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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1382/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netZooR 1.4.0  (landing page)
Marouen Ben Guebila
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/netZooR
git_branch: RELEASE_3_17
git_last_commit: f2c29ff
git_last_commit_date: 2023-04-25 11:35:03 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for netZooR on kjohnson2


To the developers/maintainers of the netZooR package:
- 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.

raw results


Summary

Package: netZooR
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2023-10-18 11:25:03 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 11:38:42 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 819.4 seconds
RetCode: 0
Status:   OK  
CheckDir: netZooR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/netZooR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.4.0’
* 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 ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
monsterBereFull 4.046  0.166   6.455
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/netZooR.Rcheck/00check.log’
for details.



Installation output

netZooR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netZooR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)

Tests output

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: aarch64-apple-darwin20 (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 0.0210526315789472"
[1] "Q = 0.0263157894736842"
[1] "Q = 0.0263157894736842"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 100 communities"
[1] 1
[1] 2
[1] 3
[1] 4
[1] "Merging 2 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
[1] "modularity of projected graph 0.144628099173554"
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0"
[1] "Q = 0"
[1] "Q = 0.15702479338843"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] 0.1983471 0.2314050 0.2314050
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "Q = 0.140495867768595"
[1] "Q = 0.140495867768595"
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0.525346928655047"
[1] "Q = 0.52666696475026"
[1] "Q = 0.52666696475026"
[1] 0.79 0.00
final  value 375.120000 
converged
[1] 0.31 0.29
final  value 36.897493 
converged
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[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"
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100 27822  100 27822    0     0  46129      0 --:--:-- --:--:-- --:--:-- 49593
[1] "Computing network for sample  1"
[1] "Computing network for sample  2"
[1] "Computing network for sample  3"
[1] "Computing network for sample  4"
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Time difference of 2.098083e-05 secs
Time difference of 1.422564 secs
Time difference of 3.131706 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.
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100 27822  100 27822    0     0   4077      0  0:00:06  0:00:06 --:--:--  5985
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: 0.13 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.14 sec.
intersection /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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: 0.3794232904911041
step: 3, hamming: 0.3818596303462982
step: 4, hamming: 0.38526612520217896
step: 5, hamming: 0.3832989037036896
step: 6, hamming: 0.36915773153305054
step: 7, hamming: 0.34574782848358154
step: 8, hamming: 0.31520816683769226
step: 9, hamming: 0.2818054258823395
step: 10, hamming: 0.24849660694599152
step: 11, hamming: 0.21666744351387024
step: 12, hamming: 0.18729539215564728
step: 13, hamming: 0.16079427301883698
step: 14, hamming: 0.13726864755153656
step: 15, hamming: 0.11666569113731384
step: 16, hamming: 0.09877120703458786
step: 17, hamming: 0.08336563408374786
step: 18, hamming: 0.07016085088253021
step: 19, hamming: 0.058891184628009796
step: 20, hamming: 0.04931585118174553
step: 21, hamming: 0.041211165487766266
step: 22, hamming: 0.03437766060233116
step: 23, hamming: 0.02863147109746933
step: 24, hamming: 0.0238089170306921
step: 25, hamming: 0.019770871847867966
step: 26, hamming: 0.016396749764680862
step: 27, hamming: 0.01358273159712553
step: 28, hamming: 0.011239762417972088
step: 29, hamming: 0.009291956201195717
step: 30, hamming: 0.0076749688014388084
step: 31, hamming: 0.0063342684879899025
step: 32, hamming: 0.005223971791565418
step: 33, hamming: 0.004305408801883459
step: 34, hamming: 0.0035461909137666225
step: 35, hamming: 0.002919200574979186
step: 36, hamming: 0.0024018811527639627
step: 37, hamming: 0.0019753146916627884
step: 38, hamming: 0.0016238073585554957
step: 39, hamming: 0.001334344851784408
step: 40, hamming: 0.0010961124207824469
step: 41, hamming: 0.0009001471335068345
Running panda took: 0.04 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.
Calculating coexpression network ...
  Elapsed time: 0.01 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.16 sec.
legacy /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False False
Normalizing networks ...
  Elapsed time: 0.02 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.5867745269558597
step: 1, hamming: 0.47709480696171547
step: 2, hamming: 0.4695616866661462
step: 3, hamming: 0.45425003629838684
step: 4, hamming: 0.41874277251518716
step: 5, hamming: 0.36797241244238355
step: 6, hamming: 0.31337190961143313
step: 7, hamming: 0.2640386174641925
step: 8, hamming: 0.2239999232789824
step: 9, hamming: 0.19253176059893798
step: 10, hamming: 0.1676553667649102
step: 11, hamming: 0.14730006142326466
step: 12, hamming: 0.12982159089839332
step: 13, hamming: 0.11459157116297605
step: 14, hamming: 0.10108821391424128
step: 15, hamming: 0.08890364507467009
step: 16, hamming: 0.0778724445647805
step: 17, hamming: 0.06785464923123909
step: 18, hamming: 0.058787964712381395
step: 19, hamming: 0.0506215574480977
step: 20, hamming: 0.043332393809259025
step: 21, hamming: 0.03689257494016053
step: 22, hamming: 0.0312620601212167
step: 23, hamming: 0.026384280403921753
step: 24, hamming: 0.022190961740915584
step: 25, hamming: 0.018609229885172114
step: 26, hamming: 0.01556665218826011
step: 27, hamming: 0.012993283312056436
step: 28, hamming: 0.010824919177296194
step: 29, hamming: 0.009003507268894198
step: 30, hamming: 0.007477552910889812
step: 31, hamming: 0.006202062894110503
step: 32, hamming: 0.005138069423501669
step: 33, hamming: 0.00425208599353795
step: 34, hamming: 0.0035154788596479616
step: 35, hamming: 0.0029039267439058794
step: 36, hamming: 0.002396852136799839
step: 37, hamming: 0.0019768786344578084
step: 38, hamming: 0.0016294013136896595
step: 39, hamming: 0.0013421799963357498
step: 40, hamming: 0.0011049738470584913
step: 41, hamming: 0.0009092279973180417
Running panda took: 0.12 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: 0.14 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/4.3-arm64/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: 0.00 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: 0.04 seconds!
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.471004488691679"
[1] "Q = 0.471024100010188"
[1] "Q = 0.471024100010188"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 386 communities"
[1] 1
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[1] "Merging 201 communities"
[1] 1
[1] "Computing node scores..."
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Read 7424 items
WARNING: Score threshold is not specified. We will be using medium stringency cut-off of 400.
trying URL 'https://stringdb-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 
 61.211   4.034 152.142 

Example timings

netZooR.Rcheck/netZooR-Ex.timings

nameusersystemelapsed
alpaca1.2260.0301.919
alpacaCommunityStructureRotation0.0010.0000.000
alpacaComputeDWBMmatmScale000
alpacaComputeWBMmat000
alpacaCrane0.0000.0000.001
alpacaDeltaZAnalysis0.0000.0010.000
alpacaDeltaZAnalysisLouvain000
alpacaExtractTopGenes0.5780.0110.901
alpacaGOtabtogenes000
alpacaGenLouvain000
alpacaGoToGenes0.0010.0000.000
alpacaListToGo0.0000.0000.002
alpacaMetaNetwork000
alpacaNodeToGene0.0000.0000.001
alpacaRotationAnalysis000
alpacaRotationAnalysisLouvain0.0000.0010.000
alpacaSimulateNetwork0.0000.0000.001
alpacaTestNodeRank0.0000.0000.001
alpacaTidyConfig0.0010.0000.000
alpacaTopEnsembltoTopSym000
alpacaWBMlouvain000
condorCluster1.0220.0111.570
condorCoreEnrich1.9690.0943.138
condorMatrixModularity0.0120.0020.021
condorModularityMax0.0290.0040.050
condorPlotCommunities1.0300.0191.601
condorPlotHeatmap0.1920.0280.335
condorQscore0.9840.0081.521
craneBipartite000
createCondorObject0.0030.0010.008
createPandaStyle0.0000.0000.001
lioness2.6560.1244.229
lionessPy0.0040.0010.009
monster0.0220.0020.036
monsterBereFull4.0460.1666.455
monsterCalculateTmPValues0.0180.0040.032
monsterCheckDataType0.2230.4931.106
monsterGetTm0.0040.0020.006
monsterHclHeatmapPlot0.9190.0291.462
monsterMonsterNI1.7460.0452.696
monsterPlotMonsterAnalysis0.0200.0020.036
monsterPrintMonsterAnalysis0.0210.0030.037
monsterTransformationMatrix0.6940.0301.100
monsterTransitionNetworkPlot0.2860.0100.446
monsterTransitionPCAPlot0.1850.0050.297
monsterdTFIPlot0.3060.0120.481
otter0.0030.0010.006
pandaDiffEdges0.0040.0020.011
pandaPy0.0050.0020.013
pandaToAlpaca0.0060.0030.012
pandaToCondorObject0.0030.0020.006
runEgret0.0160.0070.036
sambar2.1950.0783.489
sourcePPI0.0100.0020.017
spider0.0110.0020.020
visPandaInCytoscape0.0000.0000.001