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This page was generated on 2024-04-17 11:36:11 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 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 -0400 (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
merida1macOS 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 nebbiolo2


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: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings netZooR_1.6.0.tar.gz
StartedAt: 2024-04-16 01:31:56 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 01:40:53 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 537.3 seconds
RetCode: 0
Status:   OK  
CheckDir: netZooR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings netZooR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/netZooR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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   2.9Mb
* 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 loading without being on the library search path ... 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 ...
  ‘CONDOR.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/netZooR.Rcheck/00check.log’
for details.



Installation output

netZooR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL netZooR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 0.0236842105263165"
[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
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100   355  100   355    0     0   2017      0 --:--:-- --:--:-- --:--:--  2028
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100   569  100   569    0     0   3326      0 --:--:-- --:--:-- --:--:--  3347
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100   840  100   840    0     0   4667      0 --:--:-- --:--:-- --:--:--  4692
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100   222  100   222    0     0   1225      0 --:--:-- --:--:-- --:--:--  1226
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 24 1438k   24  356k    0     0   513k      0  0:00:02 --:--:--  0:00:02  513k
100 1438k  100 1438k    0     0  1029k      0  0:00:01  0:00:01 --:--:-- 1030k
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100   578  100   578    0     0   2670      0 --:--:-- --:--:-- --:--:--  2675
[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
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 27822  100 27822    0     0   123k      0 --:--:-- --:--:-- --:--:--  123k
[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
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 82 1079k   82  887k    0     0  1310k      0 --:--:-- --:--:-- --:--:-- 1308k
100 1079k  100 1079k    0     0  1534k      0 --:--:-- --:--:-- --:--:-- 1533k
Time difference of 2.145767e-05 secs
Time difference of 1.765572 secs
Time difference of 0.6664031 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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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 27822  100 27822    0     0   122k      0 --:--:-- --:--:-- --:--:--  122k
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: 0.07 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.07 sec.
intersection /home/biocbuild/bbs-3.18-bioc/R/site-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: 0.3794232904911041
step: 3, hamming: 0.3818596303462982
step: 4, hamming: 0.38526612520217896
step: 5, hamming: 0.3832989037036896
step: 6, hamming: 0.36915773153305054
step: 7, hamming: 0.34574782848358154
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: 0.16079427301883698
step: 14, hamming: 0.13726867735385895
step: 15, hamming: 0.11666569113731384
step: 16, hamming: 0.09877119958400726
step: 17, hamming: 0.08336563408374786
step: 18, hamming: 0.07016085088253021
step: 19, hamming: 0.0588911734521389
step: 20, hamming: 0.04931586608290672
step: 21, hamming: 0.04121116176247597
step: 22, hamming: 0.03437766060233116
step: 23, hamming: 0.028631482273340225
step: 24, hamming: 0.023808928206562996
step: 25, hamming: 0.019770875573158264
step: 26, hamming: 0.01639675162732601
step: 27, hamming: 0.01358273159712553
step: 28, hamming: 0.011239764280617237
step: 29, hamming: 0.009291954338550568
step: 30, hamming: 0.0076749688014388084
step: 31, hamming: 0.0063342684879899025
step: 32, hamming: 0.005223970860242844
step: 33, hamming: 0.0043054018169641495
step: 34, hamming: 0.003546181134879589
step: 35, hamming: 0.0029191910289227962
step: 36, hamming: 0.0024018590338528156
step: 37, hamming: 0.001975312363356352
step: 38, hamming: 0.0016238141106441617
step: 39, hamming: 0.001334351603873074
step: 40, hamming: 0.0010961128864437342
step: 41, hamming: 0.0009001469006761909
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: 0.07 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.07 sec.
legacy /home/biocbuild/bbs-3.18-bioc/R/site-library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False False
Normalizing networks ...
  Elapsed time: 0.06 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.5867745269558597
step: 1, hamming: 0.47709480696171547
step: 2, hamming: 0.4695616866661461
step: 3, hamming: 0.45425003629838684
step: 4, hamming: 0.4187427725151872
step: 5, hamming: 0.36797241244238343
step: 6, hamming: 0.31337190961143313
step: 7, hamming: 0.26403861746419255
step: 8, hamming: 0.2239999232789824
step: 9, hamming: 0.19253176059893798
step: 10, hamming: 0.16765536676491025
step: 11, hamming: 0.14730006142326466
step: 12, hamming: 0.12982159089839335
step: 13, hamming: 0.11459157116297607
step: 14, hamming: 0.10108821391424129
step: 15, hamming: 0.0889036450746701
step: 16, hamming: 0.0778724445647805
step: 17, hamming: 0.06785464923123909
step: 18, hamming: 0.05878796471238138
step: 19, hamming: 0.0506215574480977
step: 20, hamming: 0.04333239380925903
step: 21, hamming: 0.03689257494016052
step: 22, hamming: 0.03126206012121671
step: 23, hamming: 0.026384280403921757
step: 24, hamming: 0.02219096174091556
step: 25, hamming: 0.018609229885172118
step: 26, hamming: 0.015566652188260114
step: 27, hamming: 0.012993283312056434
step: 28, hamming: 0.010824919177296216
step: 29, hamming: 0.009003507268894182
step: 30, hamming: 0.007477552910889806
step: 31, hamming: 0.006202062894110499
step: 32, hamming: 0.005138069423501644
step: 33, hamming: 0.00425208599353795
step: 34, hamming: 0.0035154788596479833
step: 35, hamming: 0.0029039267439058755
step: 36, hamming: 0.0023968521367998463
step: 37, hamming: 0.0019768786344577984
step: 38, hamming: 0.0016294013136896753
step: 39, hamming: 0.0013421799963357418
step: 40, hamming: 0.001104973847058476
step: 41, hamming: 0.0009092279973180601
Running panda took: 0.08 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: 0.07 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 /home/biocbuild/bbs-3.18-bioc/R/site-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: 0.4081852233215105
step: 9, hamming: 0.363060630725845
step: 10, hamming: 0.3189123247409479
step: 11, hamming: 0.2773389585437183
step: 12, hamming: 0.23925292481822666
step: 13, hamming: 0.20518316158337407
step: 14, hamming: 0.17501658473943316
step: 15, hamming: 0.14854288648840216
step: 16, hamming: 0.12553582999076407
step: 17, hamming: 0.10573284427875863
step: 18, hamming: 0.08878386418920356
step: 19, hamming: 0.07436882705115157
step: 20, hamming: 0.06217241239091747
step: 21, hamming: 0.05188071541370957
step: 22, hamming: 0.04322032231952041
step: 23, hamming: 0.03594946787636905
step: 24, hamming: 0.0298598954759094
step: 25, hamming: 0.024770938396293202
step: 26, hamming: 0.020525756048994252
step: 27, hamming: 0.016990787588434902
step: 28, hamming: 0.014051171275167211
step: 29, hamming: 0.011609873894851033
step: 30, hamming: 0.009584973156032744
step: 31, hamming: 0.00790737427936001
step: 32, hamming: 0.006518966440957102
step: 33, hamming: 0.0053709991568694606
step: 34, hamming: 0.00442266609021128
step: 35, hamming: 0.003639879247818433
step: 36, hamming: 0.002994214649903007
step: 37, hamming: 0.0024620102843806047
step: 38, hamming: 0.002023597846720663
step: 39, hamming: 0.0016626509987884234
step: 40, hamming: 0.0013656343876712767
step: 41, hamming: 0.0011213392761822275
step: 42, hamming: 0.000920493242564561
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
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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 
 53.914   3.972  97.037 

Example timings

netZooR.Rcheck/netZooR-Ex.timings

nameusersystemelapsed
alpaca0.5760.0120.588
alpacaCommunityStructureRotation000
alpacaComputeDWBMmatmScale000
alpacaComputeWBMmat000
alpacaCrane000
alpacaDeltaZAnalysis000
alpacaDeltaZAnalysisLouvain000
alpacaExtractTopGenes1.7280.0611.789
alpacaGOtabtogenes000
alpacaGenLouvain000
alpacaGoToGenes000
alpacaListToGo000
alpacaMetaNetwork000
alpacaNodeToGene000
alpacaRotationAnalysis000
alpacaRotationAnalysisLouvain000
alpacaSimulateNetwork000
alpacaTestNodeRank000
alpacaTidyConfig000
alpacaTopEnsembltoTopSym000
alpacaWBMlouvain000
condorCluster1.3710.0201.391
condorCoreEnrich2.1840.1082.292
condorMatrixModularity0.0060.0080.015
condorModularityMax0.0220.0040.026
condorPlotCommunities1.4610.0121.474
condorPlotHeatmap0.2310.0110.243
condorQscore1.320.001.32
craneBipartite000
createCondorObject0.0060.0000.006
createPandaStyle000
lioness3.5480.1763.726
lionessPy0.0020.0000.002
monster0.0230.0000.023
monsterBereFull3.4470.0163.464
monsterCalculateTmPValues0.0160.0000.015
monsterCheckDataType0.1610.1360.296
monsterGetTm0.0040.0000.004
monsterHclHeatmapPlot0.5180.0440.562
monsterMonsterNI2.6160.0722.689
monsterPlotMonsterAnalysis0.0220.0000.023
monsterPrintMonsterAnalysis0.0190.0040.023
monsterTransformationMatrix0.7660.0160.783
monsterTransitionNetworkPlot0.2810.0000.281
monsterTransitionPCAPlot0.1450.0120.156
monsterdTFIPlot0.3230.0160.339
otter0.0020.0000.003
pandaDiffEdges0.0030.0000.004
pandaPy0.0030.0000.003
pandaToAlpaca0.0030.0000.003
pandaToCondorObject0.0020.0000.003
runEgret0.0540.0000.056
sambar3.0160.1603.177
sourcePPI0.0080.0000.008
spider0.0100.0000.009
visPandaInCytoscape000