Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-09 12:05 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 859/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggkegg 1.7.0 (landing page) Noriaki Sato
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 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: 1.7.0 |
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_1.7.0.tar.gz |
StartedAt: 2025-08-08 22:51:14 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 22:53:40 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 146.2 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_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ggkegg.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘ggkegg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ggkegg’ version ‘1.7.0’ * 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 ... 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 5.465 0.386 12.475 pathway_abundance 1.270 0.158 16.639 rawMap 1.130 0.289 7.768 * 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: 1 NOTE 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 ‘1.7.0’ ** 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 (2025-06-13) -- "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 270 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 4.404 0.548 10.256
ggkegg.Rcheck/ggkegg-Ex.timings
name | user | system | elapsed | |
append_cp | 5.465 | 0.386 | 12.475 | |
append_label_position | 0.056 | 0.006 | 0.062 | |
assign_deseq2 | 0.008 | 0.001 | 0.009 | |
carrow | 0.000 | 0.001 | 0.001 | |
combine_with_bnlearn | 0.081 | 0.006 | 0.087 | |
convert_id | 0.243 | 0.022 | 0.253 | |
create_test_module | 0.003 | 0.000 | 0.004 | |
create_test_network | 0.002 | 0.000 | 0.002 | |
create_test_pathway | 0.078 | 0.000 | 0.078 | |
edge_matrix | 0.021 | 0.008 | 0.029 | |
edge_numeric | 0.010 | 0.004 | 0.014 | |
edge_numeric_sum | 0.025 | 0.001 | 0.026 | |
geom_kegg | 0.049 | 0.015 | 0.064 | |
geom_node_rect | 0.016 | 0.001 | 0.016 | |
geom_node_rect_kegg | 0.018 | 0.002 | 0.020 | |
geom_node_rect_multi | 0.179 | 0.057 | 0.237 | |
geom_node_shadowtext | 0.016 | 0.000 | 0.016 | |
ggkegg | 0.267 | 0.014 | 1.684 | |
ggplot_add.geom_kegg | 0.030 | 0.001 | 0.031 | |
ggplot_add.geom_node_rect_kegg | 0.014 | 0.003 | 0.017 | |
ggplot_add.geom_node_rect_multi | 0.055 | 0.010 | 0.065 | |
ggplot_add.overlay_raw_map | 0.936 | 0.146 | 1.040 | |
ggplot_add.stamp | 0.015 | 0.000 | 0.015 | |
highlight_entities | 0.594 | 0.068 | 0.625 | |
highlight_module | 0.016 | 0.000 | 0.016 | |
highlight_set_edges | 0.007 | 0.000 | 0.007 | |
highlight_set_nodes | 0.009 | 0.000 | 0.010 | |
module | 0.923 | 0.107 | 4.227 | |
module_abundance | 0.270 | 0.016 | 0.286 | |
module_completeness | 0.004 | 0.000 | 0.004 | |
module_text | 0.006 | 0.000 | 0.005 | |
multi_pathway_native | 0.300 | 0.004 | 1.184 | |
network | 0.055 | 0.002 | 0.759 | |
network_graph | 0.024 | 0.000 | 0.024 | |
node_matrix | 0.023 | 0.000 | 0.022 | |
node_numeric | 0.011 | 0.000 | 0.011 | |
obtain_sequential_module_definition | 0.018 | 0.000 | 0.018 | |
output_overlay_image | 0 | 0 | 0 | |
overlay_raw_map | 0.449 | 0.029 | 0.438 | |
pathway | 0.141 | 0.019 | 0.160 | |
pathway_abundance | 1.270 | 0.158 | 16.639 | |
pathway_info | 0.067 | 0.011 | 1.359 | |
plot_kegg_network | 0.065 | 0.006 | 0.071 | |
plot_module_blocks | 0.057 | 0.006 | 0.063 | |
plot_module_text | 0.068 | 0.006 | 0.075 | |
process_line | 0.011 | 0.001 | 0.012 | |
process_reaction | 0.007 | 0.001 | 0.008 | |
rawMap | 1.130 | 0.289 | 7.768 | |
rawValue | 0.021 | 0.001 | 0.022 | |
return_line_compounds | 0.015 | 0.000 | 0.014 | |
stamp | 0.016 | 0.000 | 0.015 | |