| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:43 -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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netZooR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings netZooR_1.2.0.tar.gz |
| StartedAt: 2023-04-11 03:57:21 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 04:11:13 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 831.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: netZooR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netZooR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings netZooR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/netZooR.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 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
monsterPlotMonsterAnalysis 40.32 1.32 41.64
monsterPrintMonsterAnalysis 37.01 0.94 37.96
monster 6.53 0.66 7.18
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/netZooR.Rcheck/00check.log'
for details.
netZooR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL netZooR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 0.0250000000000004"
[1] "Q = 0.0263157894736842"
[1] "Q = 0.0263157894736842"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 100 communities"
[1] 1
[1] 2
[1] 3
[1] 4
[1] "Merging 2 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
[1] "modularity of projected graph 0.144628099173554"
[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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 355 100 355 0 0 2391 0 --:--:-- --:--:-- --:--:-- 2398
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 569 100 569 0 0 3841 0 --:--:-- --:--:-- --:--:-- 3870
% 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 7167 0 --:--:-- --:--:-- --:--:-- 7241
% 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 29073 0 --:--:-- --:--:-- --:--:-- 29472
% 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 3538 0 --:--:-- --:--:-- --:--:-- 3565
% 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 2269 0 --:--:-- --:--:-- --:--:-- 2288
% 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 1438k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1438k 100 1438k 0 0 5345k 0 --:--:-- --:--:-- --:--:-- 5346k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 578 100 578 0 0 6039 0 --:--:-- --:--:-- --:--:-- 6084
[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 234k 0 --:--:-- --:--:-- --:--:-- 236k
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,)
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.
C:\Python39\lib\site-packages\numpy\lib\function_base.py:2691: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[:, None]
C:\Python39\lib\site-packages\numpy\lib\function_base.py:2692: RuntimeWarning: invalid value encountered in true_divide
c /= stddev[None, :]
Loading motif data ...
Elapsed time: 0.00 sec.
Loading expression data ...
Elapsed time: 0.02 sec.
No PPI data given: ppi matrix will be an identity matrix of size 5
Calculating coexpression network ...
Elapsed time: 0.03 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: 0.3008717441926665
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: 0.005828962967549391
step: 31, hamming: 0.004813469251228287
step: 32, hamming: 0.003971733841541358
step: 33, hamming: 0.003274823735478184
step: 34, hamming: 0.002698421842219443
step: 35, hamming: 0.002222141197914948
step: 36, hamming: 0.0018289290757055085
step: 37, hamming: 0.0015045517890993699
step: 38, hamming: 0.001237148633830058
step: 39, hamming: 0.0010168547681778833
step: 40, hamming: 0.0008354772054776418
Running panda took: 0.69 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: 0.02 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: 0.3245939713292134
step: 6, hamming: 0.2989655066138038
step: 7, hamming: 0.27062058204102246
step: 8, hamming: 0.24148327279879642
step: 9, hamming: 0.21304028351555665
step: 10, hamming: 0.18620484129483603
step: 11, hamming: 0.1614836666882501
step: 12, hamming: 0.13913925776650915
step: 13, hamming: 0.1192705526210247
step: 14, hamming: 0.10186083999388719
step: 15, hamming: 0.0867061558174197
step: 16, hamming: 0.0735398859822866
step: 17, hamming: 0.06215811356512186
step: 18, hamming: 0.05241372809810256
step: 19, hamming: 0.04410977556767985
step: 20, hamming: 0.03702457033326145
step: 21, hamming: 0.031005003311004847
step: 22, hamming: 0.02590957296357105
step: 23, hamming: 0.021610559908641202
step: 24, hamming: 0.01799395112713222
step: 25, hamming: 0.014959350583484143
step: 26, hamming: 0.012419036091497034
step: 27, hamming: 0.010296989659986456
step: 28, hamming: 0.00852768414504873
step: 29, hamming: 0.007054962882501573
step: 30, hamming: 0.005830983737417465
step: 31, hamming: 0.004815151202585597
step: 32, hamming: 0.003973130484197424
step: 33, hamming: 0.0032759823203917893
step: 34, hamming: 0.0026993820286105494
step: 35, hamming: 0.0022229362315468095
step: 36, hamming: 0.0018295867892865773
step: 37, hamming: 0.0015050947585658215
step: 38, hamming: 0.0012375965038720221
step: 39, hamming: 0.001017223969926159
step: 40, hamming: 0.0008357813833837506
Elapsed time: 0.70 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: 0.02 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: 0.02 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.09 sec.
Normalizing networks ...
Elapsed time: 1.13 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 1.34 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: 0.036830333937534133
step: 9, hamming: 0.03280131999197774
step: 10, hamming: 0.02895800229188848
step: 11, hamming: 0.025365652761878358
step: 12, hamming: 0.022066636023677574
step: 13, hamming: 0.019078836711277743
step: 14, hamming: 0.016405313028879685
step: 15, hamming: 0.014037779400693116
step: 16, hamming: 0.01195982841838061
step: 17, hamming: 0.01015009070774131
step: 18, hamming: 0.008584499851559681
step: 19, hamming: 0.007238007589517707
step: 20, hamming: 0.00608586224867506
step: 21, hamming: 0.005104411138700386
step: 22, hamming: 0.004271661591718609
step: 23, hamming: 0.003567561174685126
step: 24, hamming: 0.002974084885079086
step: 25, hamming: 0.002475243890114065
step: 26, hamming: 0.002056989100113543
step: 27, hamming: 0.0017070859535523232
step: 28, hamming: 0.0014149533300699651
step: 29, hamming: 0.0011714963862095031
step: 30, hamming: 0.000968936912293422
Running panda took: 28.80 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: 0.03 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: 0.053045294463774983
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: 0.02536789474365321
step: 12, hamming: 0.022069009727623188
step: 13, hamming: 0.019081318203819215
step: 14, hamming: 0.016407788201894247
step: 15, hamming: 0.014040090736288896
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: 0.002974559350795157
step: 25, hamming: 0.002475628259651009
step: 26, hamming: 0.0020572999963523056
step: 27, hamming: 0.0017073373347909835
step: 28, hamming: 0.00141515656139142
step: 29, hamming: 0.0011716607762849165
step: 30, hamming: 0.0009690701447933722
Elapsed time: 29.83 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: 0.11 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: 0.3794232904911041
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: 0.02 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: 0.6829624252643024
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: 0.31596767563237377
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: 0.02 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: 0.02 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: 0.02 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.08 sec.
Normalizing networks ...
Elapsed time: 0.00 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.02 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: 0.06 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: 0.5875614098660666
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: 0.06 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: 0.08 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: 0.02 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.6201117836163109
step: 1, hamming: 0.48938385169250487
step: 2, hamming: 0.49937220814370314
step: 3, hamming: 0.5234998024292964
step: 4, hamming: 0.5316279091580729
step: 5, hamming: 0.5196461826284899
step: 6, hamming: 0.49096615680840516
step: 7, hamming: 0.45136867762995053
step: 8, hamming: 0.4081852233215105
step: 9, hamming: 0.363060630725845
step: 10, hamming: 0.3189123247409479
step: 11, hamming: 0.27733895854371826
step: 12, hamming: 0.23925292481822666
step: 13, hamming: 0.20518316158337402
step: 14, hamming: 0.17501658473943316
step: 15, hamming: 0.14854288648840214
step: 16, hamming: 0.12553582999076404
step: 17, hamming: 0.10573284427875865
step: 18, hamming: 0.08878386418920353
step: 19, hamming: 0.07436882705115158
step: 20, hamming: 0.062172412390917475
step: 21, hamming: 0.051880715413709574
step: 22, hamming: 0.043220322319520395
step: 23, hamming: 0.03594946787636906
step: 24, hamming: 0.029859895475909407
step: 25, hamming: 0.0247709383962932
step: 26, hamming: 0.02052575604899425
step: 27, hamming: 0.016990787588434916
step: 28, hamming: 0.014051171275167215
step: 29, hamming: 0.011609873894851033
step: 30, hamming: 0.009584973156032758
step: 31, hamming: 0.007907374279360044
step: 32, hamming: 0.006518966440957067
step: 33, hamming: 0.00537099915686947
step: 34, hamming: 0.004422666090211263
step: 35, hamming: 0.003639879247818417
step: 36, hamming: 0.002994214649903011
step: 37, hamming: 0.002462010284380626
step: 38, hamming: 0.0020235978467206613
step: 39, hamming: 0.001662650998788406
step: 40, hamming: 0.0013656343876712778
step: 41, hamming: 0.001121339276182217
step: 42, hamming: 0.0009204932425645662
Running panda took: 0.02 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: 0.4945006816241802
step: 7, hamming: 0.45361576992526725
step: 8, hamming: 0.40948805442896147
step: 9, hamming: 0.364314775944606
step: 10, hamming: 0.3202827156746967
step: 11, hamming: 0.27889575055839505
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: 0.10605108373830612
step: 18, hamming: 0.08898835303868327
step: 19, hamming: 0.07448950012171325
step: 20, hamming: 0.06222491628833415
step: 21, hamming: 0.05188708455543115
step: 22, hamming: 0.04319809393977557
step: 23, hamming: 0.03591255015730086
step: 24, hamming: 0.02981582036436827
step: 25, hamming: 0.024724122666490836
step: 26, hamming: 0.020479690684899493
step: 27, hamming: 0.016946966247749058
step: 28, hamming: 0.014010645315880806
step: 29, hamming: 0.011573255021910579
step: 30, hamming: 0.009552447322836884
step: 31, hamming: 0.00787886102785467
step: 32, hamming: 0.006494227871820657
step: 33, hamming: 0.00534971327882381
step: 34, hamming: 0.004404475166617579
step: 35, hamming: 0.0036244207432898318
step: 36, hamming: 0.0029811401934302546
step: 37, hamming: 0.002450996487900658
step: 38, hamming: 0.002014351683946002
step: 39, hamming: 0.0016549116365250542
step: 40, hamming: 0.0013591727817255587
step: 41, hamming: 0.0011159564314784573
step: 42, hamming: 0.0009160177452470277
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
100 1079k 100 1079k 0 0 4331k 0 --:--:-- --:--:-- --:--:-- 4352k
[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 0.0001449585 secs
[1] "More data cleaning"
[1] "Main calculation"
.....................................................[1] "Initializing and validating"
[1] "Verified adequate samples, calculating correlation matrix"
Time difference of 0.0001950264 secs
[1] "More data cleaning"
[1] "Main calculation"
.....................................................[1] "Using OLS method"
[1] "Finished running iteration 1"
Time difference of 3.791374 secs
Time difference of 0.1340618 secs
Time difference of 0.142334 secs
Time difference of 0.1116581 secs
Time difference of 0.09046912 secs
[1] "Using OLS method"
Time difference of 2.002716e-05 secs
Time difference of 1.429778 secs
Time difference of 0.6964889 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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 27822 100 27822 0 0 71841 0 --:--:-- --:--:-- --:--:-- 71891
Loading expression data ...
Elapsed time: 0.20 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 motif data ...
Elapsed time: 0.02 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: 0.02 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: 0.3008717441926665
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: 0.005828962967549391
step: 31, hamming: 0.004813469251228287
step: 32, hamming: 0.003971733841541358
step: 33, hamming: 0.003274823735478184
step: 34, hamming: 0.002698421842219443
step: 35, hamming: 0.002222141197914948
step: 36, hamming: 0.0018289290757055085
step: 37, hamming: 0.0015045517890993699
step: 38, hamming: 0.001237148633830058
step: 39, hamming: 0.0010168547681778833
step: 40, hamming: 0.0008354772054776418
Running panda took: 0.75 seconds!
Loading motif data ...
Elapsed time: 0.00 sec.
Loading expression data ...
Elapsed time: 0.00 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.34 sec.
Calculating coexpression network ...
Elapsed time: 0.02 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.11 sec.
Normalizing networks ...
Elapsed time: 1.11 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 1.27 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: 0.036830333937534133
step: 9, hamming: 0.03280131999197774
step: 10, hamming: 0.02895800229188848
step: 11, hamming: 0.025365652761878358
step: 12, hamming: 0.022066636023677574
step: 13, hamming: 0.019078836711277743
step: 14, hamming: 0.016405313028879685
step: 15, hamming: 0.014037779400693116
step: 16, hamming: 0.01195982841838061
step: 17, hamming: 0.01015009070774131
step: 18, hamming: 0.008584499851559681
step: 19, hamming: 0.007238007589517707
step: 20, hamming: 0.00608586224867506
step: 21, hamming: 0.005104411138700386
step: 22, hamming: 0.004271661591718609
step: 23, hamming: 0.003567561174685126
step: 24, hamming: 0.002974084885079086
step: 25, hamming: 0.002475243890114065
step: 26, hamming: 0.002056989100113543
step: 27, hamming: 0.0017070859535523232
step: 28, hamming: 0.0014149533300699651
step: 29, hamming: 0.0011714963862095031
step: 30, hamming: 0.000968936912293422
Running panda took: 29.70 seconds!
Loading motif data ...
Elapsed time: 0.02 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.
Clearing motif and ppi data, unique tfs, and gene names for speed
Running PANDA algorithm ...
step: 0, hamming: 0.6788049340248108
step: 1, hamming: 0.4237635135650635
step: 2, hamming: 0.3794232904911041
step: 3, hamming: 0.3818596303462982
step: 4, hamming: 0.38526612520217896
step: 5, hamming: 0.3832989037036896
step: 6, hamming: 0.36915773153305054
step: 7, hamming: 0.34574782848358154
step: 8, hamming: 0.31520816683769226
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: 0.02 seconds!
Loading motif data ...
Elapsed time: 0.00 sec.
Loading expression data ...
Elapsed time: 0.00 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.13 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: 0.02 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: 0.06 seconds!
Loading motif data ...
Elapsed time: 0.00 sec.
Loading expression data ...
Elapsed time: 0.00 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.06 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: 0.49937220814370314
step: 3, hamming: 0.5234998024292964
step: 4, hamming: 0.5316279091580729
step: 5, hamming: 0.5196461826284899
step: 6, hamming: 0.49096615680840516
step: 7, hamming: 0.45136867762995053
step: 8, hamming: 0.4081852233215105
step: 9, hamming: 0.363060630725845
step: 10, hamming: 0.3189123247409479
step: 11, hamming: 0.27733895854371826
step: 12, hamming: 0.23925292481822666
step: 13, hamming: 0.20518316158337402
step: 14, hamming: 0.17501658473943316
step: 15, hamming: 0.14854288648840214
step: 16, hamming: 0.12553582999076404
step: 17, hamming: 0.10573284427875865
step: 18, hamming: 0.08878386418920353
step: 19, hamming: 0.07436882705115158
step: 20, hamming: 0.062172412390917475
step: 21, hamming: 0.051880715413709574
step: 22, hamming: 0.043220322319520395
step: 23, hamming: 0.03594946787636906
step: 24, hamming: 0.029859895475909407
step: 25, hamming: 0.0247709383962932
step: 26, hamming: 0.02052575604899425
step: 27, hamming: 0.016990787588434916
step: 28, hamming: 0.014051171275167215
step: 29, hamming: 0.011609873894851033
step: 30, hamming: 0.009584973156032758
step: 31, hamming: 0.007907374279360044
step: 32, hamming: 0.006518966440957067
step: 33, hamming: 0.00537099915686947
step: 34, hamming: 0.004422666090211263
step: 35, hamming: 0.003639879247818417
step: 36, hamming: 0.002994214649903011
step: 37, hamming: 0.002462010284380626
step: 38, hamming: 0.0020235978467206613
step: 39, hamming: 0.001662650998788406
step: 40, hamming: 0.0013656343876712778
step: 41, hamming: 0.001121339276182217
step: 42, hamming: 0.0009204932425645662
Running panda took: 0.02 seconds!
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.471004488691679"
[1] "Q = 0.471024100010188"
[1] "Q = 0.471024100010188"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 386 communities"
[1] 1
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[1] "Merging 201 communities"
[1] 1
[1] "Computing node scores..."
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Read 7424 items
WARNING: Score threshold is not specified. We will be using medium stringency cut-off of 400.
trying URL 'https://stringdb-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
341.45 25.46 355.67
netZooR.Rcheck/netZooR-Ex.timings
| name | user | system | elapsed | |
| alpaca | 0.96 | 0.03 | 0.99 | |
| alpacaCommunityStructureRotation | 0 | 0 | 0 | |
| alpacaComputeDWBMmatmScale | 0 | 0 | 0 | |
| alpacaComputeWBMmat | 0 | 0 | 0 | |
| alpacaCrane | 0 | 0 | 0 | |
| alpacaDeltaZAnalysis | 0 | 0 | 0 | |
| alpacaDeltaZAnalysisLouvain | 0 | 0 | 0 | |
| alpacaExtractTopGenes | 0.49 | 0.00 | 0.49 | |
| 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 | 0 | 0 | |
| alpacaTestNodeRank | 0 | 0 | 0 | |
| alpacaTidyConfig | 0 | 0 | 0 | |
| alpacaTopEnsembltoTopSym | 0 | 0 | 0 | |
| alpacaWBMlouvain | 0 | 0 | 0 | |
| condorCluster | 1.22 | 0.00 | 1.22 | |
| condorCoreEnrich | 2.08 | 0.07 | 2.27 | |
| condorMatrixModularity | 0.00 | 0.01 | 0.01 | |
| condorModularityMax | 0.01 | 0.02 | 0.03 | |
| condorPlotCommunities | 1.22 | 0.00 | 1.22 | |
| condorPlotHeatmap | 0.24 | 0.00 | 0.23 | |
| condorQscore | 1.14 | 0.00 | 1.14 | |
| craneBipartite | 0 | 0 | 0 | |
| createCondorObject | 0 | 0 | 0 | |
| createPandaStyle | 0 | 0 | 0 | |
| lioness | 4.36 | 0.11 | 4.61 | |
| lionessPy | 0 | 0 | 0 | |
| monster | 6.53 | 0.66 | 7.18 | |
| monsterBereFull | 3.36 | 0.31 | 3.68 | |
| monsterCalculateTmPValues | 0.02 | 0.00 | 0.01 | |
| monsterCheckDataType | 0.37 | 0.27 | 0.64 | |
| monsterGetTm | 0 | 0 | 0 | |
| monsterHclHeatmapPlot | 0.86 | 0.06 | 0.92 | |
| monsterMonsterNI | 2.39 | 0.08 | 2.47 | |
| monsterPlotMonsterAnalysis | 40.32 | 1.32 | 41.64 | |
| monsterPrintMonsterAnalysis | 37.01 | 0.94 | 37.96 | |
| monsterTransformationMatrix | 0.74 | 0.03 | 0.76 | |
| monsterTransitionNetworkPlot | 0.25 | 0.02 | 0.27 | |
| monsterTransitionPCAPlot | 0.15 | 0.00 | 0.15 | |
| monsterdTFIPlot | 0.21 | 0.01 | 0.22 | |
| otter | 0.01 | 0.00 | 0.02 | |
| pandaPy | 0 | 0 | 0 | |
| pandaToAlpaca | 0 | 0 | 0 | |
| pandaToCondorObject | 0 | 0 | 0 | |
| runEgret | 0.00 | 0.02 | 0.02 | |
| sambar | 1.76 | 0.05 | 1.81 | |
| sourcePPI | 0.00 | 0.01 | 0.02 | |
| visPandaInCytoscape | 0 | 0 | 0 | |