Multiple platform build/check report for BioC 3.11 - CHECK report for EGAD on tokay2

Package: EGAD

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EGAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings EGAD_1.16.0.tar.gz

StartedAt: 2020-10-17 03:39:27 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 03:45:08 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 340.5 seconds

RetCode: 0

Status: OK

CheckDir: EGAD.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EGAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings EGAD_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/EGAD.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.16.0'
* 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 41.6Mb
  sub-directories of 1Mb or more:
    data  41.1Mb
* checking package directory ... OK
* checking 'build' 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 ... NOTE
Namespaces in Imports field not imported from:
  'Matrix' 'affy'
  All declared Imports should be used.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* 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 for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/EGAD.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/EGAD_1.16.0.tar.gz && rm -rf EGAD.buildbin-libdir && mkdir EGAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EGAD.buildbin-libdir EGAD_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL EGAD_1.16.0.zip && rm EGAD_1.16.0.tar.gz EGAD_1.16.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 73 39.4M   73 29.0M    0     0  84.9M      0 --:--:-- --:--:-- --:--:-- 86.5M
100 39.4M  100 39.4M    0     0  90.7M      0 --:--:-- --:--:-- --:--:-- 92.1M

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_1.16.0.zip
* DONE (EGAD)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'EGAD' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 9 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   9.54    0.85   10.37


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 9 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   9.89    0.60   10.48

name	user	system	elapsed
assortativity	0	0	0
auc_multifunc	0	0	0
auprc	0.02	0.00	0.02
auroc_analytic	0	0	0
build_binary_network	0	0	0
build_coexp_expressionSet	0.01	0.00	0.02
build_coexp_network	0	0	0
build_semantic_similarity_network	0	0	0
build_weighted_network	0	0	0
calculate_multifunc	0	0	0
conv_smoother	0.03	0.00	0.03
extend_network	0	0	0
filter_network	0	0	0
filter_network_cols	0.01	0.00	0.02
filter_network_rows	0	0	0
filter_orthologs	0	0	0
fmeasure	0	0	0
get_auc	0	0	0
get_counts	0.02	0.00	0.01
get_density	0	0	0
get_prc	0	0	0
get_roc	0	0	0
make_annotations	0	0	0
make_gene_network	0	0	0
make_genelist	0	0	0
neighbor_voting	0.05	0.00	0.05
node_degree	0	0	0
plot_densities	0.03	0.00	0.03
plot_density_compare	0.01	0.00	0.02
plot_distribution	0	0	0
plot_network_heatmap	0.10	0.00	0.09
plot_prc	0.01	0.00	0.02
plot_roc	0.02	0.00	0.01
plot_roc_overlay	0.19	0.00	0.19
predictions	0.01	0.00	0.02
repmat	0	0	0
run_GBA	0.03	0.00	0.03

name	user	system	elapsed
assortativity	0	0	0
auc_multifunc	0	0	0
auprc	0	0	0
auroc_analytic	0.02	0.00	0.02
build_binary_network	0	0	0
build_coexp_expressionSet	0	0	0
build_coexp_network	0	0	0
build_semantic_similarity_network	0	0	0
build_weighted_network	0	0	0
calculate_multifunc	0.00	0.02	0.01
conv_smoother	0	0	0
extend_network	0	0	0
filter_network	0	0	0
filter_network_cols	0	0	0
filter_network_rows	0.04	0.00	0.03
filter_orthologs	0	0	0
fmeasure	0	0	0
get_auc	0	0	0
get_counts	0	0	0
get_density	0	0	0
get_prc	0	0	0
get_roc	0	0	0
make_annotations	0	0	0
make_gene_network	0	0	0
make_genelist	0	0	0
neighbor_voting	0.02	0.00	0.02
node_degree	0	0	0
plot_densities	0.03	0.00	0.03
plot_density_compare	0.01	0.00	0.02
plot_distribution	0	0	0
plot_network_heatmap	0.05	0.00	0.04
plot_prc	0.02	0.00	0.02
plot_roc	0	0	0
plot_roc_overlay	0.07	0.00	0.08
predictions	0	0	0
repmat	0	0	0
run_GBA	0.02	0.00	0.01

CHECK report for EGAD on tokay2

Summary

Command output

Installation output

Tests output

Example timings