| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:17 -0400 (Wed, 12 Apr 2023).
| 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 | ||||
|
To the developers/maintainers of the netZooR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netZooR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1350/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netZooR 1.2.0 (landing page) Marouen Ben Guebila
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: netZooR |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2023-04-10 21:32:27 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 21:47:09 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 881.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: netZooR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/netZooR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.2.0’
* 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 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 28.247 2.972 31.325
monsterPlotMonsterAnalysis 28.138 2.699 30.938
monster 5.616 0.471 6.126
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/netZooR.Rcheck/00check.log’
for details.
netZooR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netZooR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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)
netZooR.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(netZooR)
Loading required package: igraph
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: reticulate
Loading required package: pandaR
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:igraph':
normalize, path, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: yarn
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> #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 0.0223684210526322"
[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
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 355 100 355 0 0 1703 0 --:--:-- --:--:-- --:--:-- 1811
% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 569 100 569 0 0 3116 0 --:--:-- --:--:-- --:--:-- 3308
% 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 3210 0 --:--:-- --:--:-- --:--:-- 3346
% 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 21757 0 --:--:-- --:--:-- --:--:-- 23323
% 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 2101 0 --:--:-- --:--:-- --:--:-- 2228
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 222 100 222 0 0 1263 0 --:--:-- --:--:-- --:--:-- 1361
% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
14 1438k 14 203k 0 0 350k 0 0:00:04 --:--:-- 0:00:04 356k
96 1438k 96 1392k 0 0 873k 0 0:00:01 0:00:01 --:--:-- 878k
100 1438k 100 1438k 0 0 888k 0 0:00:01 0:00:01 --:--:-- 893k
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 578 100 578 0 0 2478 0 --:--:-- --:--:-- --:--:-- 2603
[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 114k 0 --:--:-- --:--:-- --:--:-- 120k
Loading expression data ...
Elapsed time: 0.02 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,)
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/netZooR/extdata/lioness.py:346: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
indDF = indDF.append(
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: 0.01 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.
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2829: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[:, None]
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2830: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[None, :]
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: 0.02 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.3008717441926667
step: 1, hamming: 0.32577840239393496
step: 2, hamming: 0.36046547993298544
step: 3, hamming: 0.36058526850894806
step: 4, hamming: 0.3466240823512555
step: 5, hamming: 0.32456269443005165
step: 6, hamming: 0.29894345984218645
step: 7, hamming: 0.27060190935086686
step: 8, hamming: 0.24146225569326282
step: 9, hamming: 0.21301541796450388
step: 10, hamming: 0.1861874742812892
step: 11, hamming: 0.16147381450104845
step: 12, hamming: 0.1391332489588238
step: 13, hamming: 0.11926159237252484
step: 14, hamming: 0.10185246481285452
step: 15, hamming: 0.08669455519421998
step: 16, hamming: 0.07353017763220182
step: 17, hamming: 0.06215000422873348
step: 18, hamming: 0.052396181784803826
step: 19, hamming: 0.04409487478206075
step: 20, hamming: 0.03701196105540119
step: 21, hamming: 0.03099423061137564
step: 22, hamming: 0.025900515663656483
step: 23, hamming: 0.021602975736465913
step: 24, hamming: 0.01798763913772466
step: 25, hamming: 0.014954147174028844
step: 26, hamming: 0.01241474935607606
step: 27, hamming: 0.010293476645032596
step: 28, hamming: 0.008524772832534808
step: 29, hamming: 0.007052536065331863
step: 30, hamming: 0.005828962967548954
step: 31, hamming: 0.00481346925122789
step: 32, hamming: 0.003971733841541235
step: 33, hamming: 0.0032748237354783805
step: 34, hamming: 0.00269842184221958
step: 35, hamming: 0.0022221411979144803
step: 36, hamming: 0.0018289290757053124
step: 37, hamming: 0.001504551789099312
step: 38, hamming: 0.0012371486338297601
step: 39, hamming: 0.0010168547681782068
step: 40, hamming: 0.0008354772054775502
Running panda took: 0.81 seconds!
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2829: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[:, None]
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2830: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[None, :]
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/netZooR/extdata/lioness.py:337: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
indDF = indDF.append(
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: 0.02 sec.
Inferring LIONESS network:
step: 0, hamming: 0.30159324227999135
step: 1, hamming: 0.326744782398401
step: 2, hamming: 0.36109248186970094
step: 3, hamming: 0.3608089428450733
step: 4, hamming: 0.34665241776678835
step: 5, hamming: 0.3245939713292128
step: 6, hamming: 0.2989655066138042
step: 7, hamming: 0.27062058204102235
step: 8, hamming: 0.241483272798797
step: 9, hamming: 0.21304028351555637
step: 10, hamming: 0.18620484129483533
step: 11, hamming: 0.16148366668824993
step: 12, hamming: 0.13913925776650846
step: 13, hamming: 0.11927055262102387
step: 14, hamming: 0.10186083999388643
step: 15, hamming: 0.08670615581741928
step: 16, hamming: 0.07353988598228602
step: 17, hamming: 0.06215811356512138
step: 18, hamming: 0.05241372809810218
step: 19, hamming: 0.04410977556767987
step: 20, hamming: 0.03702457033326206
step: 21, hamming: 0.031005003311005128
step: 22, hamming: 0.025909572963571176
step: 23, hamming: 0.021610559908641705
step: 24, hamming: 0.017993951127132018
step: 25, hamming: 0.014959350583484184
step: 26, hamming: 0.012419036091497044
step: 27, hamming: 0.010296989659985933
step: 28, hamming: 0.008527684145048432
step: 29, hamming: 0.007054962882501581
step: 30, hamming: 0.005830983737417126
step: 31, hamming: 0.0048151512025851
step: 32, hamming: 0.003973130484198018
step: 33, hamming: 0.0032759823203924406
step: 34, hamming: 0.002699382028610703
step: 35, hamming: 0.002222936231546537
step: 36, hamming: 0.0018295867892866126
step: 37, hamming: 0.0015050947585650975
step: 38, hamming: 0.0012375965038721236
step: 39, hamming: 0.0010172239699258487
step: 40, hamming: 0.0008357813833839833
Elapsed time: 0.74 sec.
Saving LIONESS network 1 to lioness_output using no format:
Unknown format no! File will not be saved.
Elapsed time: 0.00 sec.
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2829: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[:, None]
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2830: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[None, :]
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: 0.97 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.19 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.08748661874955622
step: 1, hamming: 0.06888714365861337
step: 2, hamming: 0.062114312778413824
step: 3, hamming: 0.057133530904466975
step: 4, hamming: 0.05304016922455829
step: 5, hamming: 0.049101138022894876
step: 6, hamming: 0.045074438192725504
step: 7, hamming: 0.04095526634659025
step: 8, hamming: 0.036830333937534133
step: 9, hamming: 0.03280131999197774
step: 10, hamming: 0.02895800229188848
step: 11, hamming: 0.025365652761878358
step: 12, hamming: 0.022066636023677574
step: 13, hamming: 0.01907883671127774
step: 14, hamming: 0.01640531302887969
step: 15, hamming: 0.014037779400693125
step: 16, hamming: 0.01195982841838061
step: 17, hamming: 0.010150090707741312
step: 18, hamming: 0.008584499851559678
step: 19, hamming: 0.0072380075895177075
step: 20, hamming: 0.0060858622486750545
step: 21, hamming: 0.005104411138700387
step: 22, hamming: 0.004271661591718607
step: 23, hamming: 0.003567561174685129
step: 24, hamming: 0.002974084885079093
step: 25, hamming: 0.0024752438901140686
step: 26, hamming: 0.0020569891001135433
step: 27, hamming: 0.0017070859535523305
step: 28, hamming: 0.0014149533300699603
step: 29, hamming: 0.0011714963862094997
step: 30, hamming: 0.0009689369122934191
Running panda took: 28.22 seconds!
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2829: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[:, None]
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2830: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[None, :]
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/netZooR/extdata/lioness.py:337: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
indDF = indDF.append(
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: 0.02 sec.
Inferring LIONESS network:
step: 0, hamming: 0.0874818573175637
step: 1, hamming: 0.06891282897076391
step: 2, hamming: 0.062130587348151134
step: 3, hamming: 0.05714118386838519
step: 4, hamming: 0.05304529446377499
step: 5, hamming: 0.04910525549313265
step: 6, hamming: 0.045077507937550505
step: 7, hamming: 0.04095716825335454
step: 8, hamming: 0.036831755781812706
step: 9, hamming: 0.032802826977823545
step: 10, hamming: 0.02895992049443768
step: 11, hamming: 0.025367894743653203
step: 12, hamming: 0.022069009727623188
step: 13, hamming: 0.01908131820381921
step: 14, hamming: 0.01640778820189424
step: 15, hamming: 0.014040090736288887
step: 16, hamming: 0.011961875397219704
step: 17, hamming: 0.010151865216875243
step: 18, hamming: 0.008586011382256616
step: 19, hamming: 0.007239278751699699
step: 20, hamming: 0.006086920160262563
step: 21, hamming: 0.0051052834701504814
step: 22, hamming: 0.004272377006570677
step: 23, hamming: 0.0035681447767932518
step: 24, hamming: 0.002974559350795158
step: 25, hamming: 0.0024756282596510126
step: 26, hamming: 0.002057299996352307
step: 27, hamming: 0.0017073373347909885
step: 28, hamming: 0.00141515656139143
step: 29, hamming: 0.0011716607762849135
step: 30, hamming: 0.0009690701447933819
Elapsed time: 29.32 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: 0.00 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.06 sec.
Normalizing networks ...
Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.6788049340248108
step: 1, hamming: 0.4237635135650635
step: 2, hamming: 0.37942326068878174
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: 0.03 seconds!
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/netZooR/extdata/lioness.py:337: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
indDF = indDF.append(
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: 0.6829624252643024
step: 1, hamming: 0.43097386969737467
step: 2, hamming: 0.3855310332972826
step: 3, hamming: 0.38637191344546506
step: 4, hamming: 0.3900182026704469
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: 0.18751291931754166
step: 13, hamming: 0.16097018362231139
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: 0.04944784893620859
step: 21, hamming: 0.04133266535809628
step: 22, hamming: 0.03448368388232095
step: 23, hamming: 0.028720375548938085
step: 24, hamming: 0.02388327219797364
step: 25, hamming: 0.01983295871646228
step: 26, hamming: 0.016448511057472175
step: 27, hamming: 0.013625773339477055
step: 28, hamming: 0.011275503429549744
step: 29, hamming: 0.009321615661804521
step: 30, hamming: 0.007699524683027153
step: 31, hamming: 0.006354585216875871
step: 32, hamming: 0.00524073243580051
step: 33, hamming: 0.004319230981273431
step: 34, hamming: 0.003557580755210523
step: 35, hamming: 0.0029286114077763654
step: 36, hamming: 0.002409612680693885
step: 37, hamming: 0.0019816823742853846
step: 38, hamming: 0.0016290920553380472
step: 39, hamming: 0.0013387284639915446
step: 40, hamming: 0.0010997294054595052
step: 41, hamming: 0.0009031298195247481
Elapsed time: 0.02 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: 0.00 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.06 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: 0.5867745269558597
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: 0.06 seconds!
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/netZooR/extdata/lioness.py:337: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
indDF = indDF.append(
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: 0.5875614098660666
step: 1, hamming: 0.4829466848764663
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: 0.08963435266941025
step: 16, hamming: 0.07811460526211583
step: 17, hamming: 0.06770343603846223
step: 18, hamming: 0.05834298311519195
step: 19, hamming: 0.04999398523930743
step: 20, hamming: 0.042616168208077454
step: 21, hamming: 0.03616034696677988
step: 22, hamming: 0.030559142027366405
step: 23, hamming: 0.025737009029274744
step: 24, hamming: 0.021610772222598038
step: 25, hamming: 0.018099099845240614
step: 26, hamming: 0.01512391162922806
step: 27, hamming: 0.01261301971521904
step: 28, hamming: 0.010500738712116991
step: 29, hamming: 0.008728774744404807
step: 30, hamming: 0.00724574630911598
step: 31, hamming: 0.006007158777935759
step: 32, hamming: 0.004974647163777016
step: 33, hamming: 0.004115358386599994
step: 34, hamming: 0.0034013063275367293
step: 35, hamming: 0.002808749172176152
step: 36, hamming: 0.0023176215646632894
step: 37, hamming: 0.00191101153272212
step: 38, hamming: 0.0015747162820157828
step: 39, hamming: 0.0012968334760169711
step: 40, hamming: 0.001067413379763626
step: 41, hamming: 0.0008781471581459417
Elapsed time: 0.07 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.
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: 0.02 seconds!
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/netZooR/extdata/lioness.py:337: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
indDF = indDF.append(
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: 0.02 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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
45 1079k 45 492k 0 0 420k 0 0:00:02 0:00:01 0:00:01 440k
100 1079k 100 1079k 0 0 676k 0 0:00:01 0:00:01 --:--:-- 699k
[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 0.0001540184 secs
[1] "More data cleaning"
[1] "Main calculation"
.....................................................[1] "Initializing and validating"
[1] "Verified adequate samples, calculating correlation matrix"
Time difference of 0.0001299381 secs
[1] "More data cleaning"
[1] "Main calculation"
.....................................................[1] "Using OLS method"
[1] "Finished running iteration 1"
Time difference of 3.052107 secs
Time difference of 0.103281 secs
Time difference of 0.08460402 secs
Time difference of 0.1005139 secs
Time difference of 0.08251309 secs
[1] "Using OLS method"
Time difference of 2.098083e-05 secs
Time difference of 1.643885 secs
Time difference of 0.6141 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 91930 0 --:--:-- --:--:-- --:--:-- 94955
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,)
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2829: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[:, None]
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2830: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[None, :]
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: 0.02 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.3008717441926667
step: 1, hamming: 0.32577840239393496
step: 2, hamming: 0.36046547993298544
step: 3, hamming: 0.36058526850894806
step: 4, hamming: 0.3466240823512555
step: 5, hamming: 0.32456269443005165
step: 6, hamming: 0.29894345984218645
step: 7, hamming: 0.27060190935086686
step: 8, hamming: 0.24146225569326282
step: 9, hamming: 0.21301541796450388
step: 10, hamming: 0.1861874742812892
step: 11, hamming: 0.16147381450104845
step: 12, hamming: 0.1391332489588238
step: 13, hamming: 0.11926159237252484
step: 14, hamming: 0.10185246481285452
step: 15, hamming: 0.08669455519421998
step: 16, hamming: 0.07353017763220182
step: 17, hamming: 0.06215000422873348
step: 18, hamming: 0.052396181784803826
step: 19, hamming: 0.04409487478206075
step: 20, hamming: 0.03701196105540119
step: 21, hamming: 0.03099423061137564
step: 22, hamming: 0.025900515663656483
step: 23, hamming: 0.021602975736465913
step: 24, hamming: 0.01798763913772466
step: 25, hamming: 0.014954147174028844
step: 26, hamming: 0.01241474935607606
step: 27, hamming: 0.010293476645032596
step: 28, hamming: 0.008524772832534808
step: 29, hamming: 0.007052536065331863
step: 30, hamming: 0.005828962967548954
step: 31, hamming: 0.00481346925122789
step: 32, hamming: 0.003971733841541235
step: 33, hamming: 0.0032748237354783805
step: 34, hamming: 0.00269842184221958
step: 35, hamming: 0.0022221411979144803
step: 36, hamming: 0.0018289290757053124
step: 37, hamming: 0.001504551789099312
step: 38, hamming: 0.0012371486338297601
step: 39, hamming: 0.0010168547681782068
step: 40, hamming: 0.0008354772054775502
Running panda took: 0.82 seconds!
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2829: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[:, None]
/usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2830: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[None, :]
Loading motif data ...
Elapsed time: 0.01 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: 0.01 sec.
Creating motif network ...
Elapsed time: 0.01 sec.
Creating PPI network ...
Elapsed time: 0.11 sec.
Normalizing networks ...
Elapsed time: 0.99 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.21 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.08748661874955622
step: 1, hamming: 0.06888714365861337
step: 2, hamming: 0.062114312778413824
step: 3, hamming: 0.057133530904466975
step: 4, hamming: 0.05304016922455829
step: 5, hamming: 0.049101138022894876
step: 6, hamming: 0.045074438192725504
step: 7, hamming: 0.04095526634659025
step: 8, hamming: 0.036830333937534133
step: 9, hamming: 0.03280131999197774
step: 10, hamming: 0.02895800229188848
step: 11, hamming: 0.025365652761878358
step: 12, hamming: 0.022066636023677574
step: 13, hamming: 0.01907883671127774
step: 14, hamming: 0.01640531302887969
step: 15, hamming: 0.014037779400693125
step: 16, hamming: 0.01195982841838061
step: 17, hamming: 0.010150090707741312
step: 18, hamming: 0.008584499851559678
step: 19, hamming: 0.0072380075895177075
step: 20, hamming: 0.0060858622486750545
step: 21, hamming: 0.005104411138700387
step: 22, hamming: 0.004271661591718607
step: 23, hamming: 0.003567561174685129
step: 24, hamming: 0.002974084885079093
step: 25, hamming: 0.0024752438901140686
step: 26, hamming: 0.0020569891001135433
step: 27, hamming: 0.0017070859535523305
step: 28, hamming: 0.0014149533300699603
step: 29, hamming: 0.0011714963862094997
step: 30, hamming: 0.0009689369122934191
Running panda took: 42.30 seconds!
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: 0.17 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.
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: 0.06 seconds!
Loading motif data ...
Elapsed time: 0.01 sec.
Loading expression data ...
Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.15 sec.
Calculating coexpression network ...
Elapsed time: 0.01 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.18 sec.
Normalizing networks ...
Elapsed time: 0.01 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.02 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: 0.50 seconds!
Loading motif data ...
Elapsed time: 0.01 sec.
Loading expression data ...
Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.16 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: 0.07 seconds!
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.471004488691679"
[1] "Q = 0.471024100010188"
[1] "Q = 0.471024100010188"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 386 communities"
[1] 1
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[1] "Merging 201 communities"
[1] 1
[1] "Computing node scores..."
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Read 7424 items
WARNING: Score threshold is not specified. We will be using medium stringency cut-off of 400.
trying URL 'https://stringdb-static.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-static.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-static.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 1 | SKIP 0 | PASS 61 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 61 ]
>
> proc.time()
user system elapsed
395.957 45.582 467.474
netZooR.Rcheck/netZooR-Ex.timings
| name | user | system | elapsed | |
| alpaca | 0.814 | 0.021 | 0.837 | |
| alpacaCommunityStructureRotation | 0 | 0 | 0 | |
| alpacaComputeDWBMmatmScale | 0 | 0 | 0 | |
| alpacaComputeWBMmat | 0.001 | 0.000 | 0.000 | |
| alpacaCrane | 0 | 0 | 0 | |
| alpacaDeltaZAnalysis | 0 | 0 | 0 | |
| alpacaDeltaZAnalysisLouvain | 0 | 0 | 0 | |
| alpacaExtractTopGenes | 0.316 | 0.004 | 0.320 | |
| alpacaGOtabtogenes | 0 | 0 | 0 | |
| alpacaGenLouvain | 0 | 0 | 0 | |
| alpacaGoToGenes | 0 | 0 | 0 | |
| alpacaListToGo | 0 | 0 | 0 | |
| alpacaMetaNetwork | 0 | 0 | 0 | |
| alpacaNodeToGene | 0.001 | 0.000 | 0.000 | |
| alpacaRotationAnalysis | 0.000 | 0.001 | 0.000 | |
| alpacaRotationAnalysisLouvain | 0 | 0 | 0 | |
| alpacaSimulateNetwork | 0 | 0 | 0 | |
| alpacaTestNodeRank | 0 | 0 | 0 | |
| alpacaTidyConfig | 0 | 0 | 0 | |
| alpacaTopEnsembltoTopSym | 0 | 0 | 0 | |
| alpacaWBMlouvain | 0 | 0 | 0 | |
| condorCluster | 1.072 | 0.006 | 1.080 | |
| condorCoreEnrich | 1.693 | 0.057 | 1.761 | |
| condorMatrixModularity | 0.007 | 0.002 | 0.009 | |
| condorModularityMax | 0.022 | 0.004 | 0.025 | |
| condorPlotCommunities | 1.045 | 0.009 | 1.056 | |
| condorPlotHeatmap | 0.149 | 0.019 | 0.169 | |
| condorQscore | 1.008 | 0.007 | 1.017 | |
| craneBipartite | 0 | 0 | 0 | |
| createCondorObject | 0.002 | 0.000 | 0.002 | |
| createPandaStyle | 0 | 0 | 0 | |
| lioness | 3.754 | 0.248 | 4.011 | |
| lionessPy | 0.002 | 0.001 | 0.002 | |
| monster | 5.616 | 0.471 | 6.126 | |
| monsterBereFull | 2.616 | 0.217 | 2.840 | |
| monsterCalculateTmPValues | 0.011 | 0.002 | 0.013 | |
| monsterCheckDataType | 0.155 | 0.378 | 0.537 | |
| monsterGetTm | 0.002 | 0.002 | 0.004 | |
| monsterHclHeatmapPlot | 0.616 | 0.027 | 0.645 | |
| monsterMonsterNI | 2.319 | 0.064 | 2.391 | |
| monsterPlotMonsterAnalysis | 28.138 | 2.699 | 30.938 | |
| monsterPrintMonsterAnalysis | 28.247 | 2.972 | 31.325 | |
| monsterTransformationMatrix | 0.624 | 0.027 | 0.653 | |
| monsterTransitionNetworkPlot | 0.193 | 0.007 | 0.200 | |
| monsterTransitionPCAPlot | 0.130 | 0.004 | 0.135 | |
| monsterdTFIPlot | 0.189 | 0.004 | 0.193 | |
| otter | 0.002 | 0.001 | 0.002 | |
| pandaPy | 0.002 | 0.001 | 0.003 | |
| pandaToAlpaca | 0.003 | 0.001 | 0.004 | |
| pandaToCondorObject | 0.002 | 0.000 | 0.002 | |
| runEgret | 0.012 | 0.003 | 0.017 | |
| sambar | 1.532 | 0.183 | 1.725 | |
| sourcePPI | 0.007 | 0.001 | 0.008 | |
| visPandaInCytoscape | 0.000 | 0.000 | 0.001 | |