Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:06:08 -0400 (Fri, 24 Sep 2021).

CHECK results for EGAD on tokay2

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 559/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EGAD 1.20.0  (landing page)
Sara Ballouz
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/EGAD
git_branch: RELEASE_3_13
git_last_commit: 948910f
git_last_commit_date: 2021-05-19 12:20:29 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.20.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EGAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EGAD_1.20.0.tar.gz
StartedAt: 2021-09-23 21:54:51 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 21:56:48 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 116.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: EGAD.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EGAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EGAD_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/EGAD.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EGAD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EGAD' version '1.20.0'
* 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 'EGAD' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 39.5Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/EGAD.Rcheck/00check.log'
for details.



Installation output

EGAD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/EGAD_1.20.0.tar.gz && rm -rf EGAD.buildbin-libdir && mkdir EGAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EGAD.buildbin-libdir EGAD_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL EGAD_1.20.0.zip && rm EGAD_1.20.0.tar.gz EGAD_1.20.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  4 14.5M    4  738k    0     0  1401k      0  0:00:10 --:--:--  0:00:10 1400k
 21 14.5M   21 3141k    0     0  2082k      0  0:00:07  0:00:01  0:00:06 2083k
 43 14.5M   43 6546k    0     0  2610k      0  0:00:05  0:00:02  0:00:03 2610k
 71 14.5M   71 10.4M    0     0  3030k      0  0:00:04  0:00:03  0:00:01 3030k
100 14.5M  100 14.5M    0     0  3428k      0  0:00:04  0:00:04 --:--:-- 3429k

install for i386

* 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
  converting help for package 'EGAD'
    finding HTML links ... done
    GO.human                                html  
    GO.mouse                                html  
    GO.voc                                  html  
    assortativity                           html  
    atrr.human                              html  
    attr.mouse                              html  
    auc_multifunc                           html  
    auprc                                   html  
    auroc_analytic                          html  
    biogrid                                 html  
    build_binary_network                    html  
    build_coexp_GEOID                       html  
    build_coexp_expressionSet               html  
    build_coexp_network                     html  
    build_semantic_similarity_network       html  
    build_weighted_network                  html  
    calculate_multifunc                     html  
    conv_smoother                           html  
    example_annotations                     html  
    example_binary_network                  html  
    example_coexpression                    html  
    example_neighbor_voting                 html  
    extend_network                          html  
    filter_network                          html  
    filter_network_cols                     html  
    filter_network_rows                     html  
    filter_orthologs                        html  
    fmeasure                                html  
    genes                                   html  
    get_auc                                 html  
    get_biogrid                             html  
    get_counts                              html  
    get_density                             html  
    get_expression_data_gemma               html  
    get_expression_matrix_from_GEO          html  
    get_phenocarta                          html  
    get_prc                                 html  
    get_roc                                 html  
    make_annotations                        html  
    make_gene_network                       html  
    make_genelist                           html  
    make_transparent                        html  
    neighbor_voting                         html  
    node_degree                             html  
    ortho                                   html  
    pheno                                   html  
    plot_densities                          html  
    plot_density_compare                    html  
    plot_distribution                       html  
    plot_network_heatmap                    html  
    plot_prc                                html  
    plot_roc                                html  
    plot_roc_overlay                        html  
    plot_value_compare                      html  
    predictions                             html  
    repmat                                  html  
    run_GBA                                 html  
** 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

install for x64

* installing *source* package 'EGAD' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EGAD' as EGAD_1.20.0.zip
* DONE (EGAD)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'EGAD' successfully unpacked and MD5 sums checked

Tests output

EGAD.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   2.46    0.23    2.87 

EGAD.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   2.54    0.25    2.78 

Example timings

EGAD.Rcheck/examples_i386/EGAD-Ex.timings

nameusersystemelapsed
assortativity000
auc_multifunc000
auprc0.010.000.02
auroc_analytic000
build_binary_network000
build_coexp_expressionSet000
build_coexp_network0.020.000.01
build_semantic_similarity_network000
build_weighted_network000
calculate_multifunc000
conv_smoother0.010.020.03
extend_network000
filter_network000
filter_network_cols0.020.000.02
filter_network_rows000
filter_orthologs000
fmeasure0.010.000.01
get_auc000
get_counts000
get_density000
get_prc000
get_roc000
make_annotations000
make_gene_network000
make_genelist000
neighbor_voting0.030.030.06
node_degree000
plot_densities0.050.000.05
plot_density_compare0.000.010.01
plot_distribution0.010.000.02
plot_network_heatmap0.080.020.09
plot_prc0.030.000.04
plot_roc000
plot_roc_overlay0.170.030.20
predictions0.020.000.01
repmat000
run_GBA0.020.020.04

EGAD.Rcheck/examples_x64/EGAD-Ex.timings

nameusersystemelapsed
assortativity000
auc_multifunc000
auprc000
auroc_analytic000
build_binary_network000
build_coexp_expressionSet0.020.000.02
build_coexp_network000
build_semantic_similarity_network000
build_weighted_network000
calculate_multifunc000
conv_smoother0.010.000.02
extend_network000
filter_network0.020.000.01
filter_network_cols000
filter_network_rows000
filter_orthologs000
fmeasure000
get_auc000
get_counts000
get_density000
get_prc000
get_roc0.010.000.02
make_annotations000
make_gene_network000
make_genelist000
neighbor_voting0.020.000.01
node_degree000
plot_densities0.010.000.01
plot_density_compare0.020.000.02
plot_distribution000
plot_network_heatmap0.030.000.08
plot_prc0.010.000.02
plot_roc000
plot_roc_overlay0.160.000.16
predictions0.020.000.01
repmat000
run_GBA0.010.010.03