Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 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" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1396/2255 | 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 | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.9.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netZooR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings netZooR_1.9.0.tar.gz |
StartedAt: 2024-08-21 03:18:03 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 03:27:56 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 593.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: netZooR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netZooR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings netZooR_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed monsterBereFull 5.17 0.14 5.31 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/netZooR.Rcheck/00check.log' for details.
netZooR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL netZooR ### ############################################################################## ############################################################################## * installing to library 'F:/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 0.022368421052632" [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 1703 0 --:--:-- --:--:-- --:--:-- 1748 % 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 4107 0 --:--:-- --:--:-- --:--:-- 4246 % 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 5373 0 --:--:-- --:--:-- --:--:-- 5562 % 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 18327 0 --:--:-- --:--:-- --:--:-- 18739 % 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 2573 0 --:--:-- --:--:-- --:--:-- 2628 % 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 1549 0 --:--:-- --:--:-- --:--:-- 1608 % 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 4847k 0 --:--:-- --:--:-- --:--:-- 4942k % 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 3445 0 --:--:-- --:--:-- --:--:-- 3567 [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 170k 0 --:--:-- --:--:-- --:--:-- 176k [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 3500k 0 --:--:-- --:--:-- --:--:-- 3562k Time difference of 2.69413e-05 secs Time difference of 1.848337 secs Time difference of 0.854099 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 123k 0 --:--:-- --:--:-- --:--:-- 126k Loading motif data ... Elapsed time: 0.03 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: 0.05 sec. intersection F:/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: 0.3794232904911041 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: 0.3152081370353699 step: 9, hamming: 0.2818054258823395 step: 10, hamming: 0.24849660694599152 step: 11, hamming: 0.21666744351387024 step: 12, hamming: 0.18729539215564728 step: 13, hamming: 0.16079427301883698 step: 14, hamming: 0.13726867735385895 step: 15, hamming: 0.11666569113731384 step: 16, hamming: 0.09877119958400726 step: 17, hamming: 0.08336563408374786 step: 18, hamming: 0.07016085088253021 step: 19, hamming: 0.0588911734521389 step: 20, hamming: 0.04931586608290672 step: 21, hamming: 0.04121116176247597 step: 22, hamming: 0.03437766060233116 step: 23, hamming: 0.028631482273340225 step: 24, hamming: 0.023808928206562996 step: 25, hamming: 0.019770875573158264 step: 26, hamming: 0.01639675162732601 step: 27, hamming: 0.01358273159712553 step: 28, hamming: 0.011239764280617237 step: 29, hamming: 0.009291954338550568 step: 30, hamming: 0.0076749688014388084 step: 31, hamming: 0.0063342684879899025 step: 32, hamming: 0.005223970860242844 step: 33, hamming: 0.0043054018169641495 step: 34, hamming: 0.003546181134879589 step: 35, hamming: 0.0029191910289227962 step: 36, hamming: 0.0024018590338528156 step: 37, hamming: 0.001975312363356352 step: 38, hamming: 0.0016238141106441617 step: 39, hamming: 0.001334351603873074 step: 40, hamming: 0.0010961128864437342 step: 41, hamming: 0.0009001469006761909 Running panda took: 0.02 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: 0.02 sec. Creating motif network ... Elapsed time: 0.00 sec. Creating PPI network ... Elapsed time: 0.05 sec. legacy F:/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: 0.4770948069617154 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: 0.02 sec. Loading PPI data ... Number of PPIs: 100019 Elapsed time: 0.11 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 F:/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: 0.49937220814370314 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: 0.12553582999076407 step: 17, hamming: 0.10573284427875865 step: 18, hamming: 0.08878386418920353 step: 19, hamming: 0.07436882705115155 step: 20, hamming: 0.06217241239091747 step: 21, hamming: 0.05188071541370957 step: 22, hamming: 0.043220322319520416 step: 23, hamming: 0.035949467876369046 step: 24, hamming: 0.029859895475909407 step: 25, hamming: 0.024770938396293216 step: 26, hamming: 0.020525756048994273 step: 27, hamming: 0.01699078758843491 step: 28, hamming: 0.014051171275167211 step: 29, hamming: 0.011609873894851028 step: 30, hamming: 0.009584973156032751 step: 31, hamming: 0.007907374279360021 step: 32, hamming: 0.0065189664409571 step: 33, hamming: 0.0053709991568694675 step: 34, hamming: 0.004422666090211269 step: 35, hamming: 0.0036398792478184454 step: 36, hamming: 0.0029942146499029884 step: 37, hamming: 0.002462010284380603 step: 38, hamming: 0.0020235978467206643 step: 39, hamming: 0.0016626509987884173 step: 40, hamming: 0.0013656343876712693 step: 41, hamming: 0.0011213392761822323 step: 42, hamming: 0.0009204932425645518 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 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 61.96 4.62 93.92
netZooR.Rcheck/netZooR-Ex.timings
name | user | system | elapsed | |
alpaca | 0.74 | 0.02 | 0.77 | |
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 | 0.36 | 0.00 | 0.36 | |
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 | 1.36 | 0.00 | 1.36 | |
condorCoreEnrich | 2.44 | 0.03 | 2.46 | |
condorMatrixModularity | 0.01 | 0.00 | 0.02 | |
condorModularityMax | 0.05 | 0.00 | 0.05 | |
condorPlotCommunities | 1.42 | 0.00 | 1.42 | |
condorPlotHeatmap | 0.30 | 0.01 | 0.31 | |
condorQscore | 1.36 | 0.00 | 1.36 | |
craneBipartite | 0 | 0 | 0 | |
createCondorObject | 0.01 | 0.00 | 0.02 | |
createPandaStyle | 0 | 0 | 0 | |
lioness | 3.57 | 0.13 | 3.87 | |
lionessPy | 0 | 0 | 0 | |
monster | 0.03 | 0.00 | 0.03 | |
monsterBereFull | 5.17 | 0.14 | 5.31 | |
monsterCalculateTmPValues | 0.02 | 0.00 | 0.02 | |
monsterCheckDataType | 0.45 | 0.33 | 0.78 | |
monsterGetTm | 0.01 | 0.00 | 0.02 | |
monsterHclHeatmapPlot | 0.65 | 0.06 | 0.73 | |
monsterMonsterNI | 4.25 | 0.05 | 4.30 | |
monsterPlotMonsterAnalysis | 0.01 | 0.01 | 0.03 | |
monsterPrintMonsterAnalysis | 0.03 | 0.02 | 0.05 | |
monsterTransformationMatrix | 0.91 | 0.03 | 0.93 | |
monsterTransitionNetworkPlot | 0.34 | 0.00 | 0.35 | |
monsterTransitionPCAPlot | 0.24 | 0.00 | 0.23 | |
monsterdTFIPlot | 0.36 | 0.03 | 0.39 | |
otter | 0.00 | 0.02 | 0.02 | |
pandaDiffEdges | 0 | 0 | 0 | |
pandaPy | 0.00 | 0.01 | 0.01 | |
pandaToAlpaca | 0.00 | 0.02 | 0.02 | |
pandaToCondorObject | 0 | 0 | 0 | |
runEgret | 0.01 | 0.00 | 0.11 | |
sambar | 2.22 | 0.25 | 2.50 | |
sourcePPI | 0.02 | 0.02 | 0.05 | |
spider | 0.01 | 0.00 | 0.02 | |
visPandaInCytoscape | 0 | 0 | 0 | |