Multiple platform build/check report for BioC 3.12 - CHECK report for GWENA on tokay1

Package: GWENA

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GWENA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GWENA_1.0.1.tar.gz

StartedAt: 2021-05-06 03:31:31 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 03:48:46 -0400 (Thu, 06 May 2021)

EllapsedTime: 1035.5 seconds

RetCode: 0

Status: OK

CheckDir: GWENA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GWENA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GWENA_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GWENA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.0.1'
* 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 ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
* 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 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                12.40   0.09   16.39
compare_conditions        8.31   0.29    8.93
plot_expression_profiles  3.25   0.17    7.77
plot_enrichment           1.38   0.33    7.72
bio_enrich                0.15   0.01   11.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
z_summary          14.69   0.06   16.39
compare_conditions  9.06   0.05   11.70
plot_enrichment     2.08   0.20    8.48
bio_enrich          0.14   0.03   10.20
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/GWENA.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GWENA_1.0.1.tar.gz && rm -rf GWENA.buildbin-libdir && mkdir GWENA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GWENA.buildbin-libdir GWENA_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GWENA_1.0.1.zip && rm GWENA_1.0.1.tar.gz GWENA_1.0.1.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
100 2579k  100 2579k    0     0  25.2M      0 --:--:-- --:--:-- --:--:-- 25.4M

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  
    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_1.0.1.zip
* DONE (GWENA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GWENA' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 
 579.62    6.96  275.90


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 
 560.06    4.95  272.85

name	user	system	elapsed
associate_phenotype	0.04	0.00	0.03
bio_enrich	0.15	0.01	11.13
build_graph_from_sq_mat	0.20	0.00	0.21
build_net	2.36	0.03	2.65
compare_conditions	8.31	0.29	8.93
detect_modules	2.03	0.03	2.06
filter_RNA_seq	0	0	0
filter_low_var	0.04	0.00	0.03
get_fit.cor	0.87	0.01	0.89
get_fit.expr	0.88	0.00	0.87
get_hub_degree	0.15	0.00	0.16
get_hub_genes	0	0	0
get_hub_high_co	0	0	0
get_hub_kleinberg	0.3	0.0	0.3
is_data_expr	0	0	0
is_gost	0.05	0.00	2.40
is_module	0	0	0
is_network	0	0	0
join_gost	0.00	0.00	1.07
plot_comparison_stats	0.31	0.08	0.39
plot_enrichment	1.38	0.33	7.72
plot_expression_profiles	3.25	0.17	7.77
plot_module	0.33	0.00	0.37
plot_modules_merge	2.01	0.05	2.99
plot_modules_phenotype	0.31	0.00	0.36
z_summary	12.40	0.09	16.39

name	user	system	elapsed
associate_phenotype	0.03	0.00	0.03
bio_enrich	0.14	0.03	10.20
build_graph_from_sq_mat	0.14	0.00	0.14
build_net	3.31	0.00	3.31
compare_conditions	9.06	0.05	11.70
detect_modules	1.74	0.01	1.91
filter_RNA_seq	0	0	0
filter_low_var	0.01	0.00	0.01
get_fit.cor	0.91	0.00	0.91
get_fit.expr	0.89	0.00	4.88
get_hub_degree	0.19	0.00	0.18
get_hub_genes	0	0	0
get_hub_high_co	0	0	0
get_hub_kleinberg	0.39	0.00	0.39
is_data_expr	0	0	0
is_gost	0.04	0.00	2.38
is_module	0	0	0
is_network	0	0	0
join_gost	0.04	0.00	1.03
plot_comparison_stats	0.36	0.02	0.37
plot_enrichment	2.08	0.20	8.48
plot_expression_profiles	3.45	0.02	3.54
plot_module	0.19	0.00	0.18
plot_modules_merge	1.84	0.03	1.96
plot_modules_phenotype	0.32	0.00	0.32
z_summary	14.69	0.06	16.39

CHECK report for GWENA on tokay1

Summary

Command output

Installation output

Tests output

Example timings