Multiple platform build/check report for BioC 3.13 - CHECK results for GWENA on tokay2

Package: GWENA

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GWENA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GWENA_1.2.0.tar.gz

StartedAt: 2021-10-15 00:14:07 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 00:29:28 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 921.1 seconds

RetCode: 0

Status: OK

CheckDir: GWENA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GWENA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GWENA_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GWENA.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 'GWENA/DESCRIPTION' ... OK
* this is package 'GWENA' version '1.2.0'
* 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          9.96   0.08   11.53
compare_conditions 6.40   0.13    7.52
plot_enrichment    1.55   0.48    8.55
bio_enrich         0.25   0.03   10.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
z_summary          11.83   0.05   13.18
compare_conditions  7.46   0.06    8.30
plot_enrichment     1.47   0.15    7.63
bio_enrich          0.20   0.00   11.29
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GWENA_1.2.0.tar.gz && rm -rf GWENA.buildbin-libdir && mkdir GWENA.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GWENA.buildbin-libdir GWENA_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GWENA_1.2.0.zip && rm GWENA_1.2.0.tar.gz GWENA_1.2.0.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
 43 2581k   43 1110k    0     0  1759k      0  0:00:01 --:--:--  0:00:01 1759k
100 2581k  100 2581k    0     0  2233k      0  0:00:01  0:00:01 --:--:-- 2235k

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_1.2.0.zip
* DONE (GWENA)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GWENA' successfully unpacked and MD5 sums checked


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(GWENA)

> 
> test_check("GWENA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 275 ]
> 
> proc.time()
   user  system elapsed 
 598.01    5.96  251.48


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(GWENA)

> 
> test_check("GWENA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 275 ]
> 
> proc.time()
   user  system elapsed 
 584.03    4.73  251.71

name	user	system	elapsed
associate_phenotype	0.02	0.00	0.02
bio_enrich	0.25	0.03	10.89
build_graph_from_sq_mat	0.19	0.00	0.18
build_net	2.66	0.06	2.72
compare_conditions	6.40	0.13	7.52
detect_modules	1.24	0.03	1.26
filter_RNA_seq	0	0	0
filter_low_var	0.01	0.00	0.02
get_fit.cor	0.58	0.00	0.58
get_fit.expr	0.66	0.00	0.65
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	0.15	0.00	0.16
get_sub_clusters	1.18	0.07	1.25
is_data_expr	0	0	0
is_gost	0.04	0.00	2.36
is_module	0	0	0
is_network	0	0	0
join_gost	0.01	0.00	1.05
plot_comparison_stats	0.39	0.02	0.40
plot_enrichment	1.55	0.48	8.55
plot_expression_profiles	2.32	0.05	2.39
plot_module	0.15	0.05	0.19
plot_modules_merge	1.26	0.00	1.26
plot_modules_phenotype	0.17	0.01	0.19
z_summary	9.96	0.08	11.53

name	user	system	elapsed
associate_phenotype	0.02	0.00	0.02
bio_enrich	0.20	0.00	11.29
build_graph_from_sq_mat	0.2	0.0	0.2
build_net	2.88	0.03	2.91
compare_conditions	7.46	0.06	8.30
detect_modules	1.33	0.00	1.32
filter_RNA_seq	0	0	0
filter_low_var	0.02	0.00	0.02
get_fit.cor	0.62	0.00	0.63
get_fit.expr	0.67	0.00	0.67
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	1.44	0.02	1.45
is_data_expr	0	0	0
is_gost	0.05	0.02	2.47
is_module	0	0	0
is_network	0	0	0
join_gost	0.05	0.00	1.03
plot_comparison_stats	0.39	0.00	0.39
plot_enrichment	1.47	0.15	7.63
plot_expression_profiles	2.28	0.00	2.28
plot_module	0.14	0.00	0.14
plot_modules_merge	1.47	0.00	1.47
plot_modules_phenotype	0.18	0.00	0.18
z_summary	11.83	0.05	13.18

CHECK results for GWENA on tokay2

Summary

Command output

Installation output

Tests output

Example timings