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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 846/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggkegg 1.5.0  (landing page)
Noriaki Sato
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/ggkegg
git_branch: devel
git_last_commit: 5ce3db0
git_last_commit_date: 2024-10-29 11:23:07 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for ggkegg on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ggkegg
Version: 1.5.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ggkegg.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ggkegg_1.5.0.tar.gz
StartedAt: 2024-12-23 08:11:00 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 08:16:13 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 313.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ggkegg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ggkegg.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ggkegg_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ggkegg.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggkegg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggkegg’ version ‘1.5.0’
* 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         7.441  0.236  10.031
rawMap            1.453  0.180   8.486
pathway_abundance 0.499  0.144  75.516
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ggkegg.Rcheck/00check.log’
for details.


Installation output

ggkegg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ggkegg
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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

ggkegg.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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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 
  5.470   0.299   7.895 

Example timings

ggkegg.Rcheck/ggkegg-Ex.timings

nameusersystemelapsed
append_cp 7.441 0.23610.031
append_label_position0.0960.0040.100
assign_deseq20.0100.0000.011
carrow0.0010.0000.001
combine_with_bnlearn0.1030.0040.107
convert_id0.2760.0040.298
create_test_module0.1440.0280.172
create_test_network0.0050.0000.005
create_test_pathway0.1090.0000.109
edge_matrix0.0270.0040.031
edge_numeric0.0120.0000.012
edge_numeric_sum0.0320.0000.032
geom_kegg0.0650.0000.065
geom_node_rect0.0190.0000.019
geom_node_rect_kegg0.0250.0000.025
geom_node_rect_multi0.1090.0040.113
geom_node_shadowtext0.0240.0000.024
ggkegg1.0300.4502.258
ggplot_add.geom_kegg0.0410.0010.041
ggplot_add.geom_node_rect_kegg0.0210.0000.022
ggplot_add.geom_node_rect_multi0.080.000.08
ggplot_add.overlay_raw_map0.7700.0920.764
ggplot_add.stamp0.0320.0000.032
highlight_entities1.0670.1431.095
highlight_module0.0250.0010.025
highlight_set_edges0.0120.0000.012
highlight_set_nodes0.0160.0000.016
module0.0790.0160.426
module_abundance0.0360.0120.048
module_completeness0.0070.0000.007
module_text0.0090.0000.009
multi_pathway_native0.3660.0800.806
network0.0430.0230.378
network_graph0.0170.0080.025
node_matrix0.0110.0110.022
node_numeric0.0160.0000.016
obtain_sequential_module_definition0.0290.0000.029
output_overlay_image000
overlay_raw_map0.8750.0830.845
pathway0.2230.0040.227
pathway_abundance 0.499 0.14475.516
pathway_info0.0400.0030.456
plot_kegg_network0.7950.4231.220
plot_module_blocks0.0830.0080.092
plot_module_text0.0930.0000.093
process_line0.0160.0000.016
process_reaction0.0120.0000.012
rawMap1.4530.1808.486
rawValue0.0310.0080.039
return_line_compounds0.0230.0040.027
stamp0.0280.0000.028