Noriaki Sato
| Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ggkegg |
| git_branch: RELEASE_3_22 |
| git_last_commit: c13dd11 |
| git_last_commit_date: 2025-10-29 11:24:48 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-01 12:03 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 875/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ggkegg 1.8.0 (landing page) Noriaki Sato
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: ggkegg |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ggkegg.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ggkegg_1.8.0.tar.gz |
| StartedAt: 2025-11-01 00:13:01 -0400 (Sat, 01 Nov 2025) |
| EndedAt: 2025-11-01 00:15:39 -0400 (Sat, 01 Nov 2025) |
| EllapsedTime: 158.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ggkegg.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ggkegg.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ggkegg_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ggkegg.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ggkegg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggkegg’ version ‘1.8.0’
* 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 ‘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 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
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘x’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘y’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘xend’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘yend’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘group’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘label’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘angle2’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘angle’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘x1’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘y1’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘x2’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘y2’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘mx’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘my’
ggplot_add.add_readable_edge_label: no visible binding for global
variable ‘ma’
Undefined global functions or variables:
angle angle2 group label ma mx my x x1 x2 xend y y1 y2 yend
* 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 5.895 0.643 14.293
pathway_abundance 1.198 0.084 16.745
rawMap 1.187 0.088 8.552
module 0.995 0.136 5.098
* 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-3.22-bioc/meat/ggkegg.Rcheck/00check.log’
for details.
ggkegg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ggkegg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ggkegg’ ... ** this is package ‘ggkegg’ version ‘1.8.0’ ** 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)
ggkegg.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.
> # 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 276 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
4.913 0.326 11.517
ggkegg.Rcheck/ggkegg-Ex.timings
| name | user | system | elapsed | |
| add_readable_edge_label | 0.188 | 0.012 | 0.200 | |
| append_cp | 5.895 | 0.643 | 14.293 | |
| append_label_position | 0.043 | 0.001 | 0.044 | |
| assign_deseq2 | 0.008 | 0.013 | 0.020 | |
| carrow | 0.001 | 0.001 | 0.001 | |
| combine_with_bnlearn | 0.079 | 0.010 | 0.089 | |
| convert_id | 0.236 | 0.030 | 0.256 | |
| create_test_module | 0.002 | 0.002 | 0.003 | |
| create_test_network | 0.002 | 0.000 | 0.002 | |
| create_test_pathway | 0.072 | 0.013 | 0.085 | |
| edge_matrix | 0.043 | 0.011 | 0.054 | |
| edge_numeric | 0.007 | 0.000 | 0.007 | |
| edge_numeric_sum | 0.019 | 0.000 | 0.019 | |
| geom_kegg | 0.054 | 0.001 | 0.055 | |
| geom_node_rect | 0.019 | 0.000 | 0.019 | |
| geom_node_rect_kegg | 0.021 | 0.000 | 0.021 | |
| geom_node_rect_multi | 0.064 | 0.011 | 0.075 | |
| geom_node_shadowtext | 0.02 | 0.00 | 0.02 | |
| ggkegg | 0.301 | 0.021 | 1.797 | |
| ggplot_add.add_readable_edge_label | 0.106 | 0.017 | 0.122 | |
| ggplot_add.geom_kegg | 0.056 | 0.009 | 0.065 | |
| ggplot_add.geom_node_rect_kegg | 0.023 | 0.003 | 0.025 | |
| ggplot_add.geom_node_rect_multi | 0.066 | 0.008 | 0.073 | |
| ggplot_add.overlay_raw_map | 0.455 | 0.070 | 0.491 | |
| ggplot_add.stamp | 0.020 | 0.002 | 0.022 | |
| highlight_entities | 0.711 | 0.055 | 0.729 | |
| highlight_module | 0.017 | 0.003 | 0.020 | |
| highlight_set_edges | 0.007 | 0.000 | 0.008 | |
| highlight_set_nodes | 0.057 | 0.012 | 0.069 | |
| module | 0.995 | 0.136 | 5.098 | |
| module_abundance | 0.295 | 0.026 | 0.321 | |
| module_completeness | 0.004 | 0.000 | 0.004 | |
| module_text | 0.006 | 0.000 | 0.005 | |
| multi_pathway_native | 0.314 | 0.022 | 1.427 | |
| network | 0.060 | 0.006 | 0.909 | |
| network_graph | 0.025 | 0.001 | 0.026 | |
| node_matrix | 0.02 | 0.00 | 0.02 | |
| node_numeric | 0.009 | 0.001 | 0.010 | |
| obtain_sequential_module_definition | 0.018 | 0.000 | 0.018 | |
| output_overlay_image | 0 | 0 | 0 | |
| overlay_raw_map | 0.466 | 0.027 | 0.456 | |
| pathway | 0.139 | 0.008 | 0.147 | |
| pathway_abundance | 1.198 | 0.084 | 16.745 | |
| pathway_info | 0.070 | 0.004 | 1.698 | |
| plot_kegg_network | 0.113 | 0.002 | 0.115 | |
| plot_module_blocks | 0.081 | 0.006 | 0.088 | |
| plot_module_text | 0.120 | 0.014 | 0.134 | |
| process_line | 0.012 | 0.001 | 0.013 | |
| process_reaction | 0.008 | 0.000 | 0.008 | |
| rawMap | 1.187 | 0.088 | 8.552 | |
| rawValue | 0.041 | 0.000 | 0.041 | |
| return_line_compounds | 0.012 | 0.001 | 0.013 | |
| stamp | 0.019 | 0.000 | 0.019 | |