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This page was generated on 2024-02-28 11:39:18 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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 1396/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netZooR 1.7.0  (landing page)
Marouen Ben Guebila
Snapshot Date: 2024-02-26 14:39:26 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/netZooR
git_branch: devel
git_last_commit: 78a6970
git_last_commit_date: 2023-10-24 11:38:39 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for netZooR on merida1


To the developers/maintainers of the netZooR package:
- 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 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: netZooR
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2024-02-27 09:36:42 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 09:53:56 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 1034.6 seconds
RetCode: 0
Status:   OK  
CheckDir: netZooR.Rcheck
Warnings: 0

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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/netZooR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.7.0’
* 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 ‘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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
monsterBereFull  5.402  0.337   6.789
monsterMonsterNI 4.998  0.143   6.191
sambar           4.068  0.335   5.285
lioness          3.829  0.332   5.604
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/netZooR.Rcheck/00check.log’
for details.



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/4.4-x86_64/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) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(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, 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 3.5 MB

> 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 14.5 MB

> 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 114 bytes

> 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 2.4 MB

> 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 12.2 MB

> 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 8.8 MB

> 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 8.8 MB

> 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 8.8 MB

> 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 249 KB

> 
> test_check("netZooR")
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.0263157894736854"
[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] 4
[1] "Merging 2 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
[1] "modularity of projected graph 0.227272727272727"
[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] 0.231405 0.231405
[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
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100   355  100   355    0     0   2260      0 --:--:-- --:--:-- --:--:--  2500
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100   222  100   222    0     0   1535      0 --:--:-- --:--:-- --:--:--  1707
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100 1438k  100 1438k    0     0  4288k      0 --:--:-- --:--:-- --:--:-- 4466k
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[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"
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100 27822  100 27822    0     0   175k      0 --:--:-- --:--:-- --:--:--  194k
[1] "Computing network for sample  1"
[1] "Computing network for sample  2"
[1] "Computing network for sample  3"
[1] "Computing network for sample  4"
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100 1079k  100 1079k    0     0  1529k      0 --:--:-- --:--:-- --:--:-- 1557k
Time difference of 3.504753e-05 secs
Time difference of 4.199257 secs
Time difference of 1.357861 secs
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MONSTER object
2555 genes
20 baseline samples
20 final samples
Transition driven by 53 transcription factors
Run with 10 randomized permutations.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 27822  100 27822    0     0   163k      0 --:--:-- --:--:-- --:--:--  181k
Loading motif data ...
  Elapsed time: 0.04 sec.
Loading expression data ...
  Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
  Elapsed time: 0.16 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.21 sec.
intersection /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt True False True
Normalizing networks ...
  Elapsed time: 0.01 sec.
Clearing motif and ppi data, unique tfs, and gene names for speed
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: 0.08 seconds!
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: 0.15 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.20 sec.
legacy /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False False
Normalizing networks ...
  Elapsed time: 0.02 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: 0.24 seconds!
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: 0.15 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/4.4-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False True False
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: 0.07 seconds!
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.471004488691679"
[1] "Q = 0.471024100010188"
[1] "Q = 0.471024100010188"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 386 communities"
[1] 1
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[1] "Merging 201 communities"
[1] 1
[1] "Computing node scores..."
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Read 7424 items
WARNING: Score threshold is not specified. We will be using medium stringency cut-off of 400.
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.0/83332.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 614783 bytes (600 KB)
==================================================
downloaded 600 KB

trying URL 'https://stringdb-downloads.org/download/protein.info.v11.0/83332.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 442274 bytes (431 KB)
==================================================
downloaded 431 KB

trying URL 'https://stringdb-downloads.org/download/protein.links.v11.0/83332.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 7455726 bytes (7.1 MB)
==================================================
downloaded 7.1 MB

[ FAIL 0 | WARN 9 | SKIP 1 | PASS 61 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-lioness.R:44:1'

[ FAIL 0 | WARN 9 | SKIP 1 | PASS 61 ]
> 
> proc.time()
   user  system elapsed 
 93.178   6.205 131.866 

Example timings

netZooR.Rcheck/netZooR-Ex.timings

nameusersystemelapsed
alpaca2.3630.0452.909
alpacaCommunityStructureRotation0.0000.0000.001
alpacaComputeDWBMmatmScale0.0000.0000.001
alpacaComputeWBMmat0.0010.0000.000
alpacaCrane0.0000.0000.001
alpacaDeltaZAnalysis0.0000.0000.001
alpacaDeltaZAnalysisLouvain000
alpacaExtractTopGenes0.5860.0130.726
alpacaGOtabtogenes0.0000.0010.000
alpacaGenLouvain0.0000.0010.000
alpacaGoToGenes0.0010.0010.001
alpacaListToGo0.0000.0010.000
alpacaMetaNetwork0.0000.0000.001
alpacaNodeToGene0.0000.0010.000
alpacaRotationAnalysis000
alpacaRotationAnalysisLouvain0.0000.0000.001
alpacaSimulateNetwork0.0000.0000.001
alpacaTestNodeRank0.0010.0000.000
alpacaTidyConfig000
alpacaTopEnsembltoTopSym0.0000.0010.001
alpacaWBMlouvain0.0000.0010.001
condorCluster1.3790.0141.671
condorCoreEnrich3.2830.1904.171
condorMatrixModularity0.0290.0050.041
condorModularityMax0.0570.0090.082
condorPlotCommunities1.4070.0241.700
condorPlotHeatmap0.3620.0470.493
condorQscore1.3840.0171.681
craneBipartite0.0000.0010.001
createCondorObject0.0130.0010.017
createPandaStyle0.0000.0010.000
lioness3.8290.3325.604
lionessPy0.0050.0030.010
monster0.0330.0080.048
monsterBereFull5.4020.3376.789
monsterCalculateTmPValues0.0410.0080.057
monsterCheckDataType0.5991.6122.781
monsterGetTm0.0050.0040.011
monsterHclHeatmapPlot1.1220.0441.365
monsterMonsterNI4.9980.1436.191
monsterPlotMonsterAnalysis0.0310.0050.047
monsterPrintMonsterAnalysis0.0310.0040.043
monsterTransformationMatrix2.7360.1313.392
monsterTransitionNetworkPlot0.6300.0170.780
monsterTransitionPCAPlot0.3230.0090.400
monsterdTFIPlot0.7670.0150.934
otter0.0060.0020.010
pandaDiffEdges0.0060.0040.012
pandaPy0.0060.0030.009
pandaToAlpaca0.0070.0020.011
pandaToCondorObject0.0050.0020.009
runEgret0.0310.0080.056
sambar4.0680.3355.285
sourcePPI0.0150.0020.019
spider0.0160.0050.023
visPandaInCytoscape000