Marouen Ben Guebila
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/netZooR |
| git_branch: devel |
| git_last_commit: 39d320e |
| git_last_commit_date: 2024-04-30 11:39:26 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 1388/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netZooR 1.9.0 (landing page) Marouen Ben Guebila
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | 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: 1.9.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netZooR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings netZooR_1.9.0.tar.gz |
| StartedAt: 2024-07-16 02:18:08 -0400 (Tue, 16 Jul 2024) |
| EndedAt: 2024-07-16 02:25:30 -0400 (Tue, 16 Jul 2024) |
| EllapsedTime: 442.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: netZooR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netZooR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings netZooR_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/netZooR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'netZooR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'netZooR' version '1.9.0'
* 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 5.2Mb
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
* 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
'C:/Users/biocbuild/bbs-3.20-bioc/meat/netZooR.Rcheck/00check.log'
for details.
netZooR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL netZooR ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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, 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 0.0236842105263166"
[1] "Q = 0.0263157894736842"
[1] "Q = 0.0263157894736842"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 100 communities"
[1] 1
[1] 2
[1] 3
[1] "Merging 2 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0"
[1] "Q = 0"
[1] "Q = 0.15702479338843"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] 0.231405 0.231405
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "Q = 0.140495867768595"
[1] "Q = 0.140495867768595"
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0.525346928655047"
[1] "Q = 0.52666696475026"
[1] "Q = 0.52666696475026"
[1] 0.79 0.00
final value 375.120000
converged
[1] 0.31 0.29
final value 36.897493
converged
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 355 100 355 0 0 1764 0 --:--:-- --:--:-- --:--:-- 1811
% 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 5776 0 --:--:-- --:--:-- --:--:-- 6053
% 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
100 840 100 840 0 0 7618 0 --:--:-- --:--:-- --:--:-- 7850
% 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 34604 0 --:--:-- --:--:-- --:--:-- 36426
% 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 3786 0 --:--:-- --:--:-- --:--:-- 3942
% 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 2687 0 --:--:-- --:--:-- --:--:-- 2846
% 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 1438k 100 1438k 0 0 7611k 0 --:--:-- --:--:-- --:--:-- 7773k
% 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 4549 0 --:--:-- --:--:-- --:--:-- 4737
[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 224k 0 --:--:-- --:--:-- --:--:-- 232k
[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 5239k 0 --:--:-- --:--:-- --:--:-- 5343k
Time difference of 2.789497e-05 secs
Time difference of 1.000758 secs
Time difference of 0.349776 secs
.123456
.12345
.12345
.12345
.12345
.123456
.12345
.12345
.12345
.123456
.12345
.12345
.12345
.12345
.12345
.123456
.1234
.12345
.12345
.12345
.1234
.12345
.123456
.12345
.12345
.1234
.1234
.12345
.12345
.12345
.12345
.12345
.123456
.12345
.12345
.123456
.12345
.12345
.12345
.12345
.12345
.12345
.1234
.12345
.12345
.12345
.12345
.12345
.12345
.12345
.1234
.12345
.12345
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 228k 0 --:--:-- --:--:-- --:--:-- 236k
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: 0.03 sec.
intersection C:/Users/biocbuild/bbs-3.20-bioc/R/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: 0.36915773153305054
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: 0.00 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.
Calculating coexpression network ...
Elapsed time: 0.00 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.05 sec.
legacy C:/Users/biocbuild/bbs-3.20-bioc/R/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False False
Normalizing networks ...
Elapsed time: 0.00 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.5867745269558597
step: 1, hamming: 0.47709480696171536
step: 2, hamming: 0.4695616866661461
step: 3, hamming: 0.45425003629838684
step: 4, hamming: 0.41874277251518716
step: 5, hamming: 0.3679724124423835
step: 6, hamming: 0.3133719096114332
step: 7, hamming: 0.26403861746419255
step: 8, hamming: 0.22399992327898235
step: 9, hamming: 0.19253176059893798
step: 10, hamming: 0.16765536676491022
step: 11, hamming: 0.14730006142326466
step: 12, hamming: 0.12982159089839332
step: 13, hamming: 0.11459157116297604
step: 14, hamming: 0.10108821391424129
step: 15, hamming: 0.08890364507467009
step: 16, hamming: 0.0778724445647805
step: 17, hamming: 0.06785464923123909
step: 18, hamming: 0.05878796471238138
step: 19, hamming: 0.05062155744809769
step: 20, hamming: 0.04333239380925902
step: 21, hamming: 0.036892574940160516
step: 22, hamming: 0.031262060121216705
step: 23, hamming: 0.02638428040392175
step: 24, hamming: 0.022190961740915574
step: 25, hamming: 0.018609229885172118
step: 26, hamming: 0.015566652188260104
step: 27, hamming: 0.012993283312056432
step: 28, hamming: 0.010824919177296187
step: 29, hamming: 0.009003507268894194
step: 30, hamming: 0.0074775529108898125
step: 31, hamming: 0.0062020628941104996
step: 32, hamming: 0.005138069423501665
step: 33, hamming: 0.00425208599353795
step: 34, hamming: 0.0035154788596479586
step: 35, hamming: 0.0029039267439058642
step: 36, hamming: 0.002396852136799832
step: 37, hamming: 0.0019768786344578205
step: 38, hamming: 0.0016294013136896632
step: 39, hamming: 0.001342179996335748
step: 40, hamming: 0.0011049738470584945
step: 41, hamming: 0.0009092279973180455
Running panda took: 0.03 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: 0.05 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: 0.02 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.00 sec.
legacy C:/Users/biocbuild/bbs-3.20-bioc/R/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False True False
Normalizing networks ...
Elapsed time: 0.00 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.6201117836163109
step: 1, hamming: 0.48938385169250487
step: 2, hamming: 0.49937220814370303
step: 3, hamming: 0.5234998024292964
step: 4, hamming: 0.5316279091580729
step: 5, hamming: 0.5196461826284898
step: 6, hamming: 0.49096615680840516
step: 7, hamming: 0.4513686776299505
step: 8, hamming: 0.4081852233215106
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: 0.00 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
[1] 2
[1] "Merging 201 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
[1] 16
[1] 17
[1] 18
[1] 19
[1] 20
[1] 21
[1] 22
[1] 23
[1] 24
[1] 25
[1] 26
[1] 27
[1] 28
[1] 29
[1] 30
[1] 31
[1] 32
[1] 33
[1] 34
[1] 35
[1] 36
[1] 37
[1] 38
[1] 39
[1] 40
[1] 41
[1] 42
[1] 43
[1] 44
[1] 45
[1] 46
[1] 47
[1] 48
[1] 49
[1] 50
[1] 51
[1] 52
[1] 53
[1] 54
[1] 55
[1] 56
[1] 57
[1] 58
[1] 59
[1] 60
[1] 61
[1] 62
[1] 63
[1] 64
[1] 65
[1] 66
[1] 67
[1] 68
[1] 69
[1] 70
[1] 71
[1] 72
[1] 73
[1] 74
[1] 75
[1] 76
[1] 77
[1] 78
[1] 79
[1] 80
[1] 81
[1] 82
[1] 83
[1] 84
[1] 85
[1] 86
[1] 87
[1] 88
[1] 89
[1] 90
[1] 91
[1] 92
[1] 93
[1] 94
[1] 95
[1] 96
[1] 97
[1] 98
[1] 99
[1] 100
[1] 101
[1] 102
[1] 103
[1] 104
[1] 105
[1] 106
[1] 107
[1] 108
[1] 109
[1] 110
[1] 111
[1] 112
[1] 113
[1] 114
[1] 115
[1] 116
[1] 117
[1] 118
[1] 119
[1] 120
[1] 121
[1] 122
[1] 123
[1] 124
[1] 125
[1] 126
[1] 127
[1] 128
[1] 129
[1] 130
[1] 131
[1] 132
[1] 133
[1] 134
[1] 135
[1] 136
[1] 137
[1] 138
[1] 139
[1] 140
[1] 141
[1] 142
[1] 143
[1] 144
[1] 145
[1] 146
[1] 147
[1] 148
[1] 149
[1] 150
[1] 151
[1] 152
[1] 153
[1] 154
[1] 155
[1] 156
[1] 157
[1] 158
[1] 159
[1] 160
[1] 161
[1] 162
[1] 163
[1] 164
[1] 165
[1] 166
[1] 167
[1] 168
[1] 169
[1] 170
[1] 171
[1] 172
[1] 173
[1] 174
[1] 175
[1] 176
[1] 177
[1] 178
[1] 179
[1] 180
[1] 181
[1] 182
[1] 183
[1] 184
[1] 185
[1] 186
[1] 187
[1] 188
[1] 189
[1] 190
[1] 191
[1] 192
[1] 193
[1] 194
[1] 195
[1] 196
[1] 197
[1] 198
[1] 199
[1] 200
[1] 201
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
45.75 4.12 63.06
netZooR.Rcheck/netZooR-Ex.timings
| name | user | system | elapsed | |
| alpaca | 0.51 | 0.00 | 0.52 | |
| 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 | 0.17 | 0.01 | 0.19 | |
| 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 | 1.43 | 0.00 | 1.42 | |
| condorCoreEnrich | 1.86 | 0.11 | 1.97 | |
| condorMatrixModularity | 0.00 | 0.01 | 0.02 | |
| condorModularityMax | 0.01 | 0.00 | 0.01 | |
| condorPlotCommunities | 1.35 | 0.00 | 1.34 | |
| condorPlotHeatmap | 0.15 | 0.03 | 0.19 | |
| condorQscore | 1.24 | 0.00 | 1.24 | |
| craneBipartite | 0 | 0 | 0 | |
| createCondorObject | 0.01 | 0.00 | 0.01 | |
| createPandaStyle | 0 | 0 | 0 | |
| lioness | 3.13 | 0.14 | 3.41 | |
| lionessPy | 0 | 0 | 0 | |
| monster | 0.01 | 0.02 | 0.03 | |
| monsterBereFull | 2.81 | 0.20 | 3.01 | |
| monsterCalculateTmPValues | 0.04 | 0.00 | 0.04 | |
| monsterCheckDataType | 0.25 | 0.26 | 0.53 | |
| monsterGetTm | 0.01 | 0.00 | 0.01 | |
| monsterHclHeatmapPlot | 0.44 | 0.04 | 0.47 | |
| monsterMonsterNI | 1.44 | 0.06 | 1.50 | |
| monsterPlotMonsterAnalysis | 0.01 | 0.00 | 0.03 | |
| monsterPrintMonsterAnalysis | 0.02 | 0.00 | 0.02 | |
| monsterTransformationMatrix | 0.48 | 0.06 | 0.55 | |
| monsterTransitionNetworkPlot | 0.25 | 0.00 | 0.25 | |
| monsterTransitionPCAPlot | 0.19 | 0.00 | 0.19 | |
| monsterdTFIPlot | 0.29 | 0.05 | 0.34 | |
| otter | 0 | 0 | 0 | |
| pandaDiffEdges | 0.02 | 0.00 | 0.02 | |
| pandaPy | 0 | 0 | 0 | |
| pandaToAlpaca | 0.00 | 0.01 | 0.01 | |
| pandaToCondorObject | 0 | 0 | 0 | |
| runEgret | 0.00 | 0.03 | 0.03 | |
| sambar | 1.42 | 0.35 | 1.77 | |
| sourcePPI | 0 | 0 | 0 | |
| spider | 0.00 | 0.01 | 0.02 | |
| visPandaInCytoscape | 0 | 0 | 0 | |