Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 852/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggkegg 1.4.0  (landing page)
Noriaki Sato
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/ggkegg
git_branch: RELEASE_3_20
git_last_commit: 17630e2
git_last_commit_date: 2024-10-29 11:23:07 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for ggkegg on teran2

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.

raw results


Summary

Package: ggkegg
Version: 1.4.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ggkegg.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ggkegg_1.4.0.tar.gz
StartedAt: 2024-11-20 03:44:11 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 03:46:23 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 131.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ggkegg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ggkegg.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ggkegg_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ggkegg.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 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         4.805  0.269  12.032
rawMap            1.404  0.038   6.663
pathway_abundance 0.600  0.006   7.213
* 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
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ggkegg.Rcheck/00check.log’
for details.


Installation output

ggkegg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ggkegg
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 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 
  2.702   0.215   6.239 

Example timings

ggkegg.Rcheck/ggkegg-Ex.timings

nameusersystemelapsed
append_cp 4.805 0.26912.032
append_label_position0.0390.0010.079
assign_deseq20.0060.0000.014
carrow000
combine_with_bnlearn0.0590.0020.120
convert_id0.2090.0070.408
create_test_module0.0180.0000.035
create_test_network0.0030.0000.007
create_test_pathway0.0580.0000.114
edge_matrix0.0170.0000.036
edge_numeric0.0060.0000.010
edge_numeric_sum0.0160.0000.032
geom_kegg0.0320.0000.071
geom_node_rect0.0110.0000.023
geom_node_rect_kegg0.0130.0000.024
geom_node_rect_multi0.1520.0000.305
geom_node_shadowtext0.0120.0000.022
ggkegg0.1900.0111.283
ggplot_add.geom_kegg0.0180.0120.031
ggplot_add.geom_node_rect_kegg0.0110.0030.023
ggplot_add.geom_node_rect_multi0.0490.0170.131
ggplot_add.overlay_raw_map0.3050.0920.522
ggplot_add.stamp0.0120.0000.012
highlight_entities1.0260.0321.047
highlight_module0.0130.0000.013
highlight_set_edges0.0050.0000.005
highlight_set_nodes0.0070.0000.006
module0.0710.0011.555
module_abundance0.0220.0000.022
module_completeness0.0030.0000.003
module_text0.0040.0000.005
multi_pathway_native0.2020.0010.984
network0.0430.0020.730
network_graph0.0080.0000.020
node_matrix0.0080.0000.012
node_numeric0.0050.0000.013
obtain_sequential_module_definition0.0120.0010.024
output_overlay_image000
overlay_raw_map0.3330.0780.402
pathway0.1190.0240.147
pathway_abundance0.6000.0067.213
pathway_info0.0450.0021.074
plot_kegg_network0.0450.0000.062
plot_module_blocks0.0390.0010.040
plot_module_text0.0450.0000.045
process_line0.0090.0000.009
process_reaction0.0060.0000.006
rawMap1.4040.0386.663
rawValue0.0150.0000.016
return_line_compounds0.0090.0010.010
stamp0.010.000.01