Back to Multiple platform build/check report for BioC 3.20:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 210/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNERO 1.13.0  (landing page)
Fabricio Almeida-Silva
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/BioNERO
git_branch: devel
git_last_commit: 27adc4d
git_last_commit_date: 2024-04-30 11:32:29 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BioNERO on palomino4

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: 1.13.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNERO.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BioNERO_1.13.0.tar.gz
StartedAt: 2024-06-10 00:22:24 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 00:31:14 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 529.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNERO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNERO.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BioNERO_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BioNERO.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BioNERO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNERO' version '1.13.0'
* 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 code 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 ... NOTE
checkRd: (-1) SFT_fit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SFT_fit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exp2grn.Rd:28: Lost braces
    28 | say (ij), is removed if its weight is below min{(ik),(jk)} - eps. Default: 0.}
       |                                                ^
checkRd: (-1) grn_combined.Rd:27: Lost braces
    27 | is removed if its weight is below min{(ik),(jk)} - eps. Default: 0.1.}
       |                                      ^
checkRd: (-1) grn_infer.Rd:39: Lost braces
    39 | is removed if its weight is below min{(ik),(jk)} - eps. Default: 0.1.}
       |                                      ^
* 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  38.19   0.08   38.61
exp2gcn_blockwise 12.37   0.01   12.39
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/BioNERO.Rcheck/00check.log'
for details.


Installation output

BioNERO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BioNERO
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.
None of the modules in cohort1 were preserved in cohort2.
   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
Calculating number of PCs to be removed...
Number of PCs estimated to be removed: 5
Removing PCs that contribute to noise...
Number of removed samples: 1
Number of removed samples: 1
converting counts to integer mode
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
..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 150
The top number of edges that best fits the scale-free topology is 150
The top number of edges that best fits the scale-free topology is 259
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 208 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 208 ]
> 
> proc.time()
   user  system elapsed 
 129.26    3.64  132.98 

Example timings

BioNERO.Rcheck/BioNERO-Ex.timings

nameusersystemelapsed
PC_correction1.070.031.09
SFT_fit1.790.061.86
ZKfiltering0.190.020.20
check_SFT1.900.071.98
consensus_SFT_fit2.780.072.85
consensus_modules2.380.002.39
consensus_trait_cor2.280.042.33
cor2adj000
cormat_to_edgelist0.050.030.08
detect_communities0.140.050.19
dfs2one0.020.000.04
enrichment_analysis000
exp2cor000
exp2gcn0.860.050.91
exp2gcn_blockwise12.37 0.0112.39
exp2grn0.580.020.60
exp_genes2orthogroups000
exp_preprocess1.620.091.71
filt.se0.020.000.02
filter_by_variance0.310.050.36
gene_significance0.030.020.05
get_HK0.240.030.26
get_edge_list0.900.000.91
get_hubs_gcn0.960.031.00
get_hubs_grn0.510.060.58
get_neighbors1.140.051.19
grn_average_rank0.530.060.59
grn_combined0.710.030.74
grn_filter0.590.050.64
grn_infer1.170.031.20
is_singleton0.030.010.05
modPres_WGCNA000
modPres_netrep000
module_enrichment000
module_preservation000
module_stability38.19 0.0838.61
module_trait_cor0.970.031.00
net_stats000
og.zma.osa0.060.000.06
osa.se0.100.020.11
parse_orthofinder0.040.000.06
plot_PCA0.380.000.38
plot_dendro_and_colors1.610.121.73
plot_eigengene_network2.330.862.84
plot_expression_profile0.980.101.08
plot_gcn1.140.001.14
plot_gene_significance4.340.014.36
plot_grn0.480.050.53
plot_heatmap000
plot_module_trait_cor1.320.061.37
plot_ngenes_per_module1.220.001.22
plot_ppi0.50.00.5
q_normalize0.270.030.30
remove_nonexp0.180.000.19
replace_na0.190.000.19
zma.interpro0.050.000.06
zma.se0.120.000.12
zma.tfs000