Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-06 13:05:55 -0500 (Mon, 06 Dec 2021).

CHECK results for EGAD on machv2

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? here 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 568/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EGAD 1.22.0  (landing page)
Sara Ballouz
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/EGAD
git_branch: RELEASE_3_14
git_last_commit: dc2b9cc
git_last_commit_date: 2021-10-26 12:27:52 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: EGAD
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2021-12-05 14:12:19 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 14:14:05 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 106.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: EGAD.Rcheck
Warnings: 1

Command output

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###
### 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/EGAD.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.22.0’
* 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 39.3Mb
  sub-directories of 1Mb or more:
    data  39.1Mb
* 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-3.14-bioc/meat/EGAD.Rcheck/00check.log’
for details.



Installation output

EGAD.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  3.325   0.237   3.564 

Example timings

EGAD.Rcheck/EGAD-Ex.timings

nameusersystemelapsed
assortativity0.0020.0010.003
auc_multifunc0.0000.0010.001
auprc0.0070.0000.008
auroc_analytic000
build_binary_network0.0010.0000.001
build_coexp_expressionSet0.0050.0000.006
build_coexp_network0.0090.0010.011
build_semantic_similarity_network0.0010.0010.001
build_weighted_network0.0010.0000.001
calculate_multifunc0.0020.0000.002
conv_smoother0.0180.0010.020
extend_network0.0030.0000.004
filter_network0.0020.0000.002
filter_network_cols0.0030.0000.003
filter_network_rows0.0010.0000.003
filter_orthologs0.0010.0000.001
fmeasure0.0000.0000.001
get_auc0.0020.0000.002
get_counts0.0020.0000.003
get_density0.0010.0000.002
get_prc0.0010.0010.000
get_roc0.0010.0000.001
make_annotations0.0010.0000.001
make_gene_network0.0010.0010.001
make_genelist0.0010.0000.001
neighbor_voting0.0420.0060.047
node_degree0.0010.0010.001
plot_densities0.0280.0040.033
plot_density_compare0.0080.0020.010
plot_distribution0.0060.0010.007
plot_network_heatmap0.0380.0050.043
plot_prc0.0160.0020.018
plot_roc0.0020.0010.003
plot_roc_overlay0.1080.0160.125
predictions0.0110.0020.012
repmat0.0000.0010.001
run_GBA0.0200.0030.024