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This page was generated on 2024-03-04 11:38:55 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 212/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNERO 1.11.1  (landing page)
Fabricio Almeida-Silva
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/BioNERO
git_branch: devel
git_last_commit: 6b1c6e1
git_last_commit_date: 2024-02-07 06:28:35 -0500 (Wed, 07 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for BioNERO on merida1


To the developers/maintainers of the BioNERO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioNERO.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BioNERO
Version: 1.11.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNERO_1.11.1.tar.gz
StartedAt: 2024-03-02 00:53:36 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 01:08:04 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 867.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNERO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNERO_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioNERO.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNERO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNERO’ version ‘1.11.1’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
module_stability       41.324  0.350  48.529
plot_gene_significance  8.976  0.251  10.435
exp_preprocess          4.035  0.118   5.096
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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

BioNERO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNERO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BioNERO’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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
* DONE (BioNERO)

Tests output

BioNERO.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.
 mergeCloseModules: less than two proper modules.
  ..color levels are blue, grey
  ..there is nothing to merge.
[2024-03-02 01:05:52 EST] Validating user input...
[2024-03-02 01:05:52 EST]   Checking matrices for problems...
[2024-03-02 01:05:53 EST] Input ok!
[2024-03-02 01:05:53 EST] Calculating preservation of network subsets from
                          dataset "osa" in dataset "zma".
[2024-03-02 01:05:53 EST]   Pre-computing network properties in dataset
                            "osa"...
[2024-03-02 01:05:55 EST]   Calculating observed test statistics...
[2024-03-02 01:05:55 EST]   Generating null distributions from 2 permutations
                            using 1 thread...


    0% completed.
  100% completed.

[2024-03-02 01:05:56 EST]   Calculating P-values...
[2024-03-02 01:05:56 EST]   Collating results...
[2024-03-02 01:05:59 EST] Done!
2 modules in osa were preserved in zma:
NA, NA
   Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
1      5  0.00534 -0.621         0.1080   11.10     12.50   21.1
2      6  0.07230 -2.480        -0.0676   10.50     10.80   20.5
3      7  0.01870 -0.777        -0.0918   10.00      9.51   19.9
4      8  0.02070 -0.788        -0.1050    9.55      8.43   19.4
5      9  0.06560 -1.360        -0.1890    9.15      7.54   19.0
6     10  0.03530 -1.310        -0.1230    8.80      6.80   18.6
7     11  0.00722 -0.433        -0.0709    8.48      6.18   18.2
8     12  0.24400 -0.449         0.3850    8.19      5.65   17.8
9     13  0.04590 -1.130        -0.1740    7.92      5.29   17.5
10    14  0.04890 -1.140        -0.1780    7.68      5.00   17.2
11    15  0.25400 -0.442         0.3110    7.45      4.74   16.9
12    16  0.26300 -0.463         0.2150    7.24      4.51   16.6
13    17  0.02240 -0.739        -0.1300    7.04      4.30   16.3
14    18  0.02370 -0.760        -0.1380    6.85      4.12   16.0
15    19  0.02300 -0.792        -0.1280    6.68      3.95   15.8
16    20  0.02500 -0.819        -0.1280    6.51      3.79   15.6
No power reached R-squared cut-off, now choosing max R-squared based power
   Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
1      5 0.053700 -2.630        0.30600   11.90     16.50   22.4
2      6 0.017700 -1.330        0.25400   11.30     15.10   21.8
3      7 0.023200 -1.470        0.22400   10.80     13.90   21.2
4      8 0.005780 -0.636        0.15100   10.40     12.80   20.7
5      9 0.006220 -0.638        0.13800    9.98     11.80   20.2
6     10 0.007630 -0.691        0.11800    9.62     10.90   19.8
7     11 0.008810 -0.730        0.11400    9.30     10.20   19.3
8     12 0.002260  0.370        0.19400    9.00      9.47   19.0
9     13 0.004820 -0.614        0.08500    8.72      8.84   18.6
10    14 0.006750 -0.714        0.06110    8.47      8.28   18.3
11    15 0.001410  0.278        0.16100    8.23      7.77   18.0
12    16 0.000813  0.209        0.16400    8.00      7.30   17.7
13    17 0.000846  0.158       -0.00154    7.79      6.88   17.4
14    18 0.005320 -0.524       -0.01290    7.59      6.50   17.1
15    19 0.006440 -0.573       -0.02410    7.41      6.15   16.9
16    20 0.007590 -0.620       -0.03410    7.23      5.83   16.6
No power reached R-squared cut-off, now choosing max R-squared based power
   Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
1      5 0.012500 -0.655       -0.06640   12.30     15.20   21.9
2      6 0.039300 -1.430       -0.14300   11.00     13.20   20.4
3      7 0.000461 -0.120        0.02030    9.99     11.60   19.0
4      8 0.001340  0.257        0.17800    9.14     10.20   17.9
5      9 0.010800 -0.675       -0.06680    8.41      9.05   16.9
6     10 0.002830  0.270        0.09540    7.78      8.06   16.0
7     11 0.052300  1.580        0.25900    7.23      7.21   15.2
8     12 0.009940  0.761        0.27100    6.73      6.47   14.5
9     13 0.001370  0.236       -0.00272    6.29      5.83   13.9
10    14 0.000390  0.122       -0.01540    5.89      5.27   13.2
11    15 0.017200  0.585        0.07480    5.53      4.77   12.7
12    16 0.013800  0.508        0.06910    5.21      4.34   12.1
13    17 0.004920  0.393        0.19900    4.91      3.96   11.6
14    18 0.000553  0.128        0.11200    4.63      3.62   11.2
15    19 0.020800 -0.579       -0.11900    4.38      3.31   10.7
16    20 0.189000 -0.287        0.65200    4.14      3.10   10.3
No power reached R-squared cut-off, now choosing max R-squared based power
   Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
1      5 0.042000 -1.180        -0.2040   15.10     20.60   24.9
2      6 0.015800 -0.126         0.6970   13.60     18.60   23.4
3      7 0.024500 -0.909        -0.1420   12.40     16.90   22.1
4      8 0.025900 -0.899        -0.1370   11.30     15.40   20.9
5      9 0.011600 -0.567        -0.0690   10.50     14.00   19.9
6     10 0.008510 -0.509        -0.0515    9.71     12.90   18.9
7     11 0.010400 -0.527        -0.0564    9.04     11.80   18.1
8     12 0.005750 -0.537         0.0953    8.45     10.90   17.3
9     13 0.000810 -0.149         0.0368    7.92      9.99   16.5
10    14 0.000519 -0.120         0.0417    7.44      9.21   15.9
11    15 0.002240  0.326         0.2360    7.01      8.50   15.3
12    16 0.000815  0.189         0.2190    6.61      7.86   14.7
13    17 0.001540  0.265         0.2080    6.24      7.27   14.1
14    18 0.000705  0.173         0.1970    5.91      6.73   13.6
15    19 0.001480  0.181         0.0535    5.60      6.23   13.2
16    20 0.000709  0.121         0.0521    5.31      5.78   12.7
No power reached R-squared cut-off, now choosing max R-squared based power
   Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
1      5   0.0788 -0.225          0.274    9.01      9.20  17.30
2      6   0.0813 -0.238          0.238    7.98      8.19  15.70
3      7   0.1150 -0.272          0.448    7.18      7.43  14.50
4      8   0.1000 -0.285          0.374    6.54      6.83  13.50
5      9   0.0952 -0.275          0.376    6.01      6.18  12.60
6     10   0.1270 -0.270          0.351    5.57      5.61  12.00
7     11   0.1340 -0.293          0.372    5.20      5.11  11.50
8     12   0.1090 -0.276          0.340    4.87      4.67  11.00
9     13   0.1070 -0.255          0.392    4.59      4.29  10.60
10    14   0.1770 -0.285          0.425    4.34      3.95  10.20
11    15   0.2660 -0.325          0.542    4.12      3.64   9.88
12    16   0.0187 -0.713         -0.132    3.92      3.27   9.57
13    17   0.3350 -0.359          0.385    3.74      2.94   9.29
14    18   0.3150 -0.386          0.415    3.57      2.65   9.02
15    19   0.2970 -0.388          0.393    3.42      2.46   8.78
16    20   0.2540 -0.410          0.256    3.28      2.29   8.55
No power reached R-squared cut-off, now choosing max R-squared based power
   Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
1      5 0.051100 -0.2120        0.45900   12.70     15.10   23.2
2      6 0.010000 -0.6510       -0.07510   11.50     13.30   21.9
3      7 0.009570 -0.6000       -0.06850   10.60     11.90   20.7
4      8 0.000273 -0.1010       -0.01280    9.77     10.70   19.7
5      9 0.000223 -0.0938       -0.00614    9.10      9.72   18.8
6     10 0.001810 -0.4020        0.09960    8.52      8.76   18.0
7     11 0.003510 -0.5440        0.08990    8.03      7.93   17.3
8     12 0.004520 -0.6210        0.07440    7.59      7.22   16.6
9     13 0.002930  0.3120        0.01400    7.21      6.73   16.0
10    14 0.001980  0.2530        0.00897    6.87      6.30   15.4
11    15 0.001330 -0.3040       -0.00181    6.56      5.96   14.9
12    16 0.000502 -0.1820        0.00537    6.29      5.67   14.4
13    17 0.000976 -0.2510       -0.00053    6.04      5.30   14.0
14    18 0.032800 -1.0800       -0.15100    5.81      4.96   13.7
15    19 0.168000 -0.3710        0.52600    5.59      4.62   13.4
16    20 0.241000 -0.3990        0.62500    5.40      4.31   13.1
No power reached R-squared cut-off, now choosing max R-squared based power
Calculating adjacency matrix...
Calculating topological overlap matrix (TOM)...
..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 ...
 mergeCloseModules: less than two proper modules.
  ..color levels are blue, grey
  ..there is nothing to merge.
Calculating adjacency matrix...
Calculating topological overlap matrix (TOM)...
..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 ...
 mergeCloseModules: less than two proper modules.
  ..color levels are blue, grey
  ..there is nothing to merge.
Calculating adjacency matrix...
Calculating topological overlap matrix (TOM)...
..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 ...
 mergeCloseModules: less than two proper modules.
  ..color levels are blue, grey
  ..there is nothing to merge.
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  0.02190     19.0        0.20100   20.80     21.50  22.10
2      4  0.04550     30.1        0.28400   15.20     15.60  16.20
3      5  0.11000     53.3        0.21000   12.30     12.50  13.00
4      6  0.06200     57.9        0.12900   10.70     10.90  11.20
5      7  0.06170     97.3       -0.18800    9.94     10.00  10.30
6      8  0.02290     94.8       -0.24100    9.51      9.56   9.71
7      9  0.00508     73.3       -0.23900    9.28      9.31   9.41
8     10  0.01480   -201.0       -0.25300    9.15      9.17   9.24
9     11  0.02110   -388.0       -0.24300    9.09      9.09   9.14
10    12  0.02740   -715.0       -0.22900    9.05      9.05   9.08
11    13  0.15100  -2860.0        0.00526    9.03      9.03   9.05
12    14  0.16100  -4790.0        0.03130    9.02      9.02   9.03
13    15  0.16900  -7900.0        0.06080    9.01      9.01   9.02
14    16  0.18400 -13300.0        0.08190    9.00      9.00   9.01
15    17  0.12600 -19100.0        0.01680    9.00      9.00   9.01
16    18  0.12900 -31200.0        0.02000    9.00      9.00   9.00
17    19  0.14000 -52400.0        0.03260    9.00      9.00   9.00
18    20  0.14400 -87100.0        0.03750    9.00      9.00   9.00
No power reached R-squared cut-off, now choosing max R-squared based power
   Power SFT.R.sq    slope truncated.R.sq mean.k. median.k. max.k.
1      3  0.01550     14.8        -0.1650   21.00     21.30  22.80
2      4  0.07220     32.9         0.1410   15.30     15.50  16.50
3      5  0.11200     45.6         0.0304   12.30     12.50  13.20
4      6  0.01590    -29.6        -0.1050   10.80     10.90  11.40
5      7  0.00468     25.5        -0.2770    9.96     10.00  10.30
6      8  0.00971     54.0        -0.2730    9.52      9.56   9.77
7      9  0.04080   -188.0        -0.2230    9.29      9.31   9.45
8     10  0.08410   -442.0        -0.1190    9.16      9.17   9.26
9     11  0.11600   -781.0        -0.1200    9.09      9.09   9.15
10    12  0.22400  -1860.0         0.1150    9.05      9.05   9.09
11    13  0.29500  -3160.0         0.1070    9.03      9.03   9.05
12    14  0.31400  -5180.0         0.1370    9.02      9.02   9.03
13    15  0.14200  -6180.0        -0.0525    9.01      9.01   9.02
14    16  0.13800 -10100.0         0.0298    9.01      9.00   9.01
15    17  0.30700 -24200.0         0.2200    9.00      9.00   9.01
16    18  0.32200 -39100.0         0.2370    9.00      9.00   9.00
17    19  0.33500 -62800.0         0.2520    9.00      9.00   9.00
18    20  0.26000 -92600.0         0.1680    9.00      9.00   9.00
No power reached R-squared cut-off, now choosing max R-squared based power
   Power SFT.R.sq    slope truncated.R.sq mean.k. median.k. max.k.
1      3 1.10e-01     38.0        0.21000   21.10     21.50  22.90
2      4 6.62e-02     30.9        0.09390   15.40     15.60  16.70
3      5 5.66e-02     35.8        0.08640   12.40     12.50  13.30
4      6 1.30e-01     87.5        0.00830   10.80     10.90  11.40
5      7 1.09e-01    118.0       -0.00468    9.98     10.00  10.40
6      8 1.73e-01    190.0       -0.05570    9.54      9.57   9.78
7      9 2.73e-02    136.0       -0.21000    9.30      9.31   9.45
8     10 7.50e-03     99.9       -0.27500    9.16      9.17   9.26
9     11 4.59e-03    126.0       -0.27900    9.09      9.10   9.15
10    12 4.51e-05    -20.7       -0.24400    9.05      9.05   9.09
11    13 7.14e-03   -430.0       -0.17300    9.03      9.03   9.05
12    14 1.04e-02   -837.0       -0.16000    9.02      9.02   9.03
13    15 1.62e-02  -1940.0        0.03990    9.01      9.01   9.02
14    16 1.09e-01  -7020.0       -0.00229    9.01      9.01   9.01
15    17 1.40e-02  -4830.0       -0.10900    9.00      9.00   9.01
16    18 3.48e-03  -4310.0       -0.12100    9.00      9.00   9.00
17    19 5.66e-03  -8830.0       -0.11900    9.00      9.00   9.00
18    20 8.17e-03 -17000.0       -0.11600    9.00      9.00   9.00
No power reached R-squared cut-off, now choosing max R-squared based power
Calculating adjacency matrix...
Calculating topological overlap matrix (TOM)...
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
Detecting coexpression modules...
Calculating module eigengenes (MEs)...
Merging similar modules...
Calculating intramodular connectivity...
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ...working on run 1 ..
         mergeCloseModules: less than two proper modules.
          ..color levels are grey, turquoise
          ..there is nothing to merge.
 ...working on run 2 ..
         mergeCloseModules: less than two proper modules.
          ..color levels are grey, turquoise
          ..there is nothing to merge.
Enrichment analysis for module black...
Enrichment analysis for module black...
The correlation threshold that best fits the scale-free topology is 1
Could not obtain P-value for the Kolmogorov-Smirnov statistic.
The top number of edges that best fits the scale-free topology is 152
The top number of edges that best fits the scale-free topology is 152
The top number of edges that best fits the scale-free topology is 257
Could not obtain P-value for the Kolmogorov-Smirnov statistic.
Could not obtain P-value for the Kolmogorov-Smirnov statistic.
Could not obtain P-value for the Kolmogorov-Smirnov statistic.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 201 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 201 ]
> 
> proc.time()
   user  system elapsed 
126.476   4.029 155.106 

Example timings

BioNERO.Rcheck/BioNERO-Ex.timings

nameusersystemelapsed
PC_correction3.1260.1124.123
SFT_fit2.0640.1092.803
ZKfiltering0.2610.0090.338
check_SFT2.2440.2113.182
consensus_SFT_fit3.6960.1634.530
consensus_modules3.3200.1434.157
consensus_trait_cor3.4230.1084.396
cormat_to_edgelist0.1150.0220.165
detect_communities0.1810.0370.260
dfs2one0.0480.0060.064
enrichment_analysis000
exp2gcn1.2350.0721.690
exp2grn0.9490.0651.318
exp_genes2orthogroups0.0010.0000.001
exp_preprocess4.0350.1185.096
filt.se0.0120.0020.015
filter_by_variance0.6160.0170.847
gene_significance0.0430.0040.059
get_HK0.4740.0230.672
get_edge_list1.2530.0371.582
get_hubs_gcn1.2840.0391.588
get_hubs_grn0.9380.0491.180
get_neighbors1.3310.0391.612
grn_average_rank0.8340.0331.039
grn_combined0.8060.0340.981
grn_filter0.9130.0381.118
grn_infer0.7490.0360.913
is_singleton0.0910.0090.133
modPres_WGCNA0.0000.0010.000
modPres_netrep0.0000.0010.000
module_enrichment0.0000.0010.000
module_preservation0.0010.0010.000
module_stability41.324 0.35048.529
module_trait_cor1.2930.0221.495
net_stats0.0000.0000.001
og.zma.osa0.0740.0030.087
osa.se0.1180.0060.149
parse_orthofinder0.0330.0040.045
plot_PCA0.8000.0180.925
plot_dendro_and_colors3.2800.0653.812
plot_eigengene_network3.3100.0803.813
plot_expression_profile2.0280.0322.356
plot_gcn1.4490.0301.647
plot_gene_significance 8.976 0.25110.435
plot_grn1.4740.0331.782
plot_heatmap0.0000.0010.000
plot_module_trait_cor2.1620.0542.597
plot_ngenes_per_module2.0020.0802.448
plot_ppi0.9040.0151.053
q_normalize0.3340.0110.414
remove_nonexp0.2350.0090.302
replace_na0.2300.0080.267
zma.interpro0.0810.0040.100
zma.se0.1890.0080.240
zma.tfs0.0030.0030.011