Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-09-26 12:04 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
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: 2025-09-25 13:45 -0400 (Thu, 25 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: 2025-09-25 21:28:29 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 21:31:09 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 159.7 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         6.439  0.298  16.182
rawMap            1.241  0.065   7.714
pathway_abundance 1.046  0.116  16.821
* 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 
  5.746   0.443  11.855 

Example timings

ggkegg.Rcheck/ggkegg-Ex.timings

nameusersystemelapsed
append_cp 6.439 0.29816.182
append_label_position0.0610.0020.062
assign_deseq20.0080.0000.009
carrow0.0010.0000.001
combine_with_bnlearn0.0880.0060.095
convert_id0.2460.0330.299
create_test_module0.0030.0010.003
create_test_network0.0010.0010.003
create_test_pathway0.0880.0120.099
edge_matrix0.0540.0030.057
edge_numeric0.0110.0000.011
edge_numeric_sum0.0210.0000.023
geom_kegg0.0910.0000.092
geom_node_rect0.0220.0000.023
geom_node_rect_kegg0.0260.0000.027
geom_node_rect_multi0.0880.0010.089
geom_node_shadowtext0.0230.0010.024
ggkegg0.2840.0262.020
ggplot_add.geom_kegg0.0690.0080.077
ggplot_add.geom_node_rect_kegg0.0230.0030.025
ggplot_add.geom_node_rect_multi0.0720.0090.082
ggplot_add.overlay_raw_map0.4830.0400.528
ggplot_add.stamp0.0260.0010.026
highlight_entities0.8620.0550.948
highlight_module0.0160.0000.016
highlight_set_edges0.0080.0000.009
highlight_set_nodes0.0130.0010.014
module1.1230.0714.255
module_abundance0.5510.0660.627
module_completeness0.0060.0000.006
module_text0.0070.0000.008
multi_pathway_native0.2890.0071.223
network0.0210.0030.763
network_graph0.0140.0010.016
node_matrix0.0130.0010.015
node_numeric0.0090.0000.010
obtain_sequential_module_definition0.0200.0020.022
output_overlay_image0.0010.0000.000
overlay_raw_map0.5790.0360.622
pathway0.2190.0200.241
pathway_abundance 1.046 0.11616.821
pathway_info0.0250.0061.205
plot_kegg_network0.1250.0030.130
plot_module_blocks0.1020.0030.106
plot_module_text0.1420.0020.145
process_line0.0120.0010.013
process_reaction0.0110.0010.012
rawMap1.2410.0657.714
rawValue0.0510.0000.052
return_line_compounds0.0180.0010.018
stamp0.0240.0000.024