Multiple platform build/check report for BioC 3.16 - CHECK results for netZooR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4502
palomino4	Windows Server 2022 Datacenter	x64	4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"	4282
lconway	macOS 12.5.1 Monterey	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4310
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: netZooR

Version: 1.2.0

Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings netZooR_1.2.0.tar.gz

StartedAt: 2023-04-10 22:20:58 -0400 (Mon, 10 Apr 2023)

EndedAt: 2023-04-10 22:42:23 -0400 (Mon, 10 Apr 2023)

EllapsedTime: 1285.7 seconds

RetCode: 1

Status: ERROR

CheckDir: netZooR.Rcheck

Warnings: NA

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings netZooR_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/netZooR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.2.0’
* 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  5.1Mb
  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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
runEgret: no visible binding for global variable ‘NA12878’
Undefined global functions or variables:
  NA12878
* 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
monsterPrintMonsterAnalysis 35.882  0.340  36.222
monsterPlotMonsterAnalysis  32.861  0.476  33.338
monster                      6.766  0.116   6.882
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  step: 28, hamming: 0.008524772832534408
  step: 29, hamming: 0.007052536065331644
  step: 30, hamming: 0.0058289629675493905
  step: 31, hamming: 0.004813469251228287
  step: 32, hamming: 0.003971733841541358
  step: 33, hamming: 0.003274823735478185
  step: 34, hamming: 0.002698421842219443
  step: 35, hamming: 0.0022221411979149487
  step: 36, hamming: 0.0018289290757055078
  step: 37, hamming: 0.0015045517890993694
  step: 38, hamming: 0.0012371486338300583
  step: 39, hamming: 0.0010168547681778833
  step: 40, hamming: 0.0008354772054776381
  Running panda took: 4.87 seconds!
  Killed
* 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
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/netZooR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL netZooR
###
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* installing to library ‘/home/biocbuild/bbs-3.16-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)


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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)


> 
> #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

> 
> test_check("netZooR")
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.026315789473685"
[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"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100   355  100   355    0     0   1950      0 --:--:-- --:--:-- --:--:--  1939
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100  3242  100  3242    0     0  17619      0 --:--:-- --:--:-- --:--:-- 17619
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100   222  100   222    0     0   1261      0 --:--:-- --:--:-- --:--:--  1261
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 81 1438k   81 1165k    0     0  1549k      0 --:--:-- --:--:-- --:--:-- 1547k
100 1438k  100 1438k    0     0  1788k      0 --:--:-- --:--:-- --:--:-- 1786k
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100   578  100   578    0     0   3440      0 --:--:-- --:--:-- --:--:--  3440
[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   126k      0 --:--:-- --:--:-- --:--:--  126k
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: 0.00 sec.
Returning the correlation matrix of expression data in <Panda_obj>.correlation_matrix
['Rv0001' 'Rv0002' 'Rv0003' ... 'Rv0193c' 'Rv0194' 'Rv0195']
['Rv0001' 'Rv0001' 'Rv0001' ... 'Rv0195' 'Rv0195' 'Rv0195']
(40000,)
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:
  Elapsed time: 0.00 sec.
Saving LIONESS network 1 to lioness_output using no format:
Unknown format no! File will not be saved.
  Elapsed time: 0.00 sec.
Loading motif data ...
  Elapsed time: 0.00 sec.
Loading expression data ...
  Elapsed time: 0.00 sec.
No PPI data given: ppi matrix will be an identity matrix of size 5
Calculating coexpression network ...
  Elapsed time: 0.01 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Normalizing networks ...
  Elapsed time: 0.01 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.01 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.3008717441926665
step: 1, hamming: 0.32577840239393485
step: 2, hamming: 0.36046547993298506
step: 3, hamming: 0.36058526850894806
step: 4, hamming: 0.3466240823512552
step: 5, hamming: 0.32456269443005153
step: 6, hamming: 0.2989434598421862
step: 7, hamming: 0.2706019093508666
step: 8, hamming: 0.24146225569326246
step: 9, hamming: 0.21301541796450382
step: 10, hamming: 0.18618747428128857
step: 11, hamming: 0.16147381450104786
step: 12, hamming: 0.13913324895882415
step: 13, hamming: 0.11926159237252416
step: 14, hamming: 0.1018524648128548
step: 15, hamming: 0.08669455519421927
step: 16, hamming: 0.07353017763220226
step: 17, hamming: 0.06215000422873393
step: 18, hamming: 0.05239618178480344
step: 19, hamming: 0.04409487478206072
step: 20, hamming: 0.037011961055401506
step: 21, hamming: 0.03099423061137592
step: 22, hamming: 0.025900515663656126
step: 23, hamming: 0.02160297573646609
step: 24, hamming: 0.017987639137724463
step: 25, hamming: 0.01495414717402849
step: 26, hamming: 0.01241474935607542
step: 27, hamming: 0.010293476645032267
step: 28, hamming: 0.008524772832534408
step: 29, hamming: 0.007052536065331644
step: 30, hamming: 0.0058289629675493905
step: 31, hamming: 0.004813469251228287
step: 32, hamming: 0.003971733841541358
step: 33, hamming: 0.003274823735478185
step: 34, hamming: 0.002698421842219443
step: 35, hamming: 0.0022221411979149487
step: 36, hamming: 0.0018289290757055078
step: 37, hamming: 0.0015045517890993694
step: 38, hamming: 0.0012371486338300583
step: 39, hamming: 0.0010168547681778833
step: 40, hamming: 0.0008354772054776381
Running panda took: 0.36 seconds!
/usr/local/lib/python3.8/dist-packages/numpy/lib/function_base.py:2559: RuntimeWarning: invalid value encountered in true_divide
  c /= stddev[:, None]
/usr/local/lib/python3.8/dist-packages/numpy/lib/function_base.py:2560: RuntimeWarning: invalid value encountered in true_divide
  c /= stddev[None, :]
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: 0.01 sec.
Inferring LIONESS network:
step: 0, hamming: 0.3015932422799911
step: 1, hamming: 0.32674478239840066
step: 2, hamming: 0.36109248186970144
step: 3, hamming: 0.36080894284507337
step: 4, hamming: 0.34665241776678835
step: 5, hamming: 0.32459397132921336
step: 6, hamming: 0.2989655066138038
step: 7, hamming: 0.27062058204102246
step: 8, hamming: 0.24148327279879642
step: 9, hamming: 0.2130402835155567
step: 10, hamming: 0.18620484129483603
step: 11, hamming: 0.1614836666882501
step: 12, hamming: 0.13913925776650915
step: 13, hamming: 0.1192705526210247
step: 14, hamming: 0.1018608399938872
step: 15, hamming: 0.08670615581741968
step: 16, hamming: 0.0735398859822866
step: 17, hamming: 0.06215811356512186
step: 18, hamming: 0.052413728098102554
step: 19, hamming: 0.04410977556767986
step: 20, hamming: 0.037024570333261446
step: 21, hamming: 0.03100500331100484
step: 22, hamming: 0.025909572963571045
step: 23, hamming: 0.021610559908641205
step: 24, hamming: 0.01799395112713223
step: 25, hamming: 0.014959350583484143
step: 26, hamming: 0.012419036091497032
step: 27, hamming: 0.010296989659986456
step: 28, hamming: 0.00852768414504873
step: 29, hamming: 0.007054962882501573
step: 30, hamming: 0.00583098373741747
step: 31, hamming: 0.004815151202585595
step: 32, hamming: 0.003973130484197422
step: 33, hamming: 0.003275982320391778
step: 34, hamming: 0.002699382028610559
step: 35, hamming: 0.0022229362315468095
step: 36, hamming: 0.0018295867892865751
step: 37, hamming: 0.0015050947585658215
step: 38, hamming: 0.00123759650387202
step: 39, hamming: 0.0010172239699261594
step: 40, hamming: 0.0008357813833837499
  Elapsed time: 0.39 sec.
Saving LIONESS network 1 to lioness_output using no format:
Unknown format no! File will not be saved.
  Elapsed time: 0.00 sec.
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: 0.06 sec.
Calculating coexpression network ...
  Elapsed time: 0.01 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.11 sec.
Normalizing networks ...
  Elapsed time: 0.91 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.15 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: 0.049101138022894876
step: 6, hamming: 0.045074438192725504
step: 7, hamming: 0.04095526634659027
step: 8, hamming: 0.03683033393753413
step: 9, hamming: 0.03280131999197774
step: 10, hamming: 0.02895800229188848
step: 11, hamming: 0.025365652761878358
step: 12, hamming: 0.022066636023677567
step: 13, hamming: 0.019078836711277743
step: 14, hamming: 0.016405313028879685
step: 15, hamming: 0.014037779400693116
step: 16, hamming: 0.01195982841838061
step: 17, hamming: 0.01015009070774131
step: 18, hamming: 0.00858449985155968
step: 19, hamming: 0.0072380075895177075
step: 20, hamming: 0.00608586224867506
step: 21, hamming: 0.005104411138700387
step: 22, hamming: 0.004271661591718608
step: 23, hamming: 0.0035675611746851256
step: 24, hamming: 0.002974084885079086
step: 25, hamming: 0.002475243890114065
step: 26, hamming: 0.0020569891001135433
step: 27, hamming: 0.0017070859535523234
step: 28, hamming: 0.0014149533300699655
step: 29, hamming: 0.0011714963862095031
step: 30, hamming: 0.0009689369122934221
Running panda took: 31.10 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: 0.01 sec.
Normalizing networks:
  Elapsed time: 0.01 sec.
Inferring LIONESS network:
step: 0, hamming: 0.0874818573175637
step: 1, hamming: 0.06891282897076391
step: 2, hamming: 0.06213058734815114
step: 3, hamming: 0.05714118386838519
step: 4, hamming: 0.05304529446377499
step: 5, hamming: 0.04910525549313264
step: 6, hamming: 0.045077507937550505
step: 7, hamming: 0.040957168253354534
step: 8, hamming: 0.036831755781812706
step: 9, hamming: 0.032802826977823524
step: 10, hamming: 0.028959920494437665
step: 11, hamming: 0.025367894743653207
step: 12, hamming: 0.022069009727623188
step: 13, hamming: 0.019081318203819215
step: 14, hamming: 0.016407788201894247
step: 15, hamming: 0.014040090736288893
step: 16, hamming: 0.011961875397219707
step: 17, hamming: 0.010151865216875243
step: 18, hamming: 0.008586011382256611
step: 19, hamming: 0.007239278751699701
step: 20, hamming: 0.006086920160262565
step: 21, hamming: 0.005105283470150481
step: 22, hamming: 0.004272377006570679
step: 23, hamming: 0.0035681447767932513
step: 24, hamming: 0.002974559350795158
step: 25, hamming: 0.002475628259651009
step: 26, hamming: 0.0020572999963523056
step: 27, hamming: 0.0017073373347909833
step: 28, hamming: 0.0014151565613914198
step: 29, hamming: 0.0011716607762849167
step: 30, hamming: 0.0009690701447933722
  Elapsed time: 31.16 sec.
Saving LIONESS network 1 to lioness_output using no format:
Unknown format no! File will not be saved.
  Elapsed time: 0.00 sec.
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: 0.18 sec.
Normalizing networks ...
  Elapsed time: 0.00 sec.
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: 0.31520816683769226
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: 0.13726864755153656
step: 15, hamming: 0.11666569113731384
step: 16, hamming: 0.09877120703458786
step: 17, hamming: 0.08336563408374786
step: 18, hamming: 0.07016085088253021
step: 19, hamming: 0.058891184628009796
step: 20, hamming: 0.04931585118174553
step: 21, hamming: 0.041211165487766266
step: 22, hamming: 0.03437766060233116
step: 23, hamming: 0.02863147109746933
step: 24, hamming: 0.0238089170306921
step: 25, hamming: 0.019770871847867966
step: 26, hamming: 0.016396749764680862
step: 27, hamming: 0.01358273159712553
step: 28, hamming: 0.011239762417972088
step: 29, hamming: 0.009291956201195717
step: 30, hamming: 0.0076749688014388084
step: 31, hamming: 0.0063342684879899025
step: 32, hamming: 0.005223971791565418
step: 33, hamming: 0.004305408801883459
step: 34, hamming: 0.0035461909137666225
step: 35, hamming: 0.002919200574979186
step: 36, hamming: 0.0024018811527639627
step: 37, hamming: 0.0019753146916627884
step: 38, hamming: 0.0016238073585554957
step: 39, hamming: 0.001334344851784408
step: 40, hamming: 0.0010961124207824469
step: 41, hamming: 0.0009001471335068345
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: 0.01 sec.
Normalizing networks:
  Elapsed time: 0.00 sec.
Inferring LIONESS network:
step: 0, hamming: 0.6829624252643024
step: 1, hamming: 0.43097386969737467
step: 2, hamming: 0.3855310332972826
step: 3, hamming: 0.38637191344546506
step: 4, hamming: 0.39001820267044696
step: 5, hamming: 0.38601884753426646
step: 6, hamming: 0.37083627595496715
step: 7, hamming: 0.3469023721010731
step: 8, hamming: 0.3159676756323738
step: 9, hamming: 0.2823677724041992
step: 10, hamming: 0.24886232875703243
step: 11, hamming: 0.21693733016217834
step: 12, hamming: 0.1875129193175416
step: 13, hamming: 0.1609701836223114
step: 14, hamming: 0.13743834351937564
step: 15, hamming: 0.11682177402185094
step: 16, hamming: 0.0989602327792078
step: 17, hamming: 0.08353838996370484
step: 18, hamming: 0.07031459662912222
step: 19, hamming: 0.05903107230891116
step: 20, hamming: 0.049447848936208585
step: 21, hamming: 0.041332665358096286
step: 22, hamming: 0.03448368388232095
step: 23, hamming: 0.028720375548938075
step: 24, hamming: 0.02388327219797364
step: 25, hamming: 0.019832958716462273
step: 26, hamming: 0.016448511057472182
step: 27, hamming: 0.013625773339477069
step: 28, hamming: 0.011275503429549753
step: 29, hamming: 0.009321615661804542
step: 30, hamming: 0.007699524683027151
step: 31, hamming: 0.006354585216875863
step: 32, hamming: 0.00524073243580051
step: 33, hamming: 0.00431923098127344
step: 34, hamming: 0.003557580755210537
step: 35, hamming: 0.002928611407776382
step: 36, hamming: 0.0024096126806938843
step: 37, hamming: 0.001981682374285388
step: 38, hamming: 0.0016290920553380466
step: 39, hamming: 0.001338728463991543
step: 40, hamming: 0.0010997294054595165
step: 41, hamming: 0.0009031298195247417
  Elapsed time: 0.12 sec.
Saving LIONESS network 1 to lioness_output using no format:
Unknown format no! File will not be saved.
  Elapsed time: 0.00 sec.
Loading motif data ...
  Elapsed time: 0.01 sec.
Loading expression data ...
  Elapsed time: 0.03 sec.
Loading PPI data ...
Number of PPIs: 100019
  Elapsed time: 0.19 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.
Normalizing networks ...
  Elapsed time: 0.01 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.05 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.5867745269558597
step: 1, hamming: 0.4770948069617154
step: 2, hamming: 0.4695616866661462
step: 3, hamming: 0.45425003629838684
step: 4, hamming: 0.4187427725151872
step: 5, hamming: 0.3679724124423835
step: 6, hamming: 0.31337190961143313
step: 7, hamming: 0.2640386174641925
step: 8, hamming: 0.22399992327898238
step: 9, hamming: 0.19253176059893798
step: 10, hamming: 0.1676553667649102
step: 11, hamming: 0.14730006142326466
step: 12, hamming: 0.1298215908983933
step: 13, hamming: 0.11459157116297605
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: 0.05062155744809771
step: 20, hamming: 0.04333239380925903
step: 21, hamming: 0.036892574940160516
step: 22, hamming: 0.03126206012121671
step: 23, hamming: 0.02638428040392175
step: 24, hamming: 0.022190961740915574
step: 25, hamming: 0.01860922988517212
step: 26, hamming: 0.015566652188260111
step: 27, hamming: 0.012993283312056424
step: 28, hamming: 0.010824919177296213
step: 29, hamming: 0.009003507268894196
step: 30, hamming: 0.00747755291088981
step: 31, hamming: 0.0062020628941105065
step: 32, hamming: 0.005138069423501644
step: 33, hamming: 0.004252085993537948
step: 34, hamming: 0.0035154788596479672
step: 35, hamming: 0.00290392674390587
step: 36, hamming: 0.0023968521367998454
step: 37, hamming: 0.0019768786344578015
step: 38, hamming: 0.0016294013136896744
step: 39, hamming: 0.0013421799963357426
step: 40, hamming: 0.0011049738470584863
step: 41, hamming: 0.000909227997318053
Running panda took: 0.43 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: 0.00 sec.
Inferring LIONESS network:
step: 0, hamming: 0.5875614098660666
step: 1, hamming: 0.48294668487646625
step: 2, hamming: 0.4810579089105837
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: 0.22871223602816745
step: 9, hamming: 0.19638081399100335
step: 10, hamming: 0.17127585718635555
step: 11, hamming: 0.15034152043301924
step: 12, hamming: 0.1323105478668466
step: 13, hamming: 0.11649711485539004
step: 14, hamming: 0.1023563092541029
step: 15, hamming: 0.08963435266941024
step: 16, hamming: 0.07811460526211582
step: 17, hamming: 0.06770343603846223
step: 18, hamming: 0.058342983115191926
step: 19, hamming: 0.04999398523930742
step: 20, hamming: 0.04261616820807743
step: 21, hamming: 0.036160346966779874
step: 22, hamming: 0.03055914202736641
step: 23, hamming: 0.02573700902927474
step: 24, hamming: 0.021610772222598034
step: 25, hamming: 0.018099099845240618
step: 26, hamming: 0.01512391162922807
step: 27, hamming: 0.012613019715219047
step: 28, hamming: 0.010500738712116988
step: 29, hamming: 0.008728774744404807
step: 30, hamming: 0.007245746309115974
step: 31, hamming: 0.0060071587779357664
step: 32, hamming: 0.004974647163777003
step: 33, hamming: 0.004115358386600001
step: 34, hamming: 0.003401306327536735
step: 35, hamming: 0.002808749172176155
step: 36, hamming: 0.002317621564663277
step: 37, hamming: 0.0019110115327221292
step: 38, hamming: 0.0015747162820157854
step: 39, hamming: 0.0012968334760169568
step: 40, hamming: 0.0010674133797636278
step: 41, hamming: 0.0008781471581459396
  Elapsed time: 0.33 sec.
Saving LIONESS network 1 to lioness_output using no format:
Unknown format no! File will not be saved.
  Elapsed time: 0.00 sec.
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: 0.17 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
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.00 sec.
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: 0.04 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: 0.6267664063560152
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: 0.4945006816241803
step: 7, hamming: 0.4536157699252672
step: 8, hamming: 0.40948805442896147
step: 9, hamming: 0.3643147759446061
step: 10, hamming: 0.3202827156746967
step: 11, hamming: 0.2788957505583951
step: 12, hamming: 0.240869786159727
step: 13, hamming: 0.2065830558514754
step: 14, hamming: 0.17608500470506336
step: 15, hamming: 0.14929860299983969
step: 16, hamming: 0.1260432183021211
step: 17, hamming: 0.10605108373830613
step: 18, hamming: 0.08898835303868327
step: 19, hamming: 0.07448950012171324
step: 20, hamming: 0.06222491628833417
step: 21, hamming: 0.05188708455543117
step: 22, hamming: 0.04319809393977558
step: 23, hamming: 0.035912550157300875
step: 24, hamming: 0.02981582036436827
step: 25, hamming: 0.02472412266649083
step: 26, hamming: 0.020479690684899503
step: 27, hamming: 0.016946966247749072
step: 28, hamming: 0.0140106453158808
step: 29, hamming: 0.011573255021910608
step: 30, hamming: 0.009552447322836872
step: 31, hamming: 0.007878861027854666
step: 32, hamming: 0.006494227871820683
step: 33, hamming: 0.005349713278823826
step: 34, hamming: 0.0044044751666175675
step: 35, hamming: 0.0036244207432898226
step: 36, hamming: 0.0029811401934302624
step: 37, hamming: 0.0024509964879006712
step: 38, hamming: 0.0020143516839460003
step: 39, hamming: 0.0016549116365250657
step: 40, hamming: 0.0013591727817255633
step: 41, hamming: 0.0011159564314784426
step: 42, hamming: 0.0009160177452470301
  Elapsed time: 0.04 sec.
Saving LIONESS network 1 to lioness_output using no format:
Unknown format no! File will not be saved.
  Elapsed time: 0.00 sec.
[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
 40 1079k   40  434k    0     0   650k      0  0:00:01 --:--:--  0:00:01  649k
100 1079k  100 1079k    0     0  1364k      0 --:--:-- --:--:-- --:--:-- 1362k
[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 0.0002245903 secs
[1] "More data cleaning"
[1] "Main calculation"
.....................................................[1] "Initializing and validating"
[1] "Verified adequate samples, calculating correlation matrix"
Time difference of 0.0002253056 secs
[1] "More data cleaning"
[1] "Main calculation"
.....................................................[1] "Using OLS method"
[1] "Finished running iteration 1"
Time difference of 6.318054 secs
Time difference of 0.1308844 secs
Time difference of 0.178915 secs
Time difference of 0.1327913 secs
Time difference of 0.1727939 secs
[1] "Using OLS method"
Time difference of 3.170967e-05 secs
Time difference of 4.32326 secs
Time difference of 2.347293 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
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 27822  100 27822    0     0   107k      0 --:--:-- --:--:-- --:--:--  107k
Loading expression data ...
  Elapsed time: 0.03 sec.
No PPI data given: ppi matrix will be an identity matrix of size 0
Calculating coexpression network ...
  Elapsed time: 0.03 sec.
Returning the correlation matrix of expression data in <Panda_obj>.correlation_matrix
['Rv0001' 'Rv0002' 'Rv0003' ... 'Rv0193c' 'Rv0194' 'Rv0195']
['Rv0001' 'Rv0001' 'Rv0001' ... 'Rv0195' 'Rv0195' 'Rv0195']
(40000,)
Loading motif data ...
  Elapsed time: 0.03 sec.
Loading expression data ...
  Elapsed time: 0.04 sec.
No PPI data given: ppi matrix will be an identity matrix of size 5
Calculating coexpression network ...
  Elapsed time: 0.09 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Normalizing networks ...
  Elapsed time: 0.09 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.3008717441926665
step: 1, hamming: 0.32577840239393485
step: 2, hamming: 0.36046547993298506
step: 3, hamming: 0.36058526850894806
step: 4, hamming: 0.3466240823512552
step: 5, hamming: 0.32456269443005153
step: 6, hamming: 0.2989434598421862
step: 7, hamming: 0.2706019093508666
step: 8, hamming: 0.24146225569326246
step: 9, hamming: 0.21301541796450382
step: 10, hamming: 0.18618747428128857
step: 11, hamming: 0.16147381450104786
step: 12, hamming: 0.13913324895882415
step: 13, hamming: 0.11926159237252416
step: 14, hamming: 0.1018524648128548
step: 15, hamming: 0.08669455519421927
step: 16, hamming: 0.07353017763220226
step: 17, hamming: 0.06215000422873393
step: 18, hamming: 0.05239618178480344
step: 19, hamming: 0.04409487478206072
step: 20, hamming: 0.037011961055401506
step: 21, hamming: 0.03099423061137592
step: 22, hamming: 0.025900515663656126
step: 23, hamming: 0.02160297573646609
step: 24, hamming: 0.017987639137724463
step: 25, hamming: 0.01495414717402849
step: 26, hamming: 0.01241474935607542
step: 27, hamming: 0.010293476645032267
step: 28, hamming: 0.008524772832534408
step: 29, hamming: 0.007052536065331644
step: 30, hamming: 0.0058289629675493905
step: 31, hamming: 0.004813469251228287
step: 32, hamming: 0.003971733841541358
step: 33, hamming: 0.003274823735478185
step: 34, hamming: 0.002698421842219443
step: 35, hamming: 0.0022221411979149487
step: 36, hamming: 0.0018289290757055078
step: 37, hamming: 0.0015045517890993694
step: 38, hamming: 0.0012371486338300583
step: 39, hamming: 0.0010168547681778833
step: 40, hamming: 0.0008354772054776381
Running panda took: 4.87 seconds!
Killed

name	user	system	elapsed
alpaca	0.990	0.016	1.006
alpacaCommunityStructureRotation	0.001	0.000	0.000
alpacaComputeDWBMmatmScale	0	0	0
alpacaComputeWBMmat	0	0	0
alpacaCrane	0	0	0
alpacaDeltaZAnalysis	0	0	0
alpacaDeltaZAnalysisLouvain	0	0	0
alpacaExtractTopGenes	0.423	0.000	0.423
alpacaGOtabtogenes	0	0	0
alpacaGenLouvain	0	0	0
alpacaGoToGenes	0	0	0
alpacaListToGo	0	0	0
alpacaMetaNetwork	0	0	0
alpacaNodeToGene	0	0	0
alpacaRotationAnalysis	0	0	0
alpacaRotationAnalysisLouvain	0	0	0
alpacaSimulateNetwork	0.001	0.000	0.000
alpacaTestNodeRank	0	0	0
alpacaTidyConfig	0.001	0.000	0.001
alpacaTopEnsembltoTopSym	0	0	0
alpacaWBMlouvain	0	0	0
condorCluster	1.698	0.108	1.806
condorCoreEnrich	2.216	0.112	2.328
condorMatrixModularity	0.009	0.000	0.009
condorModularityMax	0.018	0.008	0.026
condorPlotCommunities	1.513	0.004	1.517
condorPlotHeatmap	0.215	0.016	0.231
condorQscore	1.584	0.000	1.584
craneBipartite	0.000	0.000	0.001
createCondorObject	0.003	0.000	0.003
createPandaStyle	0	0	0
lioness	4.470	0.236	4.708
lionessPy	0.002	0.000	0.002
monster	6.766	0.116	6.882
monsterBereFull	3.533	0.048	3.580
monsterCalculateTmPValues	0.015	0.000	0.015
monsterCheckDataType	0.168	0.140	0.307
monsterGetTm	0.004	0.000	0.004
monsterHclHeatmapPlot	0.783	0.024	0.807
monsterMonsterNI	1.852	0.044	1.896
monsterPlotMonsterAnalysis	32.861	0.476	33.338
monsterPrintMonsterAnalysis	35.882	0.340	36.222
monsterTransformationMatrix	0.593	0.012	0.606
monsterTransitionNetworkPlot	0.240	0.000	0.241
monsterTransitionPCAPlot	0.138	0.000	0.138
monsterdTFIPlot	0.227	0.000	0.227
otter	0.003	0.000	0.003
pandaPy	0.002	0.000	0.003
pandaToAlpaca	0.002	0.000	0.002
pandaToCondorObject	0.000	0.001	0.001
runEgret	0.009	0.001	0.012
sambar	1.711	0.000	1.711
sourcePPI	0.007	0.000	0.007
visPandaInCytoscape	0.001	0.000	0.000

CHECK results for netZooR on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings