Multiple platform build/check report for BioC 3.14 - CHECK results for GWENA on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: GWENA

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GWENA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GWENA_1.4.0.tar.gz

StartedAt: 2022-04-12 20:59:12 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 21:15:12 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 959.4 seconds

RetCode: 0

Status: OK

CheckDir: GWENA.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GWENA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GWENA_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GWENA.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GWENA/DESCRIPTION' ... OK
* this is package 'GWENA' version '1.4.0'
* 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 'GWENA' can be installed ... OK
* checking installed package size ... OK
* 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 ... 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
z_summary          11.58   0.06   12.94
compare_conditions  7.17   0.04    8.11
plot_enrichment     1.67   0.67    9.54
bio_enrich          0.20   0.00   11.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
z_summary          12.72   0.08   14.40
compare_conditions  7.89   0.06    8.92
plot_enrichment     1.47   0.22    8.73
bio_enrich          0.23   0.05   11.08
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GWENA_1.4.0.tar.gz && rm -rf GWENA.buildbin-libdir && mkdir GWENA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GWENA.buildbin-libdir GWENA_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GWENA_1.4.0.zip && rm GWENA_1.4.0.tar.gz GWENA_1.4.0.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
  9 2623k    9  238k    0     0   895k      0  0:00:02 --:--:--  0:00:02  896k
100 2623k  100 2623k    0     0  2263k      0  0:00:01  0:00:01 --:--:-- 2265k

install for i386

* installing *source* package 'GWENA' ...
** 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 'GWENA'
    finding HTML links ... done
    associate_phenotype                     html  
    bio_enrich                              html  
    build_graph_from_sq_mat                 html  
    build_net                               html  
    finding level-2 HTML links ... done

    compare_conditions                      html  
    detect_modules                          html  
    dot-check_data_expr                     html  
    dot-check_gost                          html  
    dot-check_module                        html  
    dot-check_network                       html  
    dot-contingencyTable                    html  
    dot-cor_func_match                      html  
    filter_RNA_seq                          html  
    filter_low_var                          html  
    get_fit.cor                             html  
    get_fit.expr                            html  
    get_hub_degree                          html  
    get_hub_genes                           html  
    get_hub_high_co                         html  
    get_hub_kleinberg                       html  
    get_sub_clusters                        html  
    gg_palette                              html  
    gtex_expr                               html  
    gtex_traits                             html  
    is_data_expr                            html  
    is_gost                                 html  
    is_module                               html  
    is_network                              html  
    join_gost                               html  
    kuehne_expr                             html  
    kuehne_traits                           html  
    matchsub                                html  
    orderAsNumeric                          html  
    plot_comparison_stats                   html  
    plot_enrichment                         html  
    plot_expression_profiles                html  
    plot_module                             html  
    plot_modules_merge                      html  
    plot_modules_phenotype                  html  
    quiet                                   html  
    z_summary                               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 'GWENA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GWENA' as GWENA_1.4.0.zip
* DONE (GWENA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GWENA' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(GWENA)

> 
> test_check("GWENA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ]
> 
> proc.time()
   user  system elapsed 
 620.92    7.01  272.09


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(GWENA)

> 
> test_check("GWENA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ]
> 
> proc.time()
   user  system elapsed 
 602.29    6.06  268.06

name	user	system	elapsed
associate_phenotype	0.04	0.00	0.03
bio_enrich	0.20	0.00	11.57
build_graph_from_sq_mat	0.22	0.01	0.23
build_net	2.88	0.07	2.94
compare_conditions	7.17	0.04	8.11
detect_modules	1.34	0.03	1.38
filter_RNA_seq	0	0	0
filter_low_var	0.02	0.00	0.01
get_fit.cor	0.62	0.00	0.63
get_fit.expr	0.62	0.00	0.63
get_hub_degree	0.08	0.00	0.08
get_hub_genes	0	0	0
get_hub_high_co	0	0	0
get_hub_kleinberg	0.17	0.00	0.17
get_sub_clusters	1.30	0.00	1.29
is_data_expr	0	0	0
is_gost	0.05	0.00	2.54
is_module	0	0	0
is_network	0	0	0
join_gost	0.01	0.00	1.00
plot_comparison_stats	0.35	0.08	0.42
plot_enrichment	1.67	0.67	9.54
plot_expression_profiles	2.20	0.14	2.35
plot_module	0.19	0.02	0.21
plot_modules_merge	1.45	0.02	1.47
plot_modules_phenotype	0.2	0.0	0.2
z_summary	11.58	0.06	12.94

name	user	system	elapsed
associate_phenotype	0.03	0.00	0.03
bio_enrich	0.23	0.05	11.08
build_graph_from_sq_mat	0.31	0.01	0.32
build_net	2.83	0.04	2.86
compare_conditions	7.89	0.06	8.92
detect_modules	1.47	0.01	1.48
filter_RNA_seq	0	0	0
filter_low_var	0.01	0.00	0.02
get_fit.cor	0.67	0.00	0.67
get_fit.expr	0.66	0.00	0.66
get_hub_degree	0.09	0.00	0.09
get_hub_genes	0	0	0
get_hub_high_co	0	0	0
get_hub_kleinberg	0.19	0.00	0.21
get_sub_clusters	1.50	0.02	1.51
is_data_expr	0.00	0.02	0.02
is_gost	0.05	0.00	2.53
is_module	0	0	0
is_network	0	0	0
join_gost	0.01	0.00	1.01
plot_comparison_stats	0.39	0.01	0.41
plot_enrichment	1.47	0.22	8.73
plot_expression_profiles	2.58	0.02	2.61
plot_module	0.15	0.01	0.17
plot_modules_merge	1.69	0.00	1.69
plot_modules_phenotype	0.22	0.00	0.22
z_summary	12.72	0.08	14.40

CHECK results for GWENA on tokay2

Summary

Command output

Installation output

Tests output

Example timings