Back to Multiple platform build/check report for BioC 3.17:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2023-03-23 11:06:59 -0400 (Thu, 23 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4536
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4298
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4290
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

CHECK results for netZooR on merida1


To the developers/maintainers of the netZooR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netZooR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1359/2189HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netZooR 1.3.14  (landing page)
Marouen Ben Guebila
Snapshot Date: 2023-03-22 14:00:17 -0400 (Wed, 22 Mar 2023)
git_url: https://git.bioconductor.org/packages/netZooR
git_branch: devel
git_last_commit: 45dbef7
git_last_commit_date: 2023-03-21 15:22:42 -0400 (Tue, 21 Mar 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    TIMEOUT  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    TIMEOUT    OK  

Summary

Package: netZooR
Version: 1.3.14
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netZooR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netZooR_1.3.14.tar.gz
StartedAt: 2023-03-23 04:59:50 -0400 (Thu, 23 Mar 2023)
EndedAt: 2023-03-23 05:39:50 -0400 (Thu, 23 Mar 2023)
EllapsedTime: 2400.3 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: netZooR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netZooR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netZooR_1.3.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/netZooR.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.3.14’
* 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 ‘netZooR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   2.8Mb
* 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 ... NOTE
Package in Depends field not imported from: ‘matrixcalc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
estimatePenaltyParameters: no visible global function definition for
  ‘matrix.trace’
runEgret: no visible binding for global variable ‘NA12878’
show,panda: no visible global function definition for ‘print.panda’
Undefined global functions or variables:
  NA12878 matrix.trace print.panda
* 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 ... ERROR
Running examples in ‘netZooR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spider
> ### Title: Seeding PANDA Interactions to Derive Epigenetic Regulation
> ### Aliases: spider
> ### Keywords: keywords
> 
> ### ** Examples
> 
> data(pandaToyData)
> spiderRes <- spider(pandaToyData$motif, pandaToyData$epifilter,
+            pandaToyData$expression,pandaToyData$ppi,hamming=.1,progress=TRUE)
[1] "Initializing and validating"
Error in Ops.data.frame(epifilter[, c(1, 2)], motif[, c(1, 2)]) : 
  ‘!=’ only defined for equally-sized data frames
Calls: spider -> Ops.data.frame
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

netZooR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘netZooR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (netZooR)

Tests output

netZooR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(netZooR)
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: reticulate
Loading required package: pandaR
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:igraph':

    normalize, path, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: yarn
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: matrixcalc

Attaching package: 'matrixcalc'

The following object is masked from 'package:igraph':

    %s%



> 
> #download test data
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/ppi_medium.txt','testthat/ppi_medium.txt')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/ppi_medium.txt'
Content type 'text/plain' length 3674311 bytes (3.5 MB)
==================================================
downloaded 3730 bytes

Warning message:
In download.file("https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/ppi_medium.txt",  :
  downloaded length 0 != reported length 0
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData','testthat/testDataset.RData')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData'
Content type 'binary/octet-stream' length 15200389 bytes (14.5 MB)
==================================================
downloaded 3730 bytes

Warning message:
In download.file("https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData",  :
  downloaded length 0 != reported length 0
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_test_get_shrunken_covariance.csv','testthat/dragon_test_get_shrunken_covariance.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_test_get_shrunken_covariance.csv'
Content type 'text/csv' length 114 bytes
==================================================
downloaded 3730 bytes

Warning message:
In download.file("https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_test_get_shrunken_covariance.csv",  :
  downloaded length 0 != reported length 0
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer1.csv','testthat/dragon_layer1.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer1.csv'
Content type 'text/csv' length 2549985 bytes (2.4 MB)
==================================================
downloaded 3730 bytes

Warning message:
In download.file("https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer1.csv",  :
  downloaded length 0 != reported length 0
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer2.csv','testthat/dragon_layer2.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer2.csv'
Content type 'text/csv' length 12749793 bytes (12.2 MB)
==================================================
downloaded 3730 bytes

Warning message:
In download.file("https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer2.csv",  :
  downloaded length 0 != reported length 0
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_cov.csv','testthat/dragon_python_cov.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_cov.csv'
Content type 'text/csv' length 9179450 bytes (8.8 MB)
==================================================
downloaded 3730 bytes

Warning message:
In download.file("https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_cov.csv",  :
  downloaded length 0 != reported length 0
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_prec.csv','testthat/dragon_python_prec.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_prec.csv'
Content type 'text/csv' length 9179450 bytes (8.8 MB)
==================================================
downloaded 3730 bytes

Warning message:
In download.file("https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_prec.csv",  :
  downloaded length 0 != reported length 0
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_parcor.csv','testthat/dragon_python_parcor.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_parcor.csv'
Content type 'text/csv' length 9179576 bytes (8.8 MB)
==================================================
downloaded 3730 bytes

Warning message:
In download.file("https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_parcor.csv",  :
  downloaded length 0 != reported length 0
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/risk_grid_netzoopy.csv','testthat/risk_grid_netzoopy.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/risk_grid_netzoopy.csv'
Content type 'text/csv' length 255025 bytes (249 KB)
==================================================
downloaded 3730 bytes

Warning message:
In download.file("https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/risk_grid_netzoopy.csv",  :
  downloaded length 0 != reported length 0
> 
> test_check("netZooR")
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.0236842105263163"
[1] "Q = 0.0263157894736842"
[1] "Q = 0.0263157894736842"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 100 communities"
[1] 1
[1] 2
[1] 3
[1] "Merging 2 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
[1] "modularity of projected graph 0.144628099173554"
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0"
[1] "Q = 0"
[1] "Q = 0.15702479338843"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] 0.1983471 0.2314050 0.2314050
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "Q = 0.140495867768595"
[1] "Q = 0.140495867768595"
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0.525346928655047"
[1] "Q = 0.52666696475026"
[1] "Q = 0.52666696475026"
[1] 0.79 0.00
final  value 375.120000 
converged
[1] 0.31 0.29
final  value 36.897493 
converged
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   355  100   355    0     0   1576      0 --:--:-- --:--:-- --:--:--  1577
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   569  100   569    0     0   3517      0 --:--:-- --:--:-- --:--:--  3534
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   840  100   840    0     0   3958      0 --:--:-- --:--:-- --:--:--  3962
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  3242    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  3242  100  3242    0     0  16071      0 --:--:-- --:--:-- --:--:-- 16049
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   410  100   410    0     0   2343      0 --:--:-- --:--:-- --:--:--  2356
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   222  100   222    0     0   1306      0 --:--:-- --:--:-- --:--:--  1313
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1438k  100 1438k    0     0  3409k      0 --:--:-- --:--:-- --:--:-- 3416k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   578  100   578    0     0   2592      0 --:--:-- --:--:-- --:--:--  2591
[1] "Initializing and validating"
[1] "Verified sufficient samples"
[1] "Normalizing networks..."
[1] "Learning Network..."
[1] "Using tanimoto similarity"
[1] "Initializing and validating"
[1] "Verified sufficient samples"
[1] "Normalizing networks..."
[1] "Learning Network..."
[1] "Using tanimoto similarity"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 27822  100 27822    0     0   133k      0 --:--:-- --:--:-- --:--:--  133k
Loading expression data ...
  Elapsed time: 0.01 sec.
No PPI data given: ppi matrix will be an identity matrix of size 0
Calculating coexpression network ...
  Elapsed time: 0.01 sec.
Returning the correlation matrix of expression data in <Panda_obj>.correlation_matrix
union None ./expr4_200_L.txt None False False True
Loading input data ...
  Elapsed time: 0.00 sec.
Number of total samples: 11
Number of computed samples: 1
Number of parallel cores: 1
Running LIONESS for sample 1:
Computing coexpression network:
  Elapsed time: 0.01 sec.
Normalizing networks:
  Elapsed time: 0.00 sec.
Inferring LIONESS network:
  Elapsed time: 0.00 sec.
Saving LIONESS network 0 (1) to lioness_output using no format:
lioness_output/lioness.1.0.no
Unknown format no! Use npy format instead.
  Elapsed time: 0.00 sec.
Trying to save lioness output. Format lioness_output/lioness.no not recognised
/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py:2853: RuntimeWarning: invalid value encountered in divide
  c /= stddev[:, None]
/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py:2854: RuntimeWarning: invalid value encountered in divide
  c /= stddev[None, :]
Loading motif data ...
  Elapsed time: 0.01 sec.
Loading expression data ...
  Elapsed time: 0.01 sec.
No PPI data given: ppi matrix will be an identity matrix of size 5
Calculating coexpression network ...
  Elapsed time: 0.04 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
union /Library/Frameworks/R.framework/Versions/4.3/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt None False False True
Normalizing networks ...
  Elapsed time: 0.04 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.3008717441926666
step: 1, hamming: 0.3257784023939347
step: 2, hamming: 0.3604654799329852
step: 3, hamming: 0.36058526850894795
step: 4, hamming: 0.34662408235125536
step: 5, hamming: 0.32456269443005176
step: 6, hamming: 0.29894345984218634
step: 7, hamming: 0.27060190935086675
step: 8, hamming: 0.24146225569326277
step: 9, hamming: 0.21301541796450388
step: 10, hamming: 0.18618747428128885
step: 11, hamming: 0.16147381450104817
step: 12, hamming: 0.13913324895882395
step: 13, hamming: 0.11926159237252454
step: 14, hamming: 0.1018524648128547
step: 15, hamming: 0.08669455519421958
step: 16, hamming: 0.07353017763220204
step: 17, hamming: 0.062150004228733687
step: 18, hamming: 0.05239618178480356
step: 19, hamming: 0.0440948747820607
step: 20, hamming: 0.03701196105540126
step: 21, hamming: 0.030994230611375673
step: 22, hamming: 0.02590051566365632
step: 23, hamming: 0.021602975736465965
step: 24, hamming: 0.017987639137724543
step: 25, hamming: 0.014954147174028647
step: 26, hamming: 0.012414749356075686
step: 27, hamming: 0.010293476645032556
step: 28, hamming: 0.008524772832534512
step: 29, hamming: 0.00705253606533178
step: 30, hamming: 0.005828962967549211
step: 31, hamming: 0.004813469251228145
step: 32, hamming: 0.003971733841541242
step: 33, hamming: 0.003274823735478386
step: 34, hamming: 0.00269842184221962
step: 35, hamming: 0.0022221411979145727
step: 36, hamming: 0.001828929075705442
step: 37, hamming: 0.0015045517890994032
step: 38, hamming: 0.0012371486338298722
step: 39, hamming: 0.0010168547681780843
step: 40, hamming: 0.0008354772054776637
Running panda took: 2.10 seconds!
Loading input data ...
  Elapsed time: 0.00 sec.
Number of total samples: 11
Number of computed samples: 1
Number of parallel cores: 1
Running LIONESS for sample 1:
Computing coexpression network:
  Elapsed time: 0.02 sec.
Normalizing networks:
  Elapsed time: 0.04 sec.
Inferring LIONESS network:
step: 0, hamming: 0.3015932422799913
step: 1, hamming: 0.3267447823984008
step: 2, hamming: 0.3610924818697011
step: 3, hamming: 0.3608089428450734
step: 4, hamming: 0.34665241776678835
step: 5, hamming: 0.3245939713292131
step: 6, hamming: 0.29896550661380406
step: 7, hamming: 0.2706205820410223
step: 8, hamming: 0.2414832727987967
step: 9, hamming: 0.2130402835155566
step: 10, hamming: 0.18620484129483578
step: 11, hamming: 0.16148366668825
step: 12, hamming: 0.1391392577665088
step: 13, hamming: 0.11927055262102428
step: 14, hamming: 0.10186083999388676
step: 15, hamming: 0.08670615581741939
step: 16, hamming: 0.07353988598228628
step: 17, hamming: 0.062158113565121506
step: 18, hamming: 0.052413728098102366
step: 19, hamming: 0.04410977556767985
step: 20, hamming: 0.03702457033326187
step: 21, hamming: 0.0310050033110051
step: 22, hamming: 0.025909572963571107
step: 23, hamming: 0.021610559908641462
step: 24, hamming: 0.017993951127132292
step: 25, hamming: 0.014959350583484257
step: 26, hamming: 0.01241903609149709
step: 27, hamming: 0.010296989659986242
step: 28, hamming: 0.008527684145048573
step: 29, hamming: 0.007054962882501563
step: 30, hamming: 0.005830983737417279
step: 31, hamming: 0.004815151202585311
step: 32, hamming: 0.003973130484197758
step: 33, hamming: 0.003275982320392084
step: 34, hamming: 0.0026993820286106336
step: 35, hamming: 0.002222936231546736
step: 36, hamming: 0.0018295867892866302
step: 37, hamming: 0.0015050947585654752
step: 38, hamming: 0.0012375965038720828
step: 39, hamming: 0.0010172239699260297
step: 40, hamming: 0.0008357813833839598
  Elapsed time: 1.79 sec.
Saving LIONESS network 0 (1) to lioness_output using no format:
lioness_output/lioness.1.0.no
Unknown format no! Use npy format instead.
  Elapsed time: 0.00 sec.
Trying to save lioness output. Format lioness_output/lioness.no not recognised
Loading motif data ...
  Elapsed time: 0.01 sec.
Loading expression data ...
  Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
  Elapsed time: 0.18 sec.
Calculating coexpression network ...
  Elapsed time: 0.02 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.30 sec.
union /Library/Frameworks/R.framework/Versions/4.3/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False True
Normalizing networks ...
  Elapsed time: 1.98 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.98 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.08748661874955622
step: 1, hamming: 0.06888714365861337
step: 2, hamming: 0.062114312778413824
step: 3, hamming: 0.05713353090446696
step: 4, hamming: 0.05304016922455829
step: 5, hamming: 0.04910113802289488
step: 6, hamming: 0.045074438192725504
step: 7, hamming: 0.04095526634659025
step: 8, hamming: 0.036830333937534133
step: 9, hamming: 0.03280131999197774
step: 10, hamming: 0.028958002291888482
step: 11, hamming: 0.02536565276187836
step: 12, hamming: 0.022066636023677578
step: 13, hamming: 0.01907883671127774
step: 14, hamming: 0.01640531302887969
step: 15, hamming: 0.014037779400693121
step: 16, hamming: 0.011959828418380612
step: 17, hamming: 0.010150090707741312
step: 18, hamming: 0.008584499851559678
step: 19, hamming: 0.0072380075895177075
step: 20, hamming: 0.0060858622486750545
step: 21, hamming: 0.005104411138700387
step: 22, hamming: 0.004271661591718607
step: 23, hamming: 0.0035675611746851287
step: 24, hamming: 0.002974084885079093
step: 25, hamming: 0.0024752438901140678
step: 26, hamming: 0.002056989100113544
step: 27, hamming: 0.0017070859535523305
step: 28, hamming: 0.0014149533300699608
step: 29, hamming: 0.001171496386209499
step: 30, hamming: 0.0009689369122934186
Running panda took: 78.41 seconds!
Loading input data ...
  Elapsed time: 0.00 sec.
Number of total samples: 11
Number of computed samples: 1
Number of parallel cores: 1
Running LIONESS for sample 1:
Computing coexpression network:
  Elapsed time: 0.03 sec.
Normalizing networks:
  Elapsed time: 0.03 sec.
Inferring LIONESS network:
step: 0, hamming: 0.08748185731756368
step: 1, hamming: 0.06891282897076392
step: 2, hamming: 0.062130587348151134
step: 3, hamming: 0.05714118386838519
step: 4, hamming: 0.05304529446377499
step: 5, hamming: 0.04910525549313265
step: 6, hamming: 0.045077507937550505
step: 7, hamming: 0.04095716825335454
step: 8, hamming: 0.036831755781812706
step: 9, hamming: 0.032802826977823545
step: 10, hamming: 0.02895992049443768
step: 11, hamming: 0.025367894743653203
step: 12, hamming: 0.022069009727623188
step: 13, hamming: 0.01908131820381921
step: 14, hamming: 0.016407788201894237
step: 15, hamming: 0.014040090736288887
step: 16, hamming: 0.011961875397219704
step: 17, hamming: 0.010151865216875243
step: 18, hamming: 0.008586011382256616
step: 19, hamming: 0.0072392787516997
step: 20, hamming: 0.006086920160262562
step: 21, hamming: 0.005105283470150479
step: 22, hamming: 0.004272377006570677
step: 23, hamming: 0.0035681447767932513
step: 24, hamming: 0.0029745593507951584
step: 25, hamming: 0.0024756282596510126
step: 26, hamming: 0.002057299996352307
step: 27, hamming: 0.001707337334790989
step: 28, hamming: 0.0014151565613914295
step: 29, hamming: 0.0011716607762849128
step: 30, hamming: 0.0009690701447933819
  Elapsed time: 79.32 sec.
Saving LIONESS network 0 (1) to lioness_output using no format:
lioness_output/lioness.1.0.no
Unknown format no! Use npy format instead.
  Elapsed time: 0.33 sec.
Trying to save lioness output. Format lioness_output/lioness.no not recognised
Loading motif data ...
  Elapsed time: 0.01 sec.
Loading expression data ...
  Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
  Elapsed time: 0.20 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.24 sec.
intersection /Library/Frameworks/R.framework/Versions/4.3/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False True
Normalizing networks ...
  Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.6788049340248108
step: 1, hamming: 0.4237635135650635
step: 2, hamming: 0.37942326068878174
step: 3, hamming: 0.3818596303462982
step: 4, hamming: 0.38526612520217896
step: 5, hamming: 0.3832989037036896
step: 6, hamming: 0.3691577613353729
step: 7, hamming: 0.34574782848358154
step: 8, hamming: 0.3152081370353699
step: 9, hamming: 0.2818053960800171
step: 10, hamming: 0.24849657714366913
step: 11, hamming: 0.21666744351387024
step: 12, hamming: 0.18729540705680847
step: 13, hamming: 0.16079428791999817
step: 14, hamming: 0.13726867735385895
step: 15, hamming: 0.11666568368673325
step: 16, hamming: 0.09877120703458786
step: 17, hamming: 0.08336561173200607
step: 18, hamming: 0.07016084343194962
step: 19, hamming: 0.0588911771774292
step: 20, hamming: 0.04931586608290672
step: 21, hamming: 0.04121115431189537
step: 22, hamming: 0.03437766805291176
step: 23, hamming: 0.028631485998630524
step: 24, hamming: 0.023808922618627548
step: 25, hamming: 0.01977088302373886
step: 26, hamming: 0.01639675535261631
step: 27, hamming: 0.013582734391093254
step: 28, hamming: 0.01123976893723011
step: 29, hamming: 0.009291954338550568
step: 30, hamming: 0.007674971595406532
step: 31, hamming: 0.006334253121167421
step: 32, hamming: 0.005223968531936407
step: 33, hamming: 0.004305415321141481
step: 34, hamming: 0.0035461809020489454
step: 35, hamming: 0.0029191956855356693
step: 36, hamming: 0.002401870209723711
step: 37, hamming: 0.001975312363356352
step: 38, hamming: 0.0016238124808296561
step: 39, hamming: 0.0013343493919819593
step: 40, hamming: 0.0010961262742057443
step: 41, hamming: 0.0009001437574625015
Running panda took: 0.11 seconds!
Loading input data ...
  Elapsed time: 0.00 sec.
Number of total samples: 11
Number of computed samples: 1
Number of parallel cores: 1
Running LIONESS for sample 1:
Computing coexpression network:
  Elapsed time: 0.00 sec.
Normalizing networks:
  Elapsed time: 0.00 sec.
Inferring LIONESS network:
step: 0, hamming: 0.6829624230448785
step: 1, hamming: 0.43097387197180576
step: 2, hamming: 0.3855310429319242
step: 3, hamming: 0.38637191135046167
step: 4, hamming: 0.3900182078494267
step: 5, hamming: 0.38601887026130727
step: 6, hamming: 0.37083628475255115
step: 7, hamming: 0.3469023786365537
step: 8, hamming: 0.31596767309078616
step: 9, hamming: 0.28236776010976555
step: 10, hamming: 0.24886232553379886
step: 11, hamming: 0.21693733215599034
step: 12, hamming: 0.18751291619111748
step: 13, hamming: 0.16097018063912635
step: 14, hamming: 0.13743834641405683
step: 15, hamming: 0.11682177613537481
step: 16, hamming: 0.09896023237174005
step: 17, hamming: 0.08353838988773093
step: 18, hamming: 0.0703146042061358
step: 19, hamming: 0.059031076247230585
step: 20, hamming: 0.04944784921567592
step: 21, hamming: 0.041332669767071145
step: 22, hamming: 0.03448368506030259
step: 23, hamming: 0.02872038151655497
step: 24, hamming: 0.023883273913207863
step: 25, hamming: 0.01983295531443069
step: 26, hamming: 0.01644851635117843
step: 27, hamming: 0.0136257745199236
step: 28, hamming: 0.011275501538387826
step: 29, hamming: 0.009321611163628719
step: 30, hamming: 0.007699522580749507
step: 31, hamming: 0.006354588057457078
step: 32, hamming: 0.005240726415107055
step: 33, hamming: 0.004319224518865088
step: 34, hamming: 0.0035575835571617143
step: 35, hamming: 0.0029286096691906534
step: 36, hamming: 0.002409612616772203
step: 37, hamming: 0.0019816919683905343
step: 38, hamming: 0.0016290847449608212
step: 39, hamming: 0.0013387267257547728
step: 40, hamming: 0.001099725068233485
step: 41, hamming: 0.0009031296566194027
  Elapsed time: 0.10 sec.
Saving LIONESS network 0 (1) to lioness_output using no format:
lioness_output/lioness.1.0.no
Unknown format no! Use npy format instead.
  Elapsed time: 0.00 sec.
Trying to save lioness output. Format lioness_output/lioness.no not recognised
Loading motif data ...
  Elapsed time: 0.01 sec.
Loading expression data ...
  Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
  Elapsed time: 0.22 sec.
Calculating coexpression network ...
  Elapsed time: 0.01 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.23 sec.
legacy /Library/Frameworks/R.framework/Versions/4.3/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False True
Normalizing networks ...
  Elapsed time: 0.01 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.5867745269558597
step: 1, hamming: 0.47709480696171536
step: 2, hamming: 0.46956168666614617
step: 3, hamming: 0.45425003629838684
step: 4, hamming: 0.4187427725151872
step: 5, hamming: 0.36797241244238355
step: 6, hamming: 0.31337190961143313
step: 7, hamming: 0.26403861746419255
step: 8, hamming: 0.22399992327898238
step: 9, hamming: 0.19253176059893798
step: 10, hamming: 0.1676553667649102
step: 11, hamming: 0.14730006142326466
step: 12, hamming: 0.12982159089839332
step: 13, hamming: 0.11459157116297604
step: 14, hamming: 0.10108821391424126
step: 15, hamming: 0.08890364507467007
step: 16, hamming: 0.07787244456478047
step: 17, hamming: 0.06785464923123904
step: 18, hamming: 0.05878796471238135
step: 19, hamming: 0.05062155744809769
step: 20, hamming: 0.04333239380925902
step: 21, hamming: 0.0368925749401605
step: 22, hamming: 0.031262060121216705
step: 23, hamming: 0.026384280403921757
step: 24, hamming: 0.022190961740915567
step: 25, hamming: 0.018609229885172118
step: 26, hamming: 0.015566652188260106
step: 27, hamming: 0.01299328331205642
step: 28, hamming: 0.010824919177296204
step: 29, hamming: 0.009003507268894189
step: 30, hamming: 0.007477552910889814
step: 31, hamming: 0.0062020628941105
step: 32, hamming: 0.005138069423501646
step: 33, hamming: 0.004252085993537942
step: 34, hamming: 0.0035154788596479716
step: 35, hamming: 0.0029039267439058773
step: 36, hamming: 0.0023968521367998406
step: 37, hamming: 0.0019768786344578015
step: 38, hamming: 0.0016294013136896712
step: 39, hamming: 0.0013421799963357374
step: 40, hamming: 0.001104973847058481
step: 41, hamming: 0.0009092279973180526
Running panda took: 0.41 seconds!
Loading input data ...
  Elapsed time: 0.00 sec.
Number of total samples: 11
Number of computed samples: 1
Number of parallel cores: 1
Running LIONESS for sample 1:
Computing coexpression network:
  Elapsed time: 0.01 sec.
Normalizing networks:
  Elapsed time: 0.00 sec.
Inferring LIONESS network:
step: 0, hamming: 0.5875614098660666
step: 1, hamming: 0.4829466848764663
step: 2, hamming: 0.48105790891058364
step: 3, hamming: 0.46847113464020446
step: 4, hamming: 0.4337012115522554
step: 5, hamming: 0.38094873330102347
step: 6, hamming: 0.32310742082399213
step: 7, hamming: 0.27060297935454153
step: 8, hamming: 0.2287122360281675
step: 9, hamming: 0.19638081399100335
step: 10, hamming: 0.17127585718635555
step: 11, hamming: 0.15034152043301924
step: 12, hamming: 0.13231054786684657
step: 13, hamming: 0.11649711485539004
step: 14, hamming: 0.10235630925410291
step: 15, hamming: 0.08963435266941025
step: 16, hamming: 0.07811460526211583
step: 17, hamming: 0.06770343603846225
step: 18, hamming: 0.05834298311519194
step: 19, hamming: 0.04999398523930743
step: 20, hamming: 0.04261616820807744
step: 21, hamming: 0.036160346966779874
step: 22, hamming: 0.030559142027366412
step: 23, hamming: 0.025737009029274747
step: 24, hamming: 0.021610772222598034
step: 25, hamming: 0.018099099845240624
step: 26, hamming: 0.015123911629228078
step: 27, hamming: 0.01261301971521905
step: 28, hamming: 0.010500738712116995
step: 29, hamming: 0.008728774744404802
step: 30, hamming: 0.007245746309115978
step: 31, hamming: 0.006007158777935765
step: 32, hamming: 0.00497464716377701
step: 33, hamming: 0.004115358386599999
step: 34, hamming: 0.003401306327536735
step: 35, hamming: 0.0028087491721761736
step: 36, hamming: 0.0023176215646632716
step: 37, hamming: 0.0019110115327221312
step: 38, hamming: 0.0015747162820157871
step: 39, hamming: 0.0012968334760169572
step: 40, hamming: 0.001067413379763634
step: 41, hamming: 0.0008781471581459415
  Elapsed time: 0.35 sec.
Saving LIONESS network 0 (1) to lioness_output using no format:
lioness_output/lioness.1.0.no
Unknown format no! Use npy format instead.
  Elapsed time: 0.00 sec.
Trying to save lioness output. Format lioness_output/lioness.no not recognised
Loading motif data ...
  Elapsed time: 0.00 sec.
Loading expression data ...
  Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
  Elapsed time: 0.19 sec.
Remove expression not in motif:
   166 rows removed from the initial 200
Remove motif not in expression data:
   467 rows removed from the initial 506
Remove ppi not in motif:
   100017 rows removed from the initial 100019
new case
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.00 sec.
legacy /Library/Frameworks/R.framework/Versions/4.3/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False True True
Normalizing networks ...
  Elapsed time: 0.00 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.6201117836163109
step: 1, hamming: 0.48938385169250487
step: 2, hamming: 0.49937220814370314
step: 3, hamming: 0.5234998024292964
step: 4, hamming: 0.5316279091580729
step: 5, hamming: 0.5196461826284898
step: 6, hamming: 0.49096615680840516
step: 7, hamming: 0.4513686776299505
step: 8, hamming: 0.40818522332151064
step: 9, hamming: 0.363060630725845
step: 10, hamming: 0.3189123247409479
step: 11, hamming: 0.2773389585437183
step: 12, hamming: 0.23925292481822674
step: 13, hamming: 0.20518316158337407
step: 14, hamming: 0.17501658473943316
step: 15, hamming: 0.1485428864884021
step: 16, hamming: 0.12553582999076404
step: 17, hamming: 0.10573284427875863
step: 18, hamming: 0.08878386418920353
step: 19, hamming: 0.07436882705115157
step: 20, hamming: 0.062172412390917454
step: 21, hamming: 0.051880715413709574
step: 22, hamming: 0.04322032231952043
step: 23, hamming: 0.03594946787636906
step: 24, hamming: 0.029859895475909407
step: 25, hamming: 0.024770938396293178
step: 26, hamming: 0.020525756048994252
step: 27, hamming: 0.01699078758843492
step: 28, hamming: 0.014051171275167217
step: 29, hamming: 0.011609873894851016
step: 30, hamming: 0.009584973156032735
step: 31, hamming: 0.007907374279360021
step: 32, hamming: 0.0065189664409571035
step: 33, hamming: 0.005370999156869475
step: 34, hamming: 0.004422666090211273
step: 35, hamming: 0.0036398792478184202
step: 36, hamming: 0.0029942146499030097
step: 37, hamming: 0.002462010284380638
step: 38, hamming: 0.0020235978467206435
step: 39, hamming: 0.0016626509987884349
step: 40, hamming: 0.001365634387671263
step: 41, hamming: 0.0011213392761822362
step: 42, hamming: 0.0009204932425645571
Running panda took: 0.08 seconds!
Loading input data ...
  Elapsed time: 0.00 sec.
Number of total samples: 11
Number of computed samples: 1
Number of parallel cores: 1
Running LIONESS for sample 1:
Computing coexpression network:
  Elapsed time: 0.00 sec.
Normalizing networks:
  Elapsed time: 0.00 sec.
Inferring LIONESS network:
step: 0, hamming: 0.626766406356015
step: 1, hamming: 0.49929052211545427
step: 2, hamming: 0.5091133020260827
step: 3, hamming: 0.5347173973757746
step: 4, hamming: 0.5397805120478006
step: 5, hamming: 0.5249527732389625
step: 6, hamming: 0.4945006816241802
step: 7, hamming: 0.4536157699252673
step: 8, hamming: 0.40948805442896147
step: 9, hamming: 0.3643147759446061
step: 10, hamming: 0.3202827156746967
step: 11, hamming: 0.27889575055839505
step: 12, hamming: 0.240869786159727
step: 13, hamming: 0.20658305585147543
step: 14, hamming: 0.17608500470506333
step: 15, hamming: 0.14929860299983969
step: 16, hamming: 0.1260432183021211
step: 17, hamming: 0.10605108373830612
step: 18, hamming: 0.08898835303868328
step: 19, hamming: 0.07448950012171324
step: 20, hamming: 0.06222491628833417
step: 21, hamming: 0.05188708455543117
step: 22, hamming: 0.04319809393977556
step: 23, hamming: 0.03591255015730087
step: 24, hamming: 0.029815820364368282
step: 25, hamming: 0.02472412266649083
step: 26, hamming: 0.02047969068489947
step: 27, hamming: 0.016946966247749065
step: 28, hamming: 0.014010645315880806
step: 29, hamming: 0.0115732550219106
step: 30, hamming: 0.009552447322836869
step: 31, hamming: 0.007878861027854678
step: 32, hamming: 0.006494227871820638
step: 33, hamming: 0.005349713278823811
step: 34, hamming: 0.004404475166617553
step: 35, hamming: 0.0036244207432898252
step: 36, hamming: 0.0029811401934302464
step: 37, hamming: 0.002450996487900651
step: 38, hamming: 0.0020143516839460037
step: 39, hamming: 0.0016549116365250675
step: 40, hamming: 0.0013591727817255344
step: 41, hamming: 0.0011159564314784107
step: 42, hamming: 0.0009160177452470136
  Elapsed time: 0.10 sec.
Saving LIONESS network 0 (1) to lioness_output using no format:
lioness_output/lioness.1.0.no
Unknown format no! Use npy format instead.
  Elapsed time: 0.00 sec.
Trying to save lioness output. Format lioness_output/lioness.no not recognised
[1] "Computing network for sample  1"
[1] "Computing network for sample  2"
[1] "Computing network for sample  3"
[1] "Computing network for sample  4"
[1] "Computing network for sample  1"
[1] "Computing network for sample  2"
[1] "Computing network for sample  3"
[1] "Computing network for sample  4"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1079k  100 1079k    0     0  2785k      0 --:--:-- --:--:-- --:--:-- 2789k
[1] "1 network transitions to be estimated"
[1] "Running iteration 1"
[1] "Initializing and validating"
[1] "Verified adequate samples, calculating correlation matrix"
Time difference of 0.0001969337 secs
[1] "More data cleaning"
[1] "Main calculation"
.....................................................[1] "Initializing and validating"
[1] "Verified adequate samples, calculating correlation matrix"
Time difference of 0.0001962185 secs
[1] "More data cleaning"
[1] "Main calculation"
.....................................................[1] "Using OLS method"
[1] "Finished running iteration 1"
Time difference of 6.40285 secs
Time difference of 0.3124371 secs
Time difference of 0.2903011 secs
Time difference of 0.31951 secs
Time difference of 0.301101 secs
[1] "Using OLS method"
Time difference of 3.886223e-05 secs
Time difference of 5.105028 secs
Time difference of 1.685934 secs
.123456
.12345
.12345
.12345
.12345
.123456
.12345
.12345
.12345
.123456
.12345
.12345
.12345
.12345
.12345
.123456
.1234
.12345
.12345
.12345
.1234
.12345
.123456
.12345
.12345
.1234
.1234
.12345
.12345
.12345
.12345
.12345
.123456
.12345
.12345
.123456
.12345
.12345
.12345
.12345
.12345
.12345
.1234
.12345
.12345
.12345
.12345
.12345
.12345
.12345
.1234
.12345
.12345
MONSTER object
2555 genes
20 baseline samples
20 final samples
Transition driven by 53 transcription factors
Run with 10 randomized permutations.

Example timings

netZooR.Rcheck/netZooR-Ex.timings

nameusersystemelapsed
alpaca1.6410.0272.286
alpacaCommunityStructureRotation000
alpacaComputeDWBMmatmScale0.0000.0000.001
alpacaComputeWBMmat000
alpacaCrane0.0000.0010.000
alpacaDeltaZAnalysis0.0000.0000.001
alpacaDeltaZAnalysisLouvain0.0000.0000.002
alpacaExtractTopGenes1.0140.0071.438
alpacaGOtabtogenes000
alpacaGenLouvain000
alpacaGoToGenes0.0000.0010.000
alpacaListToGo0.0000.0000.001
alpacaMetaNetwork000
alpacaNodeToGene0.0000.0000.001
alpacaRotationAnalysis0.0010.0000.001
alpacaRotationAnalysisLouvain000
alpacaSimulateNetwork000
alpacaTestNodeRank0.0010.0000.000
alpacaTidyConfig000
alpacaTopEnsembltoTopSym000
alpacaWBMlouvain000
condorCluster1.2850.0051.754
condorCoreEnrich3.0420.0634.231
condorMatrixModularity0.0160.0030.022
condorModularityMax0.0470.0060.077
condorPlotCommunities1.3130.0101.843
condorPlotHeatmap0.3360.0220.471
condorQscore1.2980.0071.725
craneBipartite0.0010.0000.001
createCondorObject0.0050.0000.006
createPandaStyle0.0000.0000.001
lioness3.7400.3015.631
lionessPy0.0030.0000.004
monster12.365 0.25817.542
monsterBereFull5.2420.1257.362
monsterCalculateTmPValues0.0380.0030.057
monsterCheckDataType0.4480.4811.256
monsterGetTm0.0060.0020.012
monsterHclHeatmapPlot1.7120.0202.384
monsterMonsterNI5.1550.0987.093
monsterPlotMonsterAnalysis66.528 0.84691.896
monsterPrintMonsterAnalysis60.584 0.72684.079
monsterTransformationMatrix1.4910.0242.058
monsterTransitionNetworkPlot0.6330.0060.843
monsterTransitionPCAPlot0.3440.0160.479
monsterdTFIPlot0.4740.0070.636
otter0.0050.0010.005
pandaDiffEdges48.256 4.04664.306
pandaPy0.0210.0020.028
pandaToAlpaca0.0240.0010.035
pandaToCondorObject0.0180.0010.026
runEgret0.0830.0060.103
sambar5.4000.1777.791
sourcePPI0.0290.0010.041