Fabricio Almeida-Silva
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/BioNERO |
| git_branch: devel |
| git_last_commit: 20a3539 |
| git_last_commit_date: 2024-10-29 10:57:25 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 212/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNERO 1.15.0 (landing page) Fabricio Almeida-Silva
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BioNERO |
| Version: 1.15.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BioNERO_1.15.0.tar.gz |
| StartedAt: 2024-12-24 04:54:56 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 05:05:11 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 614.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioNERO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BioNERO_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BioNERO.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNERO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNERO’ version ‘1.15.0’
* 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 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 ...Warning: program compiled against libxml 212 using older 211
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 loading without being on the library search path ... 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 44.236 0.152 44.476
exp2gcn_blockwise 14.482 0.007 14.520
check_SFT 12.013 0.191 12.223
plot_gene_significance 6.068 0.035 6.119
* 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
‘/home/biocbuild/bbs-3.21-bioc/meat/BioNERO.Rcheck/00check.log’
for details.
BioNERO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BioNERO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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)
BioNERO.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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 0.02
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 208 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 208 ]
>
> proc.time()
user system elapsed
162.673 2.654 166.693
BioNERO.Rcheck/BioNERO-Ex.timings
| name | user | system | elapsed | |
| PC_correction | 2.225 | 0.052 | 2.282 | |
| SFT_fit | 2.196 | 0.056 | 2.264 | |
| ZKfiltering | 0.180 | 0.000 | 0.182 | |
| check_SFT | 12.013 | 0.191 | 12.223 | |
| consensus_SFT_fit | 3.718 | 0.005 | 3.728 | |
| consensus_modules | 4.043 | 0.012 | 4.064 | |
| consensus_trait_cor | 4.046 | 0.076 | 4.129 | |
| cor2adj | 0.024 | 0.000 | 0.024 | |
| cormat_to_edgelist | 0.389 | 0.004 | 0.394 | |
| detect_communities | 0.450 | 0.008 | 0.458 | |
| dfs2one | 0.028 | 0.000 | 0.028 | |
| enrichment_analysis | 0 | 0 | 0 | |
| exp2cor | 0.023 | 0.000 | 0.022 | |
| exp2gcn | 1.409 | 0.059 | 1.472 | |
| exp2gcn_blockwise | 14.482 | 0.007 | 14.520 | |
| exp2grn | 1.375 | 0.008 | 1.386 | |
| exp_genes2orthogroups | 0.001 | 0.000 | 0.000 | |
| exp_preprocess | 2.258 | 0.040 | 2.303 | |
| filt.se | 0.007 | 0.000 | 0.007 | |
| filter_by_variance | 0.373 | 0.000 | 0.374 | |
| gene_significance | 0.039 | 0.000 | 0.039 | |
| get_HK | 0.291 | 0.012 | 0.303 | |
| get_edge_list | 1.429 | 0.036 | 1.469 | |
| get_hubs_gcn | 1.428 | 0.000 | 1.432 | |
| get_hubs_grn | 1.369 | 0.000 | 1.372 | |
| get_neighbors | 1.496 | 0.000 | 1.499 | |
| grn_average_rank | 1.354 | 0.000 | 1.357 | |
| grn_combined | 1.294 | 0.008 | 1.304 | |
| grn_filter | 2.259 | 0.040 | 2.304 | |
| grn_infer | 1.244 | 0.000 | 1.247 | |
| is_singleton | 0.055 | 0.000 | 0.055 | |
| modPres_WGCNA | 0.001 | 0.000 | 0.001 | |
| modPres_netrep | 0 | 0 | 0 | |
| module_enrichment | 0.000 | 0.000 | 0.001 | |
| module_preservation | 0 | 0 | 0 | |
| module_stability | 44.236 | 0.152 | 44.476 | |
| module_trait_cor | 1.451 | 0.060 | 1.514 | |
| net_stats | 0 | 0 | 0 | |
| og.zma.osa | 0.043 | 0.000 | 0.044 | |
| osa.se | 0.064 | 0.004 | 0.068 | |
| parse_orthofinder | 0.019 | 0.000 | 0.021 | |
| plot_PCA | 0.423 | 0.004 | 0.428 | |
| plot_dendro_and_colors | 2.304 | 0.016 | 2.328 | |
| plot_eigengene_network | 2.638 | 0.000 | 2.644 | |
| plot_expression_profile | 1.051 | 0.004 | 1.057 | |
| plot_gcn | 1.523 | 0.008 | 1.537 | |
| plot_gene_significance | 6.068 | 0.035 | 6.119 | |
| plot_grn | 1.391 | 0.004 | 1.398 | |
| plot_heatmap | 0 | 0 | 0 | |
| plot_module_trait_cor | 1.948 | 0.003 | 1.957 | |
| plot_ngenes_per_module | 1.659 | 0.004 | 1.666 | |
| plot_ppi | 1.040 | 0.000 | 1.042 | |
| q_normalize | 0.242 | 0.004 | 0.247 | |
| remove_nonexp | 0.142 | 0.000 | 0.143 | |
| replace_na | 0.133 | 0.004 | 0.138 | |
| zma.interpro | 0.046 | 0.000 | 0.047 | |
| zma.se | 0.105 | 0.004 | 0.109 | |
| zma.tfs | 0.002 | 0.000 | 0.003 | |