Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-04 11:39:09 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 630/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EGAD 1.31.0  (landing page)
Sara Ballouz
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/EGAD
git_branch: devel
git_last_commit: 081302d
git_last_commit_date: 2023-10-24 10:50:17 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for EGAD on merida1


To the developers/maintainers of the EGAD package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EGAD.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: EGAD
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EGAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EGAD_1.31.0.tar.gz
StartedAt: 2024-03-02 03:30:47 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 03:33:24 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 156.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: EGAD.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EGAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EGAD_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/EGAD.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 ‘EGAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EGAD’ version ‘1.31.0’
* 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 ‘EGAD’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 39.1Mb
  sub-directories of 1Mb or more:
    data  38.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘EGAD.Rmd’ ‘EGAD.bib’ ‘figures/figure_GO_comb.png’
  ‘figures/figure_aurocs_comparisons.png’
  ‘figures/figure_benchmark.png’ ‘figures/figure_degree_corr.png’
  ‘figures/figure_indirect.png’ ‘figures/figure_mf.png’
  ‘figures/figure_mf_yeast_human.png’
  ‘figures/figure_nd_yeast_human.png’ ‘figures/figure_nv.png’
  ‘figures/figure_nv_yeast_human.png’ ‘figures/figure_overlay.png’
  ‘figures/figure_pheno_comb.png’
  ‘figures/figure_pheno_degree_corr.png’ ‘figures/figure_pheno_mf.png’
  ‘figures/figure_pheno_nv.png’ ‘figures/figure_smoother.png’
  ‘figures/gba_schematic_resized.png’ ‘figures/labels_resized.png’
  ‘figures/mf_schematic.png’ ‘figures/network_resized.png’
  ‘figures/overview_resized.png’
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/EGAD.Rcheck/00check.log’
for details.



Installation output

EGAD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EGAD
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘EGAD’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (EGAD)

Tests output

EGAD.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(EGAD)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("EGAD")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test.mf.r:3:1', 'test.nv.r:3:1'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  4.626   0.402   6.069 

Example timings

EGAD.Rcheck/EGAD-Ex.timings

nameusersystemelapsed
assortativity0.0020.0010.006
auc_multifunc0.0000.0010.002
auprc0.0070.0010.011
auroc_analytic0.0000.0010.001
build_binary_network0.0010.0010.002
build_coexp_expressionSet0.0050.0010.007
build_coexp_network0.0110.0020.016
build_semantic_similarity_network0.0010.0010.003
build_weighted_network0.0010.0000.001
calculate_multifunc0.0030.0000.003
conv_smoother0.0190.0020.025
extend_network0.0210.0020.027
filter_network0.0010.0010.003
filter_network_cols0.0030.0010.004
filter_network_rows0.0030.0010.005
filter_orthologs0.0010.0010.002
fmeasure0.0000.0000.001
get_auc0.0020.0010.005
get_counts0.0040.0010.005
get_density0.0020.0010.003
get_prc0.0000.0010.001
get_roc0.0010.0000.002
make_annotations0.0010.0010.003
make_gene_network0.0020.0010.002
make_genelist0.0010.0000.001
neighbor_voting0.0600.0090.081
node_degree0.0010.0000.001
plot_densities0.0430.0080.069
plot_density_compare0.0100.0030.018
plot_distribution0.0080.0030.014
plot_network_heatmap0.0480.0100.071
plot_prc0.0180.0040.024
plot_roc0.0020.0020.004
plot_roc_overlay0.1700.0340.246
predictions0.0150.0030.022
repmat0.0000.0000.003
run_GBA0.0290.0060.040