Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:06:06 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for EGAD on lconway


To the developers/maintainers of the EGAD package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 598/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EGAD 1.26.0  (landing page)
Sara Ballouz
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/EGAD
git_branch: RELEASE_3_16
git_last_commit: f4695cc
git_last_commit_date: 2022-11-01 11:13:42 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: EGAD
Version: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2023-04-10 20:02:18 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:03:30 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 72.6 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/EGAD.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EGAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EGAD’ version ‘1.26.0’
* 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 PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-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/4.2/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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 ═══════════════════════════════════════════════════════════════
• empty test (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  1.972   0.186   2.156 

Example timings

EGAD.Rcheck/EGAD-Ex.timings

nameusersystemelapsed
assortativity0.0010.0010.001
auc_multifunc0.0000.0010.001
auprc0.0030.0010.004
auroc_analytic0.0000.0000.001
build_binary_network0.0000.0000.001
build_coexp_expressionSet0.0040.0000.003
build_coexp_network0.0060.0000.006
build_semantic_similarity_network0.0010.0000.001
build_weighted_network0.0000.0000.001
calculate_multifunc0.0010.0010.002
conv_smoother0.0110.0010.011
extend_network0.0030.0010.004
filter_network0.0020.0010.002
filter_network_cols0.0020.0010.002
filter_network_rows0.0010.0000.001
filter_orthologs0.0010.0010.001
fmeasure0.0000.0000.001
get_auc0.0000.0010.001
get_counts0.0010.0000.002
get_density0.0010.0010.001
get_prc0.0000.0000.001
get_roc0.0010.0010.001
make_annotations0.0010.0000.000
make_gene_network0.0010.0010.001
make_genelist0.0010.0000.001
neighbor_voting0.0240.0020.025
node_degree0.0010.0000.001
plot_densities0.0150.0010.016
plot_density_compare0.0060.0020.008
plot_distribution0.0050.0010.005
plot_network_heatmap0.0220.0040.026
plot_prc0.0110.0020.014
plot_roc0.0010.0010.002
plot_roc_overlay0.0630.0100.075
predictions0.0050.0010.006
repmat000
run_GBA0.0130.0020.015