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This page was generated on 2025-09-29 12:04 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4833
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4621
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4566
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 866/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggkegg 1.7.1  (landing page)
Noriaki Sato
Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025)
git_url: https://git.bioconductor.org/packages/ggkegg
git_branch: devel
git_last_commit: df43afa
git_last_commit_date: 2025-09-15 21:11:43 -0400 (Mon, 15 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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 ggkegg on lconway

To the developers/maintainers of the ggkegg package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggkegg.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.

raw results


Summary

Package: ggkegg
Version: 1.7.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggkegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggkegg_1.7.1.tar.gz
StartedAt: 2025-09-28 21:33:48 -0400 (Sun, 28 Sep 2025)
EndedAt: 2025-09-28 21:36:29 -0400 (Sun, 28 Sep 2025)
EllapsedTime: 161.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ggkegg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggkegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggkegg_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ggkegg.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggkegg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggkegg’ version ‘1.7.1’
* 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 ‘ggkegg’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
append_cp         6.328  0.293  17.075
rawMap            1.261  0.067   7.897
pathway_abundance 1.072  0.099  17.493
module            1.096  0.073   5.197
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/ggkegg.Rcheck/00check.log’
for details.


Installation output

ggkegg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ggkegg
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘ggkegg’ ...
** this is package ‘ggkegg’ version ‘1.7.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (ggkegg)

Tests output

ggkegg.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(ggkegg)
Loading required package: ggplot2
Loading required package: ggraph
Loading required package: XML
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: tidygraph

Attaching package: 'tidygraph'

The following object is masked from 'package:igraph':

    groups

The following object is masked from 'package:testthat':

    matches

The following object is masked from 'package:stats':

    filter

> 
> test_check("ggkegg")
trying URL 'https://rest.kegg.jp/get/M00004'
downloaded 273 KB

trying URL 'https://rest.kegg.jp/get/N00002'
downloaded 2119 bytes

trying URL 'https://rest.kegg.jp/get/hsa04110/kgml'
downloaded 51 KB

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 20 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
  5.871   0.471  11.886 

Example timings

ggkegg.Rcheck/ggkegg-Ex.timings

nameusersystemelapsed
append_cp 6.328 0.29317.075
append_label_position0.0660.0020.068
assign_deseq20.0100.0010.010
carrow0.0010.0000.001
combine_with_bnlearn0.0930.0080.104
convert_id0.2690.0320.317
create_test_module0.0030.0000.004
create_test_network0.0020.0010.003
create_test_pathway0.0830.0120.095
edge_matrix0.0620.0040.065
edge_numeric0.0100.0000.011
edge_numeric_sum0.0300.0000.031
geom_kegg0.1040.0010.106
geom_node_rect0.0250.0000.025
geom_node_rect_kegg0.0260.0000.026
geom_node_rect_multi0.0850.0010.087
geom_node_shadowtext0.0250.0010.026
ggkegg0.3080.0291.785
ggplot_add.geom_kegg0.0740.0090.082
ggplot_add.geom_node_rect_kegg0.0280.0030.031
ggplot_add.geom_node_rect_multi0.0740.0080.083
ggplot_add.overlay_raw_map0.5370.0420.589
ggplot_add.stamp0.0250.0010.026
highlight_entities0.9340.0570.996
highlight_module0.0210.0000.021
highlight_set_edges0.0100.0000.011
highlight_set_nodes0.0140.0010.014
module1.0960.0735.197
module_abundance0.4860.0630.555
module_completeness0.0050.0000.004
module_text0.0070.0010.007
multi_pathway_native0.2820.0061.740
network0.0180.0030.848
network_graph0.0130.0010.014
node_matrix0.0130.0010.013
node_numeric0.0100.0010.011
obtain_sequential_module_definition0.0180.0020.020
output_overlay_image0.0010.0000.000
overlay_raw_map0.5320.0310.567
pathway0.1840.0170.202
pathway_abundance 1.072 0.09917.493
pathway_info0.0220.0071.509
plot_kegg_network0.1170.0020.119
plot_module_blocks0.1050.0030.109
plot_module_text0.1410.0020.145
process_line0.0140.0010.014
process_reaction0.0100.0010.011
rawMap1.2610.0677.897
rawValue0.0470.0000.047
return_line_compounds0.0150.0000.015
stamp0.0270.0000.028