi2.0740.0032.085
gsea_data3.9480.0524.012
interactions_data0.2590.0160.279
mod_colors0.020.000.02
mod_gene_num0.0830.0040.087
mod_gsea1.7690.0241.798
mod_names0.0190.0040.023
mod_ora3.4300.0273.476
mod_summary0.1980.0040.202
module_genes0.0250.0000.026
new_cem0.0180.0000.018
nmodules0.0220.0000.023
ora_data3.9870.0004.001
plot_beta_r20.2970.0040.303
plot_gsea2.0540.0002.060
plot_hist0.5560.0000.559
plot_interactions13.861 0.04413.939
plot_mean_k0.3340.0000.335
plot_mean_var0.6920.0160.719
plot_ora5.3280.0245.371
plot_profile2.9460.0202.977
plot_qq0.6750.0000.678
plot_sample_tree0.9470.0040.954
read_gmt1.3480.0881.440
sample_annot0.0020.0000.002
sample_annotation0.0160.0020.019
save_plots0.0500.0060.055
select_genes0.2330.0000.234
show_plot0.3240.0000.325
write_files0.5520.0040.554