Marouen Ben Guebila
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/netZooR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 4cb3b30 |
| git_last_commit_date: 2024-10-29 11:07:03 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-02 12:06 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1414/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netZooR 1.10.0 (landing page) Marouen Ben Guebila
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the netZooR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netZooR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: netZooR |
| Version: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2024-12-31 07:36:23 -0500 (Tue, 31 Dec 2024) |
| EndedAt: 2024-12-31 07:58:32 -0500 (Tue, 31 Dec 2024) |
| EllapsedTime: 1328.9 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/netZooR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘netZooR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 1.5Mb
extdata 2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘matrixcalc’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
estimatePenaltyParameters: no visible global function definition for
‘matrix.trace’
runEgret: no visible binding for global variable ‘NA12878’
show,panda: no visible global function definition for ‘print.panda’
Undefined global functions or variables:
NA12878 matrix.trace print.panda
* checking Rd files ... NOTE
checkRd: (-1) condorCluster.Rd:39: Lost braces; missing escapes or markup?
39 | in the modularity for each iteration. Default is min(10^{-4},1/(number of edges)),
| ^
checkRd: (-1) dragon.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
* 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
monsterBereFull 3.398 0.259 7.136
sambar 2.479 0.374 11.638
lioness 2.597 0.190 6.304
alpaca 0.521 0.019 5.955
sourcePPI 0.010 0.004 26.188
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘netZooR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (netZooR)
netZooR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: yarn
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: matrixcalc
Attaching package: 'matrixcalc'
The following object is masked from 'package:igraph':
%s%
>
> #download test data
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/ppi_medium.txt','testthat/ppi_medium.txt')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/ppi_medium.txt'
Content type 'text/plain' length 3674311 bytes (3.5 MB)
==================================================
downloaded 3.5 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData','testthat/testDataset.RData')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData'
Content type 'binary/octet-stream' length 15200389 bytes (14.5 MB)
==================================================
downloaded 14.5 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_test_get_shrunken_covariance.csv','testthat/dragon_test_get_shrunken_covariance.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_test_get_shrunken_covariance.csv'
Content type 'text/csv' length 114 bytes
==================================================
downloaded 114 bytes
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer1.csv','testthat/dragon_layer1.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer1.csv'
Content type 'text/csv' length 2549985 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer2.csv','testthat/dragon_layer2.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer2.csv'
Content type 'text/csv' length 12749793 bytes (12.2 MB)
==================================================
downloaded 12.2 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_cov.csv','testthat/dragon_python_cov.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_cov.csv'
Content type 'text/csv' length 9179450 bytes (8.8 MB)
==================================================
downloaded 8.8 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_prec.csv','testthat/dragon_python_prec.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_prec.csv'
Content type 'text/csv' length 9179450 bytes (8.8 MB)
==================================================
downloaded 8.8 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_parcor.csv','testthat/dragon_python_parcor.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_parcor.csv'
Content type 'text/csv' length 9179576 bytes (8.8 MB)
==================================================
downloaded 8.8 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/risk_grid_netzoopy.csv','testthat/risk_grid_netzoopy.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/risk_grid_netzoopy.csv'
Content type 'text/csv' length 255025 bytes (249 KB)
==================================================
downloaded 249 KB
>
> test_check("netZooR")
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.0236842105263165"
[1] "Q = 0.0263157894736842"
[1] "Q = 0.0263157894736842"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 100 communities"
[1] 1
[1] 2
[1] 3
[1] 4
[1] "Merging 2 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0"
[1] "Q = 0"
[1] "Q = 0.132231404958678"
[1] "Q = 0.148760330578512"
[1] "Q = 0.148760330578512"
[1] 0.231405 0.231405
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "Q = 0.140495867768595"
[1] "Q = 0.140495867768595"
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0.525346928655047"
[1] "Q = 0.52666696475026"
[1] "Q = 0.52666696475026"
[1] 0.79 0.00
final value 375.120000
converged
[1] 0.31 0.29
final value 36.897493
converged
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 355 100 355 0 0 2316 0 --:--:-- --:--:-- --:--:-- 2320
% 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 4031 0 --:--:-- --:--:-- --:--:-- 4035
100 569 100 569 0 0 3980 0 --:--:-- --:--:-- --:--:-- 3979
% 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 5382 0 --:--:-- --:--:-- --:--:-- 5419
% 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 22828 0 --:--:-- --:--:-- --:--:-- 22992
% 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 2322 0 --:--:-- --:--:-- --:--:-- 2329
% 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 1414 0 --:--:-- --:--:-- --:--:-- 1423
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
83 1438k 83 1200k 0 0 2802k 0 --:--:-- --:--:-- --:--:-- 2797k
100 1438k 100 1438k 0 0 3120k 0 --:--:-- --:--:-- --:--:-- 3119k
% 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 3644 0 --:--:-- --:--:-- --:--:-- 3658
[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 152k 0 --:--:-- --:--:-- --:--:-- 153k
[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 1079k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1079k 100 1079k 0 0 2732k 0 --:--:-- --:--:-- --:--:-- 2732k
Time difference of 3.409386e-05 secs
Time difference of 3.082447 secs
Time difference of 1.178395 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 120k 0 --:--:-- --:--:-- --:--:-- 121k
Loading motif data ...
Elapsed time: 0.01 sec.
Loading expression data ...
Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.15 sec.
Calculating coexpression network ...
Elapsed time: 0.00 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.26 sec.
intersection /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt True False True
Normalizing networks ...
Elapsed time: 0.02 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: 0.3691577613353729
step: 7, hamming: 0.34574782848358154
step: 8, hamming: 0.3152081370353699
step: 9, hamming: 0.2818053960800171
step: 10, hamming: 0.24849657714366913
step: 11, hamming: 0.21666744351387024
step: 12, hamming: 0.18729540705680847
step: 13, hamming: 0.16079428791999817
step: 14, hamming: 0.13726867735385895
step: 15, hamming: 0.11666568368673325
step: 16, hamming: 0.09877120703458786
step: 17, hamming: 0.08336561173200607
step: 18, hamming: 0.07016084343194962
step: 19, hamming: 0.0588911771774292
step: 20, hamming: 0.04931586608290672
step: 21, hamming: 0.04121115431189537
step: 22, hamming: 0.03437766805291176
step: 23, hamming: 0.028631485998630524
step: 24, hamming: 0.023808922618627548
step: 25, hamming: 0.01977088302373886
step: 26, hamming: 0.01639675535261631
step: 27, hamming: 0.013582734391093254
step: 28, hamming: 0.01123976893723011
step: 29, hamming: 0.009291954338550568
step: 30, hamming: 0.007674971595406532
step: 31, hamming: 0.006334253121167421
step: 32, hamming: 0.005223968531936407
step: 33, hamming: 0.004305415321141481
step: 34, hamming: 0.0035461809020489454
step: 35, hamming: 0.0029191956855356693
step: 36, hamming: 0.002401870209723711
step: 37, hamming: 0.001975312363356352
step: 38, hamming: 0.0016238124808296561
step: 39, hamming: 0.0013343493919819593
step: 40, hamming: 0.0010961262742057443
step: 41, hamming: 0.0009001437574625015
Running panda took: 0.08 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: 0.25 sec.
Calculating coexpression network ...
Elapsed time: 0.02 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.28 sec.
legacy /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False False
Normalizing networks ...
Elapsed time: 2.26 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 1.10 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: 0.36797241244238355
step: 6, hamming: 0.31337190961143313
step: 7, hamming: 0.26403861746419255
step: 8, hamming: 0.22399992327898238
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: 0.10108821391424126
step: 15, hamming: 0.08890364507467007
step: 16, hamming: 0.07787244456478047
step: 17, hamming: 0.06785464923123904
step: 18, hamming: 0.05878796471238135
step: 19, hamming: 0.05062155744809769
step: 20, hamming: 0.04333239380925902
step: 21, hamming: 0.0368925749401605
step: 22, hamming: 0.031262060121216705
step: 23, hamming: 0.026384280403921757
step: 24, hamming: 0.022190961740915567
step: 25, hamming: 0.018609229885172118
step: 26, hamming: 0.015566652188260106
step: 27, hamming: 0.01299328331205642
step: 28, hamming: 0.010824919177296204
step: 29, hamming: 0.009003507268894189
step: 30, hamming: 0.007477552910889814
step: 31, hamming: 0.0062020628941105
step: 32, hamming: 0.005138069423501646
step: 33, hamming: 0.004252085993537942
step: 34, hamming: 0.0035154788596479716
step: 35, hamming: 0.0029039267439058773
step: 36, hamming: 0.0023968521367998406
step: 37, hamming: 0.0019768786344578015
step: 38, hamming: 0.0016294013136896712
step: 39, hamming: 0.0013421799963357374
step: 40, hamming: 0.001104973847058481
step: 41, hamming: 0.0009092279973180526
Running panda took: 0.42 seconds!
Loading motif data ...
Elapsed time: 0.00 sec.
Loading expression data ...
Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.14 sec.
Remove expression not in motif:
166 rows removed from the initial 200
Remove motif not in expression data:
467 rows removed from the initial 506
Remove ppi not in motif:
100017 rows removed from the initial 100019
new case
Calculating coexpression network ...
Elapsed time: 0.00 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.00 sec.
legacy /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False True False
Normalizing networks ...
Elapsed time: 0.00 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.96 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: 0.5196461826284898
step: 6, hamming: 0.49096615680840516
step: 7, hamming: 0.4513686776299505
step: 8, hamming: 0.40818522332151064
step: 9, hamming: 0.363060630725845
step: 10, hamming: 0.3189123247409479
step: 11, hamming: 0.2773389585437183
step: 12, hamming: 0.23925292481822674
step: 13, hamming: 0.20518316158337407
step: 14, hamming: 0.17501658473943316
step: 15, hamming: 0.1485428864884021
step: 16, hamming: 0.12553582999076404
step: 17, hamming: 0.10573284427875863
step: 18, hamming: 0.08878386418920353
step: 19, hamming: 0.07436882705115157
step: 20, hamming: 0.062172412390917454
step: 21, hamming: 0.051880715413709574
step: 22, hamming: 0.04322032231952043
step: 23, hamming: 0.03594946787636906
step: 24, hamming: 0.029859895475909407
step: 25, hamming: 0.024770938396293178
step: 26, hamming: 0.020525756048994252
step: 27, hamming: 0.01699078758843492
step: 28, hamming: 0.014051171275167217
step: 29, hamming: 0.011609873894851016
step: 30, hamming: 0.009584973156032735
step: 31, hamming: 0.007907374279360021
step: 32, hamming: 0.0065189664409571035
step: 33, hamming: 0.005370999156869475
step: 34, hamming: 0.004422666090211273
step: 35, hamming: 0.0036398792478184202
step: 36, hamming: 0.0029942146499030097
step: 37, hamming: 0.002462010284380638
step: 38, hamming: 0.0020235978467206435
step: 39, hamming: 0.0016626509987884349
step: 40, hamming: 0.001365634387671263
step: 41, hamming: 0.0011213392761822362
step: 42, hamming: 0.0009204932425645571
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"
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[1] "Merging 201 communities"
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[1] "Computing node scores..."
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Read 7424 items
WARNING: Score threshold is not specified. We will be using medium stringency cut-off of 400.
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.0/83332.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 614783 bytes (600 KB)
==================================================
downloaded 600 KB
trying URL 'https://stringdb-downloads.org/download/protein.info.v11.0/83332.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 442274 bytes (431 KB)
==================================================
downloaded 431 KB
trying URL 'https://stringdb-downloads.org/download/protein.links.v11.0/83332.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 7455726 bytes (7.1 MB)
==================================================
downloaded 7.1 MB
[ FAIL 0 | WARN 9 | SKIP 1 | PASS 61 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-lioness.R:44:1'
[ FAIL 0 | WARN 9 | SKIP 1 | PASS 61 ]
>
> proc.time()
user system elapsed
83.690 6.079 166.982
netZooR.Rcheck/netZooR-Ex.timings
| name | user | system | elapsed | |
| alpaca | 0.521 | 0.019 | 5.955 | |
| alpacaCommunityStructureRotation | 0 | 0 | 0 | |
| alpacaComputeDWBMmatmScale | 0 | 0 | 0 | |
| alpacaComputeWBMmat | 0 | 0 | 0 | |
| alpacaCrane | 0.000 | 0.001 | 0.000 | |
| alpacaDeltaZAnalysis | 0 | 0 | 0 | |
| alpacaDeltaZAnalysisLouvain | 0 | 0 | 0 | |
| alpacaExtractTopGenes | 0.509 | 0.009 | 0.518 | |
| alpacaGOtabtogenes | 0 | 0 | 0 | |
| alpacaGenLouvain | 0.000 | 0.000 | 0.001 | |
| alpacaGoToGenes | 0 | 0 | 0 | |
| alpacaListToGo | 0 | 0 | 0 | |
| alpacaMetaNetwork | 0 | 0 | 0 | |
| alpacaNodeToGene | 0 | 0 | 0 | |
| alpacaRotationAnalysis | 0 | 0 | 0 | |
| alpacaRotationAnalysisLouvain | 0.000 | 0.001 | 0.000 | |
| alpacaSimulateNetwork | 0.000 | 0.000 | 0.001 | |
| alpacaTestNodeRank | 0 | 0 | 0 | |
| alpacaTidyConfig | 0.000 | 0.001 | 0.000 | |
| alpacaTopEnsembltoTopSym | 0 | 0 | 0 | |
| alpacaWBMlouvain | 0 | 0 | 0 | |
| condorCluster | 0.911 | 0.003 | 0.914 | |
| condorCoreEnrich | 2.000 | 0.100 | 2.101 | |
| condorMatrixModularity | 0.016 | 0.001 | 0.017 | |
| condorModularityMax | 0.032 | 0.005 | 0.037 | |
| condorPlotCommunities | 1.013 | 0.013 | 1.624 | |
| condorPlotHeatmap | 0.188 | 0.017 | 3.965 | |
| condorQscore | 0.911 | 0.005 | 0.915 | |
| craneBipartite | 0 | 0 | 0 | |
| createCondorObject | 0.007 | 0.001 | 0.007 | |
| createPandaStyle | 0.000 | 0.001 | 0.000 | |
| lioness | 2.597 | 0.190 | 6.304 | |
| lionessPy | 0.003 | 0.001 | 0.730 | |
| monster | 0.020 | 0.003 | 0.023 | |
| monsterBereFull | 3.398 | 0.259 | 7.136 | |
| monsterCalculateTmPValues | 0.021 | 0.004 | 0.024 | |
| monsterCheckDataType | 0.282 | 0.711 | 0.995 | |
| monsterGetTm | 0.003 | 0.001 | 0.004 | |
| monsterHclHeatmapPlot | 0.836 | 0.042 | 1.667 | |
| monsterMonsterNI | 3.181 | 0.068 | 3.261 | |
| monsterPlotMonsterAnalysis | 0.019 | 0.002 | 0.020 | |
| monsterPrintMonsterAnalysis | 0.019 | 0.002 | 0.020 | |
| monsterTransformationMatrix | 1.758 | 0.067 | 1.826 | |
| monsterTransitionNetworkPlot | 0.465 | 0.011 | 4.913 | |
| monsterTransitionPCAPlot | 0.189 | 0.006 | 0.961 | |
| monsterdTFIPlot | 0.423 | 0.007 | 1.135 | |
| otter | 0.003 | 0.001 | 0.004 | |
| pandaDiffEdges | 0.005 | 0.002 | 0.006 | |
| pandaPy | 0.006 | 0.004 | 0.010 | |
| pandaToAlpaca | 0.004 | 0.001 | 0.005 | |
| pandaToCondorObject | 0.003 | 0.001 | 0.004 | |
| runEgret | 0.021 | 0.005 | 4.760 | |
| sambar | 2.479 | 0.374 | 11.638 | |
| sourcePPI | 0.010 | 0.004 | 26.188 | |
| spider | 0.010 | 0.003 | 0.012 | |
| visPandaInCytoscape | 0.000 | 0.000 | 0.001 | |