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

Package: BioNERO

Version: 1.0.4

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNERO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BioNERO_1.0.4.tar.gz

StartedAt: 2021-10-14 20:15:50 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 20:25:55 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 605.8 seconds

RetCode: 0

Status: OK

CheckDir: BioNERO.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNERO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BioNERO_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BioNERO.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 'BioNERO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNERO' version '1.0.4'
* 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 'BioNERO' 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 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
module_stability 18.45      0   18.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
module_stability 23.23   0.02   23.25
* 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/BioNERO_1.0.4.tar.gz && rm -rf BioNERO.buildbin-libdir && mkdir BioNERO.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioNERO.buildbin-libdir BioNERO_1.0.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BioNERO_1.0.4.zip && rm BioNERO_1.0.4.tar.gz BioNERO_1.0.4.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
 24 2478k   24  607k    0     0  1575k      0  0:00:01 --:--:--  0:00:01 1574k
100 2478k  100 2478k    0     0  2500k      0 --:--:-- --:--:-- --:--:-- 2501k

install for i386

* installing *source* package 'BioNERO' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioNERO'
    finding HTML links ... done
    PC_correction                           html  
    SFT_fit                                 html  
    ZKfiltering                             html  
    check_SFT                               html  
    consensus_SFT_fit                       html  
    consensus_modules                       html  
    consensus_trait_cor                     html  
    cormat_to_edgelist                      html  
    detect_communities                      html  
    dfs2one                                 html  
    enrichment_analysis                     html  
    exp2gcn                                 html  
    exp2grn                                 html  
    exp_genes2orthogroups                   html  
    exp_preprocess                          html  
    filt.se                                 html  
    filter_by_variance                      html  
    gene_significance                       html  
    get_HK                                  html  
    get_edge_list                           html  
    get_hubs_gcn                            html  
    get_hubs_grn                            html  
    get_neighbors                           html  
    grn_average_rank                        html  
    grn_combined                            html  
    grn_filter                              html  
    grn_infer                               html  
    is_singleton                            html  
    modPres_WGCNA                           html  
    modPres_netrep                          html  
    module_enrichment                       html  
    module_preservation                     html  
    module_stability                        html  
    module_trait_cor                        html  
    net_stats                               html  
    og.zma.osa                              html  
    osa.se                                  html  
    parse_orthofinder                       html  
    plot_PCA                                html  
    plot_dendro_and_colors                  html  
    plot_dendro_and_cons_colors             html  
    plot_eigengene_network                  html  
    plot_expression_profile                 html  
    plot_gcn                                html  
    plot_grn                                html  
    plot_heatmap                            html  
    plot_ngenes_per_module                  html  
    plot_ppi                                html  
    q_normalize                             html  
    remove_nonexp                           html  
    replace_na                              html  
    zma.interpro                            html  
    zma.se                                  html  
    zma.tfs                                 html  
*** copying figures
** 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 'BioNERO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioNERO' as BioNERO_1.0.4.zip
* DONE (BioNERO)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BioNERO' 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(BioNERO)

> 
> test_check("BioNERO")
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[2021-10-14 20:22:58 EDT] Validating user input...
[2021-10-14 20:22:58 EDT]   Checking matrices for problems...
[2021-10-14 20:22:59 EDT] Input ok!
[2021-10-14 20:22:59 EDT] Calculating preservation of network subsets from
                          dataset "osa" in dataset "zma".
[2021-10-14 20:22:59 EDT]   Pre-computing network properties in dataset
                            "osa"...
[2021-10-14 20:23:00 EDT]   Calculating observed test statistics...
[2021-10-14 20:23:00 EDT]   Generating null distributions from 2 permutations
                            using 1 thread...


    0% completed.
  100% completed.

[2021-10-14 20:23:01 EDT]   Calculating P-values...
[2021-10-14 20:23:01 EDT]   Collating results...
[2021-10-14 20:23:03 EDT] Done!
None of the modules in osa were preserved in zma.
   Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
1      5    0.162 -0.241         0.0679    49.8     39.10  120.0
2      6    0.317 -0.353         0.1980    42.9     31.60  109.0
3      7    0.504 -0.441         0.4200    37.7     26.10  101.0
4      8    0.653 -0.529         0.5950    33.5     22.50   93.7
5      9    0.720 -0.598         0.6690    30.2     19.90   87.5
6     10    0.731 -0.656         0.6590    27.4     18.80   82.1
7     11    0.872 -0.686         0.8430    25.1     17.20   77.4
8     12    0.826 -0.721         0.7800    23.1     15.40   73.1
9     13    0.832 -0.739         0.7850    21.4     13.70   69.3
10    14    0.903 -0.737         0.8780    19.9     12.80   65.8
11    15    0.875 -0.756         0.8420    18.6     11.70   62.7
12    16    0.894 -0.764         0.8680    17.4     10.90   59.8
13    17    0.908 -0.756         0.8860    16.4     10.10   57.2
14    18    0.930 -0.761         0.9180    15.4      9.36   54.7
15    19    0.941 -0.762         0.9300    14.6      8.73   52.4
16    20    0.944 -0.764         0.9340    13.8      8.20   50.3
   Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
1      5   0.0693 -0.178         -0.154    59.7      44.3  137.0
2      6   0.1920 -0.282          0.026    51.9      37.8  127.0
3      7   0.3530 -0.378          0.226    45.8      33.3  119.0
4      8   0.4680 -0.453          0.335    40.9      28.6  111.0
5      9   0.6020 -0.530          0.505    36.9      25.6  105.0
6     10   0.6560 -0.596          0.564    33.6      22.3   98.9
7     11   0.7400 -0.664          0.667    30.8      20.1   93.8
8     12   0.7690 -0.699          0.704    28.3      19.1   89.1
9     13   0.8040 -0.747          0.749    26.2      17.5   84.9
10    14   0.8060 -0.781          0.750    24.4      16.1   81.1
11    15   0.8250 -0.792          0.776    22.7      14.8   77.5
12    16   0.8510 -0.822          0.811    21.3      13.6   74.3
13    17   0.8630 -0.816          0.824    20.0      12.5   71.4
14    18   0.8360 -0.847          0.789    18.8      11.5   68.7
15    19   0.8470 -0.867          0.804    17.7      11.0   66.1
16    20   0.8720 -0.884          0.836    16.8      10.2   63.8
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..done.
 multiSetMEs: Calculating module MEs.
   Working on set 1 ...
   Working on set 2 ...
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..done.
 multiSetMEs: Calculating module MEs.
   Working on set 1 ...
   Working on set 2 ...
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..done.
 multiSetMEs: Calculating module MEs.
   Working on set 1 ...
   Working on set 2 ...
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
   Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
1      3   0.3340  1.0300        0.18900   145.0     149.0  222.0
2      4   0.2060  0.5420        0.05910   116.0     114.0  195.0
3      5   0.1460  0.3930       -0.00703    96.8      91.3  176.0
4      6   0.0556  0.1930       -0.07170    83.6      74.2  162.0
5      7   0.0209  0.1050       -0.07690    73.7      61.8  151.0
6      8   0.0015 -0.0255       -0.12100    66.0      51.9  142.0
7      9   0.0443 -0.1400       -0.16000    59.8      46.5  134.0
8     10   0.1470 -0.2570       -0.08480    54.7      43.2  127.0
9     11   0.2570 -0.3460        0.04810    50.4      39.7  121.0
10    12   0.3320 -0.3770        0.14800    46.7      36.6  116.0
11    13   0.4520 -0.4400        0.29700    43.5      32.8  111.0
12    14   0.5470 -0.4910        0.41800    40.8      30.1  107.0
13    15   0.5880 -0.5240        0.47300    38.3      27.6  103.0
14    16   0.6870 -0.5470        0.59800    36.1      24.8   99.5
15    17   0.7570 -0.5730        0.68900    34.1      22.9   96.1
16    18   0.8060 -0.5880        0.75100    32.3      21.4   93.0
17    19   0.8350 -0.6170        0.78800    30.7      20.1   90.1
18    20   0.8770 -0.6480        0.84100    29.2      19.3   87.4
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ...working on run 1 ..
The correlation threshold that best fits the scale-free topology is 0.02
Your graph fits the scale-free topology. P-value:0.999999729606805
The top number of edges that best fits the scale-free topology is 272
The top number of edges that best fits the scale-free topology is 272
The top number of edges that best fits the scale-free topology is 269
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
The top number of edges that best fits the scale-free topology is 243
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 107 ]
> 
> proc.time()
   user  system elapsed 
  75.10    3.21   83.03


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(BioNERO)

> 
> test_check("BioNERO")
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[2021-10-14 20:24:23 EDT] Validating user input...
[2021-10-14 20:24:23 EDT]   Checking matrices for problems...
[2021-10-14 20:24:24 EDT] Input ok!
[2021-10-14 20:24:24 EDT] Calculating preservation of network subsets from
                          dataset "osa" in dataset "zma".
[2021-10-14 20:24:24 EDT]   Pre-computing network properties in dataset
                            "osa"...
[2021-10-14 20:24:28 EDT]   Calculating observed test statistics...
[2021-10-14 20:24:28 EDT]   Generating null distributions from 2 permutations
                            using 1 thread...


    0% completed.
  100% completed.

[2021-10-14 20:24:29 EDT]   Calculating P-values...
[2021-10-14 20:24:29 EDT]   Collating results...
[2021-10-14 20:24:31 EDT] Done!
None of the modules in osa were preserved in zma.
   Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
1      5    0.162 -0.241         0.0679    49.8     39.10  120.0
2      6    0.317 -0.353         0.1980    42.9     31.60  109.0
3      7    0.504 -0.441         0.4200    37.7     26.10  101.0
4      8    0.653 -0.529         0.5950    33.5     22.50   93.7
5      9    0.720 -0.598         0.6690    30.2     19.90   87.5
6     10    0.731 -0.656         0.6590    27.4     18.80   82.1
7     11    0.872 -0.686         0.8430    25.1     17.20   77.4
8     12    0.826 -0.721         0.7800    23.1     15.40   73.1
9     13    0.832 -0.739         0.7850    21.4     13.70   69.3
10    14    0.903 -0.737         0.8780    19.9     12.80   65.8
11    15    0.875 -0.756         0.8420    18.6     11.70   62.7
12    16    0.894 -0.764         0.8680    17.4     10.90   59.8
13    17    0.908 -0.756         0.8860    16.4     10.10   57.2
14    18    0.930 -0.761         0.9180    15.4      9.36   54.7
15    19    0.941 -0.762         0.9300    14.6      8.73   52.4
16    20    0.944 -0.764         0.9340    13.8      8.20   50.3
   Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
1      5   0.0693 -0.178         -0.154    59.7      44.3  137.0
2      6   0.1920 -0.282          0.026    51.9      37.8  127.0
3      7   0.3530 -0.378          0.226    45.8      33.3  119.0
4      8   0.4680 -0.453          0.335    40.9      28.6  111.0
5      9   0.6020 -0.530          0.505    36.9      25.6  105.0
6     10   0.6560 -0.596          0.564    33.6      22.3   98.9
7     11   0.7400 -0.664          0.667    30.8      20.1   93.8
8     12   0.7690 -0.699          0.704    28.3      19.1   89.1
9     13   0.8040 -0.747          0.749    26.2      17.5   84.9
10    14   0.8060 -0.781          0.750    24.4      16.1   81.1
11    15   0.8250 -0.792          0.776    22.7      14.8   77.5
12    16   0.8510 -0.822          0.811    21.3      13.6   74.3
13    17   0.8630 -0.816          0.824    20.0      12.5   71.4
14    18   0.8360 -0.847          0.789    18.8      11.5   68.7
15    19   0.8470 -0.867          0.804    17.7      11.0   66.1
16    20   0.8720 -0.884          0.836    16.8      10.2   63.8
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..done.
 multiSetMEs: Calculating module MEs.
   Working on set 1 ...
   Working on set 2 ...
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..done.
 multiSetMEs: Calculating module MEs.
   Working on set 1 ...
   Working on set 2 ...
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..done.
 multiSetMEs: Calculating module MEs.
   Working on set 1 ...
   Working on set 2 ...
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
   Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
1      3   0.3340  1.0300        0.18900   145.0     149.0  222.0
2      4   0.2060  0.5420        0.05910   116.0     114.0  195.0
3      5   0.1460  0.3930       -0.00703    96.8      91.3  176.0
4      6   0.0556  0.1930       -0.07170    83.6      74.2  162.0
5      7   0.0209  0.1050       -0.07690    73.7      61.8  151.0
6      8   0.0015 -0.0255       -0.12100    66.0      51.9  142.0
7      9   0.0443 -0.1400       -0.16000    59.8      46.5  134.0
8     10   0.1470 -0.2570       -0.08480    54.7      43.2  127.0
9     11   0.2570 -0.3460        0.04810    50.4      39.7  121.0
10    12   0.3320 -0.3770        0.14800    46.7      36.6  116.0
11    13   0.4520 -0.4400        0.29700    43.5      32.8  111.0
12    14   0.5470 -0.4910        0.41800    40.8      30.1  107.0
13    15   0.5880 -0.5240        0.47300    38.3      27.6  103.0
14    16   0.6870 -0.5470        0.59800    36.1      24.8   99.5
15    17   0.7570 -0.5730        0.68900    34.1      22.9   96.1
16    18   0.8060 -0.5880        0.75100    32.3      21.4   93.0
17    19   0.8350 -0.6170        0.78800    30.7      20.1   90.1
18    20   0.8770 -0.6480        0.84100    29.2      19.3   87.4
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ...working on run 1 ..
The correlation threshold that best fits the scale-free topology is 0.02
Your graph fits the scale-free topology. P-value:0.999999729606805
The top number of edges that best fits the scale-free topology is 272
The top number of edges that best fits the scale-free topology is 272
The top number of edges that best fits the scale-free topology is 269
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
The top number of edges that best fits the scale-free topology is 243
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 107 ]
> 
> proc.time()
   user  system elapsed 
  75.12    1.00   90.07

name	user	system	elapsed
PC_correction	1.77	0.10	1.86
SFT_fit	1.95	0.08	2.03
ZKfiltering	0.20	0.00	0.21
check_SFT	2.17	0.09	2.27
consensus_SFT_fit	2.33	0.06	2.39
consensus_modules	1.86	0.05	1.90
consensus_trait_cor	1.81	0.08	2.60
cormat_to_edgelist	0.17	0.06	0.23
detect_communities	0.21	0.03	0.24
dfs2one	0.06	0.00	2.93
enrichment_analysis	0	0	0
exp2gcn	0.97	0.06	1.04
exp2grn	0.80	0.10	0.89
exp_genes2orthogroups	0	0	0
exp_preprocess	1.57	0.14	1.71
filt.se	0.02	0.00	0.02
filter_by_variance	0.37	0.06	0.44
gene_significance	1.58	0.31	1.95
get_HK	0.50	0.08	0.58
get_edge_list	0.92	0.00	0.92
get_hubs_gcn	1.05	0.02	1.06
get_hubs_grn	0.84	0.00	0.85
get_neighbors	0.91	0.00	0.90
grn_average_rank	0.52	0.00	0.52
grn_combined	0.51	0.00	0.51
grn_filter	0.71	0.00	0.97
grn_infer	0.72	0.00	0.72
is_singleton	0.08	0.00	0.08
modPres_WGCNA	0	0	0
modPres_netrep	0	0	0
module_enrichment	0	0	0
module_preservation	0	0	0
module_stability	18.45	0.00	18.45
module_trait_cor	0.75	0.00	0.75
net_stats	0	0	0
og.zma.osa	0.05	0.00	0.05
osa.se	0.09	0.00	0.09
parse_orthofinder	0.11	0.00	0.20
plot_PCA	0.59	0.01	0.61
plot_dendro_and_colors	0.88	0.02	0.89
plot_dendro_and_cons_colors	1.91	0.03	1.94
plot_eigengene_network	0.73	0.00	0.73
plot_expression_profile	0.61	0.01	0.63
plot_gcn	1.02	0.02	1.03
plot_grn	0.75	0.02	0.77
plot_heatmap	0	0	0
plot_ngenes_per_module	1.48	0.01	1.50
plot_ppi	0.03	0.00	0.03
q_normalize	0.25	0.00	0.25
remove_nonexp	0.17	0.00	0.17
replace_na	0.16	0.03	0.19
zma.interpro	0.05	0.02	0.06
zma.se	0.17	0.00	0.17
zma.tfs	0	0	0

name	user	system	elapsed
PC_correction	0.92	0.01	0.94
SFT_fit	2.14	0.00	2.14
ZKfiltering	0.17	0.00	0.17
check_SFT	1.74	0.15	1.89
consensus_SFT_fit	2.59	0.05	2.64
consensus_modules	1.88	0.02	1.89
consensus_trait_cor	1.84	0.03	1.88
cormat_to_edgelist	0.06	0.03	0.09
detect_communities	0.11	0.01	0.13
dfs2one	0.05	0.00	0.60
enrichment_analysis	0	0	0
exp2gcn	1.09	0.04	1.13
exp2grn	1.05	0.03	1.56
exp_genes2orthogroups	0	0	0
exp_preprocess	1.80	0.01	1.81
filt.se	0	0	0
filter_by_variance	0.29	0.00	0.30
gene_significance	1.64	0.07	1.70
get_HK	0.27	0.01	0.29
get_edge_list	0.97	0.00	0.96
get_hubs_gcn	0.90	0.00	0.91
get_hubs_grn	0.68	0.00	0.67
get_neighbors	0.93	0.00	0.94
grn_average_rank	0.47	0.00	0.46
grn_combined	0.47	0.00	0.47
grn_filter	0.59	0.00	0.60
grn_infer	0.41	0.00	0.41
is_singleton	0.05	0.00	0.05
modPres_WGCNA	0	0	0
modPres_netrep	0	0	0
module_enrichment	0	0	0
module_preservation	0	0	0
module_stability	23.23	0.02	23.25
module_trait_cor	0.89	0.00	0.89
net_stats	0	0	0
og.zma.osa	0.03	0.00	0.03
osa.se	0.07	0.01	0.08
parse_orthofinder	0.03	0.00	0.03
plot_PCA	0.31	0.00	0.31
plot_dendro_and_colors	0.98	0.00	0.98
plot_dendro_and_cons_colors	2.08	0.02	2.10
plot_eigengene_network	0.94	0.00	0.94
plot_expression_profile	0.56	0.01	0.59
plot_gcn	0.88	0.00	0.87
plot_grn	0.61	0.02	0.63
plot_heatmap	0	0	0
plot_ngenes_per_module	1.06	0.00	1.06
plot_ppi	0.03	0.00	0.03
q_normalize	0.19	0.00	0.19
remove_nonexp	0.14	0.00	0.14
replace_na	0.12	0.00	0.13
zma.interpro	0.03	0.00	0.03
zma.se	0.11	0.00	0.11
zma.tfs	0	0	0

CHECK results for BioNERO on tokay2

Summary

Command output

Installation output

Tests output

Example timings