Multiple platform build/check report for BioC 3.14 - CHECK results for BioNERO 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: BioNERO

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNERO.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioNERO_1.2.0.tar.gz

StartedAt: 2022-04-12 16:25:16 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 16:34:45 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 568.8 seconds

RetCode: 0

Status: OK

CheckDir: BioNERO.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNERO.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioNERO_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BioNERO.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 'BioNERO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNERO' 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 '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 21.22   0.03   21.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
module_stability 26.15   0.00   26.16
exp2grn           0.97   0.03    6.00
* 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://155.52.207.166/BBS/3.14/bioc/src/contrib/BioNERO_1.2.0.tar.gz && rm -rf BioNERO.buildbin-libdir && mkdir BioNERO.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioNERO.buildbin-libdir BioNERO_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BioNERO_1.2.0.zip && rm BioNERO_1.2.0.tar.gz BioNERO_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
 26 2496k   26  659k    0     0  1443k      0  0:00:01 --:--:--  0:00:01 1442k
100 2496k  100 2496k    0     0  2227k      0  0:00:01  0:00:01 --:--:-- 2228k

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_1.2.0.zip
* DONE (BioNERO)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BioNERO' 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(BioNERO)

> 
> test_check("BioNERO")
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[2022-04-12 16:32:43 EDT] Validating user input...
[2022-04-12 16:32:43 EDT]   Checking matrices for problems...
[2022-04-12 16:32:43 EDT] Input ok!
[2022-04-12 16:32:43 EDT] Calculating preservation of network subsets from
                          dataset "osa" in dataset "zma".
[2022-04-12 16:32:43 EDT]   Pre-computing network properties in dataset
                            "osa"...
[2022-04-12 16:32:45 EDT]   Calculating observed test statistics...
[2022-04-12 16:32:45 EDT]   Generating null distributions from 2 permutations
                            using 1 thread...


    0% completed.
  100% completed.

[2022-04-12 16:32:46 EDT]   Calculating P-values...
[2022-04-12 16:32:46 EDT]   Collating results...
[2022-04-12 16:32:48 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:0.999999729526025
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 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 107 ]
> 
> proc.time()
   user  system elapsed 
  61.34    2.79   65.12


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(BioNERO)

> 
> test_check("BioNERO")
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[2022-04-12 16:33:48 EDT] Validating user input...
[2022-04-12 16:33:48 EDT]   Checking matrices for problems...
[2022-04-12 16:33:49 EDT] Input ok!
[2022-04-12 16:33:49 EDT] Calculating preservation of network subsets from
                          dataset "osa" in dataset "zma".
[2022-04-12 16:33:49 EDT]   Pre-computing network properties in dataset
                            "osa"...
[2022-04-12 16:33:50 EDT]   Calculating observed test statistics...
[2022-04-12 16:33:50 EDT]   Generating null distributions from 2 permutations
                            using 1 thread...


    0% completed.
  100% completed.

[2022-04-12 16:33:51 EDT]   Calculating P-values...
[2022-04-12 16:33:52 EDT]   Collating results...
[2022-04-12 16:33:54 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:0.999999729526025
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 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 107 ]
> 
> proc.time()
   user  system elapsed 
  66.81    1.37   69.29

name	user	system	elapsed
PC_correction	2.03	0.07	2.10
SFT_fit	1.69	0.06	1.75
ZKfiltering	0.40	0.00	0.41
check_SFT	1.81	0.08	1.89
consensus_SFT_fit	2.83	0.05	2.87
consensus_modules	2.14	0.20	2.35
consensus_trait_cor	2.22	0.10	2.31
cormat_to_edgelist	0.67	0.03	0.70
detect_communities	0.13	0.00	0.13
dfs2one	0.06	0.00	0.06
enrichment_analysis	0	0	0
exp2gcn	0.94	0.03	0.97
exp2grn	0.81	0.05	0.86
exp_genes2orthogroups	0	0	0
exp_preprocess	1.72	0.10	1.83
filt.se	0.00	0.02	0.01
filter_by_variance	0.31	0.23	0.55
gene_significance	0.17	0.05	0.22
get_HK	0.27	0.03	0.30
get_edge_list	0.83	0.02	0.84
get_hubs_gcn	0.92	0.00	0.92
get_hubs_grn	1.09	0.00	1.09
get_neighbors	1.08	0.05	1.13
grn_average_rank	0.64	0.00	0.64
grn_combined	0.58	0.00	0.57
grn_filter	0.65	0.01	0.68
grn_infer	0.52	0.00	0.51
is_singleton	0.06	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	21.22	0.03	21.28
module_trait_cor	0.98	0.00	0.99
net_stats	0	0	0
og.zma.osa	0.07	0.00	0.06
osa.se	0.11	0.02	0.12
parse_orthofinder	0.10	0.00	0.32
plot_PCA	0.57	0.04	0.61
plot_dendro_and_colors	1.08	0.04	1.10
plot_dendro_and_cons_colors	2.14	0.00	2.15
plot_eigengene_network	1.46	0.01	1.48
plot_expression_profile	0.74	0.00	0.73
plot_gcn	1	0	1
plot_grn	0.78	0.02	0.80
plot_heatmap	0	0	0
plot_ngenes_per_module	1.28	0.01	1.30
plot_ppi	0.05	0.00	0.04
q_normalize	0.45	0.00	0.46
remove_nonexp	0.27	0.00	0.26
replace_na	0.23	0.00	0.24
zma.interpro	0.08	0.00	0.08
zma.se	0.17	0.00	0.17
zma.tfs	0	0	0

name	user	system	elapsed
PC_correction	2.13	0.03	2.16
SFT_fit	1.86	0.00	1.86
ZKfiltering	0.2	0.0	0.2
check_SFT	2.05	0.11	2.16
consensus_SFT_fit	3.01	0.03	3.04
consensus_modules	2.14	0.02	2.16
consensus_trait_cor	2.21	0.01	2.22
cormat_to_edgelist	0.07	0.05	0.12
detect_communities	0.10	0.03	0.13
dfs2one	0.08	0.00	0.12
enrichment_analysis	0	0	0
exp2gcn	1.15	0.02	1.17
exp2grn	0.97	0.03	6.00
exp_genes2orthogroups	0	0	0
exp_preprocess	1.88	0.03	1.91
filt.se	0.01	0.00	0.01
filter_by_variance	0.49	0.05	0.53
gene_significance	0.18	0.02	0.21
get_HK	0.42	0.04	0.47
get_edge_list	1.08	0.02	1.09
get_hubs_gcn	0.99	0.00	0.98
get_hubs_grn	1.40	0.01	1.43
get_neighbors	1.00	0.04	1.03
grn_average_rank	0.80	0.03	0.82
grn_combined	0.56	0.00	0.57
grn_filter	0.94	0.01	0.95
grn_infer	0.69	0.02	0.70
is_singleton	0.06	0.00	0.07
modPres_WGCNA	0	0	0
modPres_netrep	0	0	0
module_enrichment	0	0	0
module_preservation	0	0	0
module_stability	26.15	0.00	26.16
module_trait_cor	1	0	1
net_stats	0	0	0
og.zma.osa	0.05	0.00	0.04
osa.se	0.09	0.00	0.10
parse_orthofinder	0.03	0.00	0.03
plot_PCA	0.47	0.00	0.47
plot_dendro_and_colors	1.03	0.00	1.04
plot_dendro_and_cons_colors	2.37	0.01	2.39
plot_eigengene_network	1.05	0.02	1.06
plot_expression_profile	0.69	0.00	0.69
plot_gcn	1.01	0.02	1.03
plot_grn	0.77	0.00	0.76
plot_heatmap	0	0	0
plot_ngenes_per_module	1.19	0.01	1.21
plot_ppi	0.04	0.00	0.04
q_normalize	0.22	0.00	0.22
remove_nonexp	0.18	0.00	0.17
replace_na	0.26	0.05	0.32
zma.interpro	0.06	0.00	0.06
zma.se	0.18	0.01	0.19
zma.tfs	0	0	0

CHECK results for BioNERO on tokay2

Summary

Command output

Installation output

Tests output

Example timings