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This page was generated on 2021-10-15 15:06:07 -0400 (Fri, 15 Oct 2021).

CHECK results for GWENA on tokay2

To the developers/maintainers of the GWENA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GWENA.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 836/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWENA 1.2.0  (landing page)
Gwenaƫlle Lemoine
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/GWENA
git_branch: RELEASE_3_13
git_last_commit: a8f00b9
git_last_commit_date: 2021-05-19 12:53:41 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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


Installation output

GWENA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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

Tests output

GWENA.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(GWENA)

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

GWENA.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(GWENA)

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

Example timings

GWENA.Rcheck/examples_i386/GWENA-Ex.timings

nameusersystemelapsed
associate_phenotype0.020.000.02
bio_enrich 0.25 0.0310.89
build_graph_from_sq_mat0.190.000.18
build_net2.660.062.72
compare_conditions6.400.137.52
detect_modules1.240.031.26
filter_RNA_seq000
filter_low_var0.010.000.02
get_fit.cor0.580.000.58
get_fit.expr0.660.000.65
get_hub_degree0.080.000.08
get_hub_genes000
get_hub_high_co000
get_hub_kleinberg0.150.000.16
get_sub_clusters1.180.071.25
is_data_expr000
is_gost0.040.002.36
is_module000
is_network000
join_gost0.010.001.05
plot_comparison_stats0.390.020.40
plot_enrichment1.550.488.55
plot_expression_profiles2.320.052.39
plot_module0.150.050.19
plot_modules_merge1.260.001.26
plot_modules_phenotype0.170.010.19
z_summary 9.96 0.0811.53

GWENA.Rcheck/examples_x64/GWENA-Ex.timings

nameusersystemelapsed
associate_phenotype0.020.000.02
bio_enrich 0.20 0.0011.29
build_graph_from_sq_mat0.20.00.2
build_net2.880.032.91
compare_conditions7.460.068.30
detect_modules1.330.001.32
filter_RNA_seq000
filter_low_var0.020.000.02
get_fit.cor0.620.000.63
get_fit.expr0.670.000.67
get_hub_degree0.080.000.08
get_hub_genes000
get_hub_high_co000
get_hub_kleinberg0.170.000.17
get_sub_clusters1.440.021.45
is_data_expr000
is_gost0.050.022.47
is_module000
is_network000
join_gost0.050.001.03
plot_comparison_stats0.390.000.39
plot_enrichment1.470.157.63
plot_expression_profiles2.280.002.28
plot_module0.140.000.14
plot_modules_merge1.470.001.47
plot_modules_phenotype0.180.000.18
z_summary11.83 0.0513.18