Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-26 11:35:30 -0400 (Tue, 26 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 619/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EGAD 1.28.0  (landing page)
Sara Ballouz
Snapshot Date: 2023-09-25 14:00:11 -0400 (Mon, 25 Sep 2023)
git_url: https://git.bioconductor.org/packages/EGAD
git_branch: RELEASE_3_17
git_last_commit: 2fded20
git_last_commit_date: 2023-04-25 10:47:01 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for EGAD on nebbiolo1


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: 1.28.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EGAD.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings EGAD_1.28.0.tar.gz
StartedAt: 2023-09-25 21:08:00 -0400 (Mon, 25 Sep 2023)
EndedAt: 2023-09-25 21:08:58 -0400 (Mon, 25 Sep 2023)
EllapsedTime: 58.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: EGAD.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EGAD.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings EGAD_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/EGAD.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘EGAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EGAD’ version ‘1.28.0’
* 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 37.2Mb
  sub-directories of 1Mb or more:
    data  36.9Mb
* 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 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 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
  ‘/home/biocbuild/bbs-3.17-bioc/meat/EGAD.Rcheck/00check.log’
for details.



Installation output

EGAD.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL EGAD
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 (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 
  2.035   0.168   2.192 

Example timings

EGAD.Rcheck/EGAD-Ex.timings

nameusersystemelapsed
assortativity0.0020.0000.002
auc_multifunc0.0000.0000.001
auprc0.0040.0000.005
auroc_analytic0.0000.0000.001
build_binary_network0.0000.0010.001
build_coexp_expressionSet0.0000.0030.004
build_coexp_network0.0060.0000.006
build_semantic_similarity_network0.0010.0000.001
build_weighted_network0.0000.0000.001
calculate_multifunc0.0020.0000.002
conv_smoother0.0070.0040.011
extend_network0.0030.0000.003
filter_network0.0010.0000.001
filter_network_cols0.0020.0000.002
filter_network_rows0.0020.0000.001
filter_orthologs0.0010.0000.001
fmeasure000
get_auc0.0010.0000.001
get_counts0.0030.0000.002
get_density0.0010.0000.001
get_prc0.0000.0000.001
get_roc0.0000.0010.001
make_annotations0.0000.0010.001
make_gene_network0.0000.0010.001
make_genelist000
neighbor_voting0.0300.0080.038
node_degree0.0000.0000.001
plot_densities0.0120.0080.020
plot_density_compare0.0060.0000.006
plot_distribution0.0050.0000.004
plot_network_heatmap0.0320.0040.035
plot_prc0.0090.0030.012
plot_roc0.0020.0000.001
plot_roc_overlay0.0810.0040.085
predictions0.0080.0000.007
repmat000
run_GBA0.0140.0000.014