Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:34 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 1382/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
netZooR 1.4.0 (landing page) Marouen Ben Guebila
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
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: 1.4.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings netZooR_1.4.0.tar.gz |
StartedAt: 2023-10-15 23:18:22 -0400 (Sun, 15 Oct 2023) |
EndedAt: 2023-10-15 23:26:54 -0400 (Sun, 15 Oct 2023) |
EllapsedTime: 512.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: netZooR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings netZooR_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/netZooR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘netZooR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘netZooR’ version ‘1.4.0’ * 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 ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... 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 ... 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 * 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 ... ‘CONDOR.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/netZooR.Rcheck/00check.log’ for details.
netZooR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL netZooR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘netZooR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (netZooR)
netZooR.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(netZooR) Loading required package: igraph Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: reticulate Loading required package: pandaR Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:igraph': normalize, path, union The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: yarn Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) 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 0.0250000000000006" [1] "Q = 0.0263157894736842" [1] "Q = 0.0263157894736842" [1] "Computing differential modularity matrix..." [1] "Computing differential modules..." [1] "Merging 100 communities" [1] 1 [1] 2 [1] 3 [1] "Merging 2 communities" [1] 1 [1] "Computing node scores..." [1] 1 [1] 2 [1] "modularity of projected graph 0.144628099173554" [1] "Q = 0.198347107438017" [1] "Q = 0.231404958677686" [1] "Q = 0.231404958677686" [1] "modularity of projected graph 0" [1] "Q = 0" [1] "Q = 0.15702479338843" [1] "Q = 0.231404958677686" [1] "Q = 0.231404958677686" [1] 0.1983471 0.2314050 0.2314050 [1] "Q = 0.198347107438017" [1] "Q = 0.231404958677686" [1] "Q = 0.231404958677686" [1] "Q = 0.140495867768595" [1] "Q = 0.140495867768595" [1] "modularity of projected graph 0.227272727272727" [1] "Q = 0.231404958677686" [1] "Q = 0.231404958677686" [1] "modularity of projected graph 0.525346928655047" [1] "Q = 0.52666696475026" [1] "Q = 0.52666696475026" [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 1436 0 --:--:-- --:--:-- --:--:-- 1443 % 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 --:--:-- --:--:-- --:--:-- 0 100 569 100 569 0 0 2388 0 --:--:-- --:--:-- --:--:-- 2380 % 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 3607 0 --:--:-- --:--:-- --:--:-- 3620 % 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 9911 0 --:--:-- --:--:-- --:--:-- 9944 % 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 --:--:-- --:--:-- --:--:-- 0 100 410 100 410 0 0 1671 0 --:--:-- --:--:-- --:--:-- 1666 % 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 0 671 0 --:--:-- --:--:-- --:--:-- 672 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 10 1438k 10 152k 0 0 253k 0 0:00:05 --:--:-- 0:00:05 252k 95 1438k 95 1375k 0 0 863k 0 0:00:01 0:00:01 --:--:-- 863k 100 1438k 100 1438k 0 0 884k 0 0:00:01 0:00:01 --:--:-- 885k % 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 2402 0 --:--:-- --:--:-- --:--:-- 2408 [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 97k 0 --:--:-- --:--:-- --:--:-- 98k [1] "Computing network for sample 1" [1] "Computing network for sample 2" [1] "Computing network for sample 3" [1] "Computing network for sample 4" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 91 1079k 91 987k 0 0 892k 0 0:00:01 0:00:01 --:--:-- 892k 100 1079k 100 1079k 0 0 952k 0 0:00:01 0:00:01 --:--:-- 951k Time difference of 2.169609e-05 secs Time difference of 1.91504 secs Time difference of 1.966029 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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 27822 100 27822 0 0 91783 0 --:--:-- --:--:-- --:--:-- 91519 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: 0.07 sec. Calculating coexpression network ... Elapsed time: 0.00 sec. Creating motif network ... Elapsed time: 0.00 sec. Creating PPI network ... Elapsed time: 0.08 sec. intersection /home/biocbuild/bbs-3.17-bioc/R/site-library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt True False True Normalizing networks ... Elapsed time: 0.00 sec. Clearing motif and ppi data, unique tfs, and gene names for speed Running PANDA algorithm ... step: 0, hamming: 0.6788049340248108 step: 1, hamming: 0.4237635135650635 step: 2, hamming: 0.37942326068878174 step: 3, hamming: 0.3818596303462982 step: 4, hamming: 0.38526612520217896 step: 5, hamming: 0.3832989037036896 step: 6, hamming: 0.3691577613353729 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: 0.02 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: 0.07 sec. Calculating coexpression network ... Elapsed time: 0.00 sec. Creating motif network ... Elapsed time: 0.00 sec. Creating PPI network ... Elapsed time: 0.08 sec. legacy /home/biocbuild/bbs-3.17-bioc/R/site-library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False False Normalizing networks ... Elapsed time: 0.01 sec. Saving expression matrix and normalized networks ... Elapsed time: 0.00 sec. Running PANDA algorithm ... step: 0, hamming: 0.5867745269558597 step: 1, hamming: 0.47709480696171536 step: 2, hamming: 0.46956168666614617 step: 3, hamming: 0.45425003629838684 step: 4, hamming: 0.4187427725151872 step: 5, hamming: 0.36797241244238355 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: 0.06 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: 0.07 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 /home/biocbuild/bbs-3.17-bioc/R/site-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: 0.49937220814370314 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: 0.02 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 [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 1 | SKIP 1 | PASS 61 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-lioness.R:44:1' [ FAIL 0 | WARN 1 | SKIP 1 | PASS 61 ] > > proc.time() user system elapsed 52.385 3.548 98.616
netZooR.Rcheck/netZooR-Ex.timings
name | user | system | elapsed | |
alpaca | 0.613 | 0.007 | 0.621 | |
alpacaCommunityStructureRotation | 0 | 0 | 0 | |
alpacaComputeDWBMmatmScale | 0 | 0 | 0 | |
alpacaComputeWBMmat | 0.000 | 0.000 | 0.001 | |
alpacaCrane | 0.001 | 0.001 | 0.000 | |
alpacaDeltaZAnalysis | 0 | 0 | 0 | |
alpacaDeltaZAnalysisLouvain | 0 | 0 | 0 | |
alpacaExtractTopGenes | 0.476 | 0.024 | 0.500 | |
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 | 0.000 | 0.000 | 0.001 | |
alpacaTopEnsembltoTopSym | 0 | 0 | 0 | |
alpacaWBMlouvain | 0 | 0 | 0 | |
condorCluster | 1.107 | 0.058 | 1.166 | |
condorCoreEnrich | 1.904 | 0.023 | 1.927 | |
condorMatrixModularity | 0.007 | 0.001 | 0.007 | |
condorModularityMax | 0.018 | 0.000 | 0.018 | |
condorPlotCommunities | 1.238 | 0.031 | 1.269 | |
condorPlotHeatmap | 0.230 | 0.001 | 0.230 | |
condorQscore | 1.162 | 0.051 | 1.213 | |
craneBipartite | 0.001 | 0.001 | 0.000 | |
createCondorObject | 0.003 | 0.000 | 0.003 | |
createPandaStyle | 0.000 | 0.000 | 0.001 | |
lioness | 1.922 | 0.267 | 2.191 | |
lionessPy | 0.000 | 0.003 | 0.003 | |
monster | 0.038 | 0.004 | 0.042 | |
monsterBereFull | 3.218 | 0.096 | 3.314 | |
monsterCalculateTmPValues | 0.014 | 0.000 | 0.015 | |
monsterCheckDataType | 0.176 | 0.640 | 0.816 | |
monsterGetTm | 0.004 | 0.000 | 0.003 | |
monsterHclHeatmapPlot | 0.704 | 0.052 | 0.756 | |
monsterMonsterNI | 3.877 | 0.092 | 3.969 | |
monsterPlotMonsterAnalysis | 0.021 | 0.000 | 0.020 | |
monsterPrintMonsterAnalysis | 0.021 | 0.000 | 0.021 | |
monsterTransformationMatrix | 0.753 | 0.028 | 0.781 | |
monsterTransitionNetworkPlot | 0.256 | 0.004 | 0.260 | |
monsterTransitionPCAPlot | 0.155 | 0.004 | 0.159 | |
monsterdTFIPlot | 0.243 | 0.012 | 0.254 | |
otter | 0.003 | 0.000 | 0.003 | |
pandaDiffEdges | 0.002 | 0.002 | 0.004 | |
pandaPy | 0.003 | 0.001 | 0.004 | |
pandaToAlpaca | 0.004 | 0.000 | 0.003 | |
pandaToCondorObject | 0.002 | 0.000 | 0.003 | |
runEgret | 0.012 | 0.004 | 0.017 | |
sambar | 1.738 | 0.040 | 1.778 | |
sourcePPI | 0.008 | 0.001 | 0.008 | |
spider | 0.01 | 0.00 | 0.01 | |
visPandaInCytoscape | 0 | 0 | 0 | |