Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 852/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggkegg 1.4.0 (landing page) Noriaki Sato
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.4.0 |
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_1.4.0.tar.gz |
StartedAt: 2024-12-20 20:57:34 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 20:59:55 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 140.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ggkegg.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ggkegg.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ggkegg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ggkegg’ version ‘1.4.0’ * 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 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 6.828 0.249 16.050 rawMap 1.088 0.060 9.152 pathway_abundance 0.292 0.027 14.697 * 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-3.20-bioc/meat/ggkegg.Rcheck/00check.log’ for details.
ggkegg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ggkegg ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘ggkegg’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 2246 bytes 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 4.340 0.298 10.762
ggkegg.Rcheck/ggkegg-Ex.timings
name | user | system | elapsed | |
append_cp | 6.828 | 0.249 | 16.050 | |
append_label_position | 0.086 | 0.003 | 0.089 | |
assign_deseq2 | 0.011 | 0.000 | 0.011 | |
carrow | 0.001 | 0.000 | 0.001 | |
combine_with_bnlearn | 0.085 | 0.005 | 0.092 | |
convert_id | 0.312 | 0.033 | 0.314 | |
create_test_module | 0.272 | 0.019 | 0.155 | |
create_test_network | 0.009 | 0.001 | 0.006 | |
create_test_pathway | 0.097 | 0.005 | 0.085 | |
edge_matrix | 0.024 | 0.000 | 0.025 | |
edge_numeric | 0.01 | 0.00 | 0.01 | |
edge_numeric_sum | 0.023 | 0.000 | 0.024 | |
geom_kegg | 0.059 | 0.002 | 0.060 | |
geom_node_rect | 0.016 | 0.001 | 0.016 | |
geom_node_rect_kegg | 0.018 | 0.001 | 0.018 | |
geom_node_rect_multi | 0.088 | 0.007 | 0.094 | |
geom_node_shadowtext | 0.018 | 0.002 | 0.020 | |
ggkegg | 0.937 | 0.017 | 3.051 | |
ggplot_add.geom_kegg | 0.026 | 0.001 | 0.026 | |
ggplot_add.geom_node_rect_kegg | 0.016 | 0.001 | 0.016 | |
ggplot_add.geom_node_rect_multi | 0.058 | 0.001 | 0.060 | |
ggplot_add.overlay_raw_map | 0.456 | 0.034 | 0.495 | |
ggplot_add.stamp | 0.017 | 0.002 | 0.019 | |
highlight_entities | 0.706 | 0.055 | 0.761 | |
highlight_module | 0.023 | 0.000 | 0.024 | |
highlight_set_edges | 0.010 | 0.000 | 0.011 | |
highlight_set_nodes | 0.012 | 0.001 | 0.013 | |
module | 0.047 | 0.004 | 1.978 | |
module_abundance | 0.026 | 0.001 | 0.026 | |
module_completeness | 0.004 | 0.000 | 0.003 | |
module_text | 0.006 | 0.000 | 0.007 | |
multi_pathway_native | 0.227 | 0.006 | 2.112 | |
network | 0.025 | 0.003 | 1.776 | |
network_graph | 0.013 | 0.001 | 0.013 | |
node_matrix | 0.012 | 0.001 | 0.014 | |
node_numeric | 0.008 | 0.000 | 0.008 | |
obtain_sequential_module_definition | 0.015 | 0.002 | 0.017 | |
output_overlay_image | 0 | 0 | 0 | |
overlay_raw_map | 0.530 | 0.039 | 0.570 | |
pathway | 0.062 | 0.002 | 0.066 | |
pathway_abundance | 0.292 | 0.027 | 14.697 | |
pathway_info | 0.027 | 0.007 | 2.127 | |
plot_kegg_network | 0.825 | 0.011 | 0.837 | |
plot_module_blocks | 0.051 | 0.001 | 0.052 | |
plot_module_text | 0.065 | 0.001 | 0.066 | |
process_line | 0.012 | 0.001 | 0.012 | |
process_reaction | 0.008 | 0.001 | 0.009 | |
rawMap | 1.088 | 0.060 | 9.152 | |
rawValue | 0.022 | 0.001 | 0.022 | |
return_line_compounds | 0.015 | 0.001 | 0.016 | |
stamp | 0.015 | 0.000 | 0.015 | |