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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 852/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggkegg 1.4.0  (landing page)
Noriaki Sato
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 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)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ggkegg on palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggkegg.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ggkegg_1.4.0.tar.gz
StartedAt: 2024-12-20 02:01:57 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:04:20 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 143.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ggkegg.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggkegg.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ggkegg_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ggkegg.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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         6.87   0.88   12.74
rawMap            1.12   0.11    6.18
pathway_abundance 0.23   0.03    7.42
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/ggkegg.Rcheck/00check.log'
for details.


Installation output

ggkegg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ggkegg
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   4.60    1.20    7.59 

Example timings

ggkegg.Rcheck/ggkegg-Ex.timings

nameusersystemelapsed
append_cp 6.87 0.8812.74
append_label_position0.070.000.08
assign_deseq20.010.000.01
carrow000
combine_with_bnlearn0.130.000.13
convert_id0.250.050.36
create_test_module0.020.000.01
create_test_network0.010.000.02
create_test_pathway0.090.000.09
edge_matrix0.040.000.03
edge_numeric0.010.000.02
edge_numeric_sum0.030.000.03
geom_kegg0.050.020.07
geom_node_rect0.030.000.03
geom_node_rect_kegg0.140.000.14
geom_node_rect_multi0.060.030.09
geom_node_shadowtext0.040.000.03
ggkegg0.320.001.44
ggplot_add.geom_kegg0.030.020.05
ggplot_add.geom_node_rect_kegg0.040.000.03
ggplot_add.geom_node_rect_multi0.120.000.12
ggplot_add.overlay_raw_map0.560.060.72
ggplot_add.stamp0.030.000.03
highlight_entities1.500.031.54
highlight_module0.020.000.01
highlight_set_edges0.020.000.02
highlight_set_nodes0.010.000.01
module0.030.000.94
module_abundance0.030.000.03
module_completeness000
module_text0.020.000.01
multi_pathway_native0.260.021.16
network0.000.010.91
network_graph0.020.000.01
node_matrix0.020.000.01
node_numeric0.010.000.02
obtain_sequential_module_definition0.030.000.04
output_overlay_image000
overlay_raw_map0.410.060.47
pathway0.160.000.16
pathway_abundance0.230.037.42
pathway_info0.030.001.14
plot_kegg_network0.10.00.1
plot_module_blocks0.090.000.09
plot_module_text0.090.000.09
process_line0.020.000.02
process_reaction0.020.000.01
rawMap1.120.116.18
rawValue0.020.020.03
return_line_compounds0.010.000.01
stamp0.030.000.03