Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2024-03-04 11:37:37 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1410/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netZooR 1.6.0  (landing page)
Marouen Ben Guebila
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/netZooR
git_branch: RELEASE_3_18
git_last_commit: a1bfeed
git_last_commit_date: 2023-10-24 11:38:39 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for netZooR on lconway


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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2024-03-03 22:11:38 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 22:21:08 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 569.9 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/netZooR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    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 ‘1.6.0’
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-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/4.3-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 version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 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 0.022368421052632"
[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 0.227272727272727"
[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
  % 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   2525      0 --:--:-- --:--:-- --:--:--  2689
  % 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   4504      0 --:--:-- --:--:-- --:--:--  4822
  % 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   6570      0 --:--:-- --:--:-- --:--:--  7058
  % 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  3242  100  3242    0     0  25310      0 --:--:-- --:--:-- --:--:-- 27474
  % 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   3108      0 --:--:-- --:--:-- --:--:--  3306
  % 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   222  100   222    0     0   1732      0 --:--:-- --:--:-- --:--:--  1850
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 56 1438k   56  815k    0     0   953k      0  0:00:01 --:--:--  0:00:01  962k
100 1438k  100 1438k    0     0  1253k      0  0:00:01  0:00:01 --:--:-- 1263k
  % 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   578  100   578    0     0   4754      0 --:--:-- --:--:-- --:--:--  5070
[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   166k      0 --:--:-- --:--:-- --:--:--  177k
[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
 41 1079k   41  443k    0     0   694k      0  0:00:01 --:--:--  0:00:01  703k
100 1079k  100 1079k    0     0  1058k      0  0:00:01  0:00:01 --:--:-- 1068k
Time difference of 1.811981e-05 secs
Time difference of 1.919895 secs
Time difference of 0.7137659 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.
  % 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   137k      0 --:--:-- --:--:-- --:--:--  144k
Loading motif data ...
  Elapsed time: 0.02 sec.
Loading expression data ...
  Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
  Elapsed time: 0.10 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.08 sec.
intersection /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt True False True
Normalizing networks ...
  Elapsed time: 0.00 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: 0.36915773153305054
step: 7, hamming: 0.34574776887893677
step: 8, hamming: 0.3152081370353699
step: 9, hamming: 0.2818054258823395
step: 10, hamming: 0.24849660694599152
step: 11, hamming: 0.21666744351387024
step: 12, hamming: 0.18729539215564728
step: 13, hamming: 0.16079428791999817
step: 14, hamming: 0.13726867735385895
step: 15, hamming: 0.11666569113731384
step: 16, hamming: 0.09877122193574905
step: 17, hamming: 0.08336563408374786
step: 18, hamming: 0.07016084343194962
step: 19, hamming: 0.0588911771774292
step: 20, hamming: 0.04931585118174553
step: 21, hamming: 0.041211165487766266
step: 22, hamming: 0.03437765687704086
step: 23, hamming: 0.02863147482275963
step: 24, hamming: 0.023808928206562996
step: 25, hamming: 0.01977088674902916
step: 26, hamming: 0.016396764665842056
step: 27, hamming: 0.013582728803157806
step: 28, hamming: 0.011239760555326939
step: 29, hamming: 0.009291945025324821
step: 30, hamming: 0.00767497019842267
step: 31, hamming: 0.006334253121167421
step: 32, hamming: 0.005223960615694523
step: 33, hamming: 0.004305404145270586
step: 34, hamming: 0.003546181134879589
step: 35, hamming: 0.002919197781011462
step: 36, hamming: 0.002401866717264056
step: 37, hamming: 0.001975313061848283
step: 38, hamming: 0.0016238006064668298
step: 39, hamming: 0.001334363128989935
step: 40, hamming: 0.0010961104417219758
step: 41, hamming: 0.0009001354337669909
Running panda took: 0.02 seconds!
Loading motif data ...
  Elapsed time: 0.00 sec.
Loading expression data ...
  Elapsed time: 0.00 sec.
Loading PPI data ...
Number of PPIs: 100019
  Elapsed time: 0.10 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.09 sec.
legacy /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False False
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: 0.36797241244238343
step: 6, hamming: 0.31337190961143313
step: 7, hamming: 0.2640386174641925
step: 8, hamming: 0.2239999232789824
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: 0.10108821391424125
step: 15, hamming: 0.08890364507467007
step: 16, hamming: 0.07787244456478047
step: 17, hamming: 0.06785464923123906
step: 18, hamming: 0.05878796471238135
step: 19, hamming: 0.05062155744809771
step: 20, hamming: 0.04333239380925903
step: 21, hamming: 0.036892574940160516
step: 22, hamming: 0.03126206012121671
step: 23, hamming: 0.026384280403921743
step: 24, hamming: 0.02219096174091557
step: 25, hamming: 0.01860922988517212
step: 26, hamming: 0.015566652188260116
step: 27, hamming: 0.012993283312056427
step: 28, hamming: 0.010824919177296213
step: 29, hamming: 0.009003507268894196
step: 30, hamming: 0.007477552910889816
step: 31, hamming: 0.006202062894110505
step: 32, hamming: 0.005138069423501655
step: 33, hamming: 0.004252085993537945
step: 34, hamming: 0.0035154788596479794
step: 35, hamming: 0.0029039267439058677
step: 36, hamming: 0.0023968521367998463
step: 37, hamming: 0.0019768786344578106
step: 38, hamming: 0.0016294013136896753
step: 39, hamming: 0.0013421799963357426
step: 40, hamming: 0.0011049738470584863
step: 41, hamming: 0.0009092279973180559
Running panda took: 0.07 seconds!
Loading motif data ...
  Elapsed time: 0.00 sec.
Loading expression data ...
  Elapsed time: 0.00 sec.
Loading PPI data ...
Number of PPIs: 100019
  Elapsed time: 0.10 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-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: 0.49937220814370303
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: 0.4081852233215106
step: 9, hamming: 0.363060630725845
step: 10, hamming: 0.31891232474094794
step: 11, hamming: 0.27733895854371826
step: 12, hamming: 0.23925292481822666
step: 13, hamming: 0.20518316158337402
step: 14, hamming: 0.17501658473943318
step: 15, hamming: 0.14854288648840214
step: 16, hamming: 0.12553582999076407
step: 17, hamming: 0.10573284427875865
step: 18, hamming: 0.08878386418920353
step: 19, hamming: 0.0743688270511516
step: 20, hamming: 0.062172412390917475
step: 21, hamming: 0.05188071541370959
step: 22, hamming: 0.0432203223195204
step: 23, hamming: 0.03594946787636905
step: 24, hamming: 0.0298598954759094
step: 25, hamming: 0.024770938396293206
step: 26, hamming: 0.020525756048994263
step: 27, hamming: 0.016990787588434902
step: 28, hamming: 0.01405117127516721
step: 29, hamming: 0.011609873894851032
step: 30, hamming: 0.009584973156032739
step: 31, hamming: 0.007907374279360037
step: 32, hamming: 0.006518966440957099
step: 33, hamming: 0.005370999156869476
step: 34, hamming: 0.004422666090211268
step: 35, hamming: 0.0036398792478184367
step: 36, hamming: 0.0029942146499029876
step: 37, hamming: 0.002462010284380602
step: 38, hamming: 0.0020235978467206695
step: 39, hamming: 0.001662650998788413
step: 40, hamming: 0.00136563438767126
step: 41, hamming: 0.0011213392761822388
step: 42, hamming: 0.0009204932425645715
Running panda took: 0.02 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
[1] 2
[1] "Merging 201 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
[1] 16
[1] 17
[1] 18
[1] 19
[1] 20
[1] 21
[1] 22
[1] 23
[1] 24
[1] 25
[1] 26
[1] 27
[1] 28
[1] 29
[1] 30
[1] 31
[1] 32
[1] 33
[1] 34
[1] 35
[1] 36
[1] 37
[1] 38
[1] 39
[1] 40
[1] 41
[1] 42
[1] 43
[1] 44
[1] 45
[1] 46
[1] 47
[1] 48
[1] 49
[1] 50
[1] 51
[1] 52
[1] 53
[1] 54
[1] 55
[1] 56
[1] 57
[1] 58
[1] 59
[1] 60
[1] 61
[1] 62
[1] 63
[1] 64
[1] 65
[1] 66
[1] 67
[1] 68
[1] 69
[1] 70
[1] 71
[1] 72
[1] 73
[1] 74
[1] 75
[1] 76
[1] 77
[1] 78
[1] 79
[1] 80
[1] 81
[1] 82
[1] 83
[1] 84
[1] 85
[1] 86
[1] 87
[1] 88
[1] 89
[1] 90
[1] 91
[1] 92
[1] 93
[1] 94
[1] 95
[1] 96
[1] 97
[1] 98
[1] 99
[1] 100
[1] 101
[1] 102
[1] 103
[1] 104
[1] 105
[1] 106
[1] 107
[1] 108
[1] 109
[1] 110
[1] 111
[1] 112
[1] 113
[1] 114
[1] 115
[1] 116
[1] 117
[1] 118
[1] 119
[1] 120
[1] 121
[1] 122
[1] 123
[1] 124
[1] 125
[1] 126
[1] 127
[1] 128
[1] 129
[1] 130
[1] 131
[1] 132
[1] 133
[1] 134
[1] 135
[1] 136
[1] 137
[1] 138
[1] 139
[1] 140
[1] 141
[1] 142
[1] 143
[1] 144
[1] 145
[1] 146
[1] 147
[1] 148
[1] 149
[1] 150
[1] 151
[1] 152
[1] 153
[1] 154
[1] 155
[1] 156
[1] 157
[1] 158
[1] 159
[1] 160
[1] 161
[1] 162
[1] 163
[1] 164
[1] 165
[1] 166
[1] 167
[1] 168
[1] 169
[1] 170
[1] 171
[1] 172
[1] 173
[1] 174
[1] 175
[1] 176
[1] 177
[1] 178
[1] 179
[1] 180
[1] 181
[1] 182
[1] 183
[1] 184
[1] 185
[1] 186
[1] 187
[1] 188
[1] 189
[1] 190
[1] 191
[1] 192
[1] 193
[1] 194
[1] 195
[1] 196
[1] 197
[1] 198
[1] 199
[1] 200
[1] 201
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 
 58.752   5.452  98.415 

Example timings

netZooR.Rcheck/netZooR-Ex.timings

nameusersystemelapsed
alpaca0.6430.0240.676
alpacaCommunityStructureRotation0.0010.0000.000
alpacaComputeDWBMmatmScale000
alpacaComputeWBMmat000
alpacaCrane0.0000.0010.001
alpacaDeltaZAnalysis000
alpacaDeltaZAnalysisLouvain0.0000.0000.001
alpacaExtractTopGenes1.4490.0211.485
alpacaGOtabtogenes000
alpacaGenLouvain000
alpacaGoToGenes000
alpacaListToGo000
alpacaMetaNetwork000
alpacaNodeToGene0.0000.0000.001
alpacaRotationAnalysis0.0000.0000.001
alpacaRotationAnalysisLouvain000
alpacaSimulateNetwork000
alpacaTestNodeRank0.0000.0000.001
alpacaTidyConfig0.0000.0010.001
alpacaTopEnsembltoTopSym000
alpacaWBMlouvain000
condorCluster1.1140.0171.145
condorCoreEnrich1.9260.0822.028
condorMatrixModularity0.0150.0020.017
condorModularityMax0.0290.0040.034
condorPlotCommunities1.1280.0201.160
condorPlotHeatmap0.1950.0250.224
condorQscore1.0950.0191.128
craneBipartite000
createCondorObject0.0070.0010.008
createPandaStyle000
lioness4.2670.3314.657
lionessPy0.0040.0020.006
monster0.0210.0040.025
monsterBereFull3.2620.2583.561
monsterCalculateTmPValues0.0160.0040.020
monsterCheckDataType0.2050.5220.743
monsterGetTm0.0020.0020.004
monsterHclHeatmapPlot0.5580.0350.600
monsterMonsterNI2.9490.0993.081
monsterPlotMonsterAnalysis0.0200.0030.023
monsterPrintMonsterAnalysis0.0220.0020.025
monsterTransformationMatrix0.8350.0540.899
monsterTransitionNetworkPlot0.3010.0110.317
monsterTransitionPCAPlot0.1550.0040.161
monsterdTFIPlot0.4410.0110.457
otter0.0030.0010.005
pandaDiffEdges0.0050.0020.007
pandaPy0.0040.0030.006
pandaToAlpaca0.0050.0020.006
pandaToCondorObject0.0040.0020.005
runEgret0.0710.0230.097
sambar2.9940.2723.297
sourcePPI0.0080.0020.010
spider0.0110.0030.013
visPandaInCytoscape000