Multiple platform build/check report for BioC 3.19 - CHECK results for ggkegg on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4751
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4485
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4515
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*

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### Running command:
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###   /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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ggkegg.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggkegg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggkegg’ version ‘1.2.0’
* 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         3.190  0.178  11.352
pathway_abundance 0.354  0.028   7.144
* 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-3.19-bioc/meat/ggkegg.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ggkegg
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)

Tests output


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 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 7 | SKIP 0 | PASS 20 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
  8.832   0.635  12.948

Example timings

name	user	system	elapsed
append_cp	3.190	0.178	11.352
append_label_position	0.651	0.008	0.663
assign_deseq2	0.010	0.001	0.010
carrow	0.001	0.001	0.001
combine_with_bnlearn	0.102	0.008	0.111
convert_id	0.228	0.027	0.269
create_test_module	0.028	0.002	0.031
create_test_network	0.005	0.001	0.006
create_test_pathway	0.105	0.012	0.117
edge_matrix	0.037	0.004	0.040
edge_numeric	0.013	0.002	0.015
edge_numeric_sum	0.040	0.003	0.043
geom_kegg	0.077	0.008	0.086
geom_node_rect	0.029	0.003	0.031
geom_node_rect_kegg	0.025	0.002	0.028
geom_node_shadowtext	0.023	0.003	0.025
ggkegg	0.325	0.023	2.297
ggplot_add.geom_kegg	0.027	0.000	0.027
ggplot_add.geom_node_rect_kegg	0.015	0.000	0.015
ggplot_add.overlay_raw_map	0.510	0.042	0.562
ggplot_add.stamp	0.021	0.000	0.023
highlight_entities	0.720	0.055	0.783
highlight_module	0.022	0.001	0.023
highlight_set_edges	0.010	0.001	0.010
highlight_set_nodes	0.014	0.001	0.014
module	0.203	0.015	0.939
module_abundance	0.042	0.001	0.042
module_completeness	0.005	0.000	0.005
module_text	0.008	0.001	0.009
multi_pathway_native	0.307	0.008	1.239
network	0.020	0.004	0.880
network_graph	0.015	0.001	0.016
node_matrix	0.016	0.000	0.018
node_numeric	0.012	0.001	0.013
obtain_sequential_module_definition	0.025	0.003	0.028
output_overlay_image	0.001	0.000	0.001
overlay_raw_map	0.640	0.047	0.694
pathway	0.821	0.017	0.845
pathway_abundance	0.354	0.028	7.144
pathway_info	0.024	0.006	1.355
plot_kegg_network	0.067	0.001	0.070
plot_module_blocks	0.061	0.003	0.064
plot_module_text	0.081	0.007	0.088
process_line	0.015	0.002	0.018
process_reaction	0.011	0.001	0.013
rawMap	1.019	0.099	1.131
rawValue	0.028	0.001	0.031
return_line_compounds	0.019	0.000	0.019
stamp	0.020	0.001	0.021

CHECK results for ggkegg on lconway

Summary

Command output

Installation output

Tests output

Example timings