Multiple platform build/check report for BioC 3.22 - CHECK results for netZooR on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4596
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4538
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4535
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*

CHECK results for netZooR on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: netZooR

Version: 1.13.18

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings netZooR_1.13.18.tar.gz

StartedAt: 2025-08-15 09:00:35 -0000 (Fri, 15 Aug 2025)

EndedAt: 2025-08-15 09:17:16 -0000 (Fri, 15 Aug 2025)

EllapsedTime: 1001.6 seconds

RetCode: 1

Status: ERROR

CheckDir: netZooR.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings netZooR_1.13.18.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.13.18’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... INFO
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.9Mb
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘cmdstanr’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'normalizeTissueAware.Rd':
  ‘limma::qsmooth’ ‘limma::normalizeQuantiles’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bladder.Rd: ExpressionSet-class
  normalizeTissueAware.Rd: limma::qsmooth, limma::normalizeQuantiles
  skin.Rd: ExpressionSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Data with usage in Rd file 'bladder.Rd' but not in code:
  ‘bladder’

Data with usage in Rd file 'skin.Rd' but not in code:
  ‘skin’

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Output for data("bladder", package = "netZooR"):
  No dataset created in 'envir'
  Warning message:
  In utils::data(list = fileName, package = pkgname, envir = dataEnv) :
    data set ‘bladder’ not found
Output for data("skin", package = "netZooR"):
  No dataset created in 'envir'
  Warning message:
  In utils::data(list = fileName, package = pkgname, envir = dataEnv) :
    data set ‘skin’ not found
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘netZooR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tiger
> ### Title: TIGER main function
> ### Aliases: tiger
> 
> ### ** Examples
> 
> data(TIGER_expr)
> data(TIGER_prior)
> tiger(TIGER_expr,TIGER_prior)
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6787 

Error in loadNamespace(x) : there is no package called ‘cmdstanr’
Calls: tiger ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
monsterMonsterNI            42.425  0.070  43.786
normalizeTissueAware        19.199  0.155  20.004
qsmooth                     17.145  0.025  17.888
puma                        13.417  0.091  13.661
spider                      11.753  0.032  12.324
monsterTransformationMatrix  6.298  0.028   6.387
monsterBereFull              5.351  0.048   5.741
annotateFromBiomart          2.776  0.327  20.257
* 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: 1 ERROR, 4 WARNINGs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck/00check.log’
for details.

Installation output

netZooR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL netZooR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘netZooR’ ...
** this is package ‘netZooR’ version ‘1.13.18’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
--2025-08-14 21:01:05--  https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/skin.rdata
Resolving netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)... 52.219.108.82, 3.5.131.123, 52.219.93.90, ...
Connecting to netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)|52.219.108.82|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1596768 (1.5M) [binary/octet-stream]
Saving to: ‘skin.rdata’

     0K .......... .......... .......... .......... ..........  3%  205K 7s
    50K .......... .......... .......... .......... ..........  6%  205K 7s
   100K .......... .......... .......... .......... ..........  9%  171M 5s
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  1500K .......... .......... .......... .......... .......... 99%  206K 0s
  1550K .........                                             100% 17.4T=2.4s

2025-08-14 21:01:10 (640 KB/s) - ‘skin.rdata’ saved [1596768/1596768]

--2025-08-14 21:01:10--  https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/bladder.rdata
Resolving netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)... 3.5.132.248, 3.5.131.175, 52.219.177.122, ...
Connecting to netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)|3.5.132.248|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1155612 (1.1M) [binary/octet-stream]
Saving to: ‘bladder.rdata’

     0K .......... .......... .......... .......... ..........  4% 39.3K 27s
    50K .......... .......... .......... .......... ..........  8% 13.7K 51s
   100K .......... .......... .......... .......... .......... 13% 4.59K 1m43s
   150K .......... .......... .......... .......... .......... 17% 9.97K 97s
   200K .......... .......... .......... .......... .......... 22% 5.11K 1m48s
   250K .......... .......... .......... .......... .......... 26% 6.68K 1m45s
   300K .......... .......... .......... .......... .......... 31% 49.1K 87s
   350K .......... .......... .......... .......... .......... 35% 98.2K 72s
   400K .......... .......... .......... .......... .......... 39% 98.2K 61s
   450K .......... .......... .......... .......... .......... 44%  196K 51s
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  1050K .......... .......... .......... .......... .......... 97%  151M 1s
  1100K .......... .......... ........                        100%  153M=42s

2025-08-14 21:01:55 (26.8 KB/s) - ‘bladder.rdata’ saved [1155612/1155612]

** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:igraph':

    components, union

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:igraph':

    normalize, path

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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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")'.



Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> #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 0.0236842105263163"
[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 = 0.132231404958678"
[1] "Q = 0.148760330578512"
[1] "Q = 0.148760330578512"
[1] 0.231405 0.231405
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "Q = 0.140495867768595"
[1] "Q = 0.140495867768595"
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0.525346928655047"
[1] "Q = 0.52666696475026"
[1] "Q = 0.52666696475026"
[1] 0.79 0.00
final  value 375.120000 
converged
[1] 0.31 0.29
final  value 36.897493 
converged
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100 1438k  100 1438k    0     0   631k      0  0:00:02  0:00:02 --:--:--  631k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100   578  100   578    0     0    586      0 --:--:-- --:--:-- --:--:--   586
100   578  100   578    0     0    586      0 --:--:-- --:--:-- --:--:--   586
[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
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100 27822  100 27822    0     0  17995      0  0:00:01  0:00:01 --:--:-- 17996
100 27822  100 27822    0     0  17995      0  0:00:01  0:00:01 --:--:-- 17996
[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
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 34 1085k   34  375k    0     0   180k      0  0:00:06  0:00:02  0:00:04  180k
100 1085k  100 1085k    0     0   457k      0  0:00:02  0:00:02 --:--:--  457k
Time difference of 2.503395e-05 secs
Time difference of 42.83841 secs
Time difference of 0.4073434 secs
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MONSTER object
2555 genes
20 baseline samples
20 final samples
Transition driven by 53 transcription factors
Run with 10 randomized permutations.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 27822  100 27822    0     0   7226      0  0:00:03  0:00:03 --:--:--  7226
Loading motif data ...
  Elapsed time: 0.04 sec.
Loading expression data ...
  Elapsed time: 0.01 sec.
Loading PPI data ...
/home/biocbuild/R/R-4.5.0/site-library/netZooR/extdata/panda.py:278: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable.
  norm_col = zscore(x, axis=0)
Number of PPIs: 100019
  Elapsed time: 0.19 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
  Elapsed time: 0.09 sec.
intersection /home/biocbuild/R/R-4.5.0/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: 0.3794232904911041
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: 0.03 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: 0.10 sec.
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
Creating PPI network ...
/home/biocbuild/R/R-4.5.0/site-library/netZooR/extdata/panda.py:278: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable.
  norm_col = zscore(x, axis=0)
  Elapsed time: 0.10 sec.
legacy /home/biocbuild/R/R-4.5.0/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: 0.4770948069617154
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: 0.12 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: 0.11 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: 0.01 sec.
legacy /home/biocbuild/R/R-4.5.0/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: 0.49937220814370303
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: 0.05 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..."
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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 115 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-lioness.R:45:1'

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
165.045   3.334 331.599

Example timings

netZooR.Rcheck/netZooR-Ex.timings

name	user	system	elapsed
alpaca	0.703	0.005	0.779
alpacaCommunityStructureRotation	0.001	0.000	0.000
alpacaComputeDWBMmatmScale	0	0	0
alpacaComputeWBMmat	0.001	0.000	0.000
alpacaCrane	0	0	0
alpacaDeltaZAnalysis	0	0	0
alpacaDeltaZAnalysisLouvain	0	0	0
alpacaExtractTopGenes	0.425	0.051	0.480
alpacaGOtabtogenes	0.001	0.000	0.001
alpacaGenLouvain	0	0	0
alpacaGoToGenes	0	0	0
alpacaListToGo	0.001	0.000	0.001
alpacaMetaNetwork	0	0	0
alpacaNodeToGene	0	0	0
alpacaRotationAnalysis	0	0	0
alpacaRotationAnalysisLouvain	0.000	0.000	0.001
alpacaSimulateNetwork	0	0	0
alpacaTestNodeRank	0	0	0
alpacaTidyConfig	0.001	0.000	0.000
alpacaTopEnsembltoTopSym	0	0	0
alpacaWBMlouvain	0	0	0
annotateFromBiomart	2.776	0.327	20.257
bladder	0	0	0
checkMisAnnotation	0.230	0.008	0.257
checkTissuesToMerge	0.442	0.048	0.492
cobra	0.014	0.004	0.019
condorCluster	1.117	0.187	1.477
condorCoreEnrich	2.018	0.052	2.479
condorMatrixModularity	0.012	0.000	0.012
condorModularityMax	0.022	0.007	0.030
condorPlotCommunities	1.027	0.128	1.157
condorPlotHeatmap	0.180	0.015	0.195
condorQscore	0.997	0.036	1.035
craneBipartite	0.000	0.000	0.001
createCondorObject	0.004	0.000	0.004
domonster	0	0	0
downloadGTEx	0.000	0.000	0.001
extractMatrix	0.277	0.004	0.282
filterGenes	0.282	0.004	0.287
filterLowGenes	0.282	0.016	0.299
filterMissingGenes	0.241	0.012	0.270
filterSamples	0.269	0.012	0.281
lioness	3.466	0.111	3.645
lionessPy	0.003	0.000	0.003
monster	0.03	0.00	0.03
monsterBereFull	5.351	0.048	5.741
monsterCalculateTmPValues	0.022	0.000	0.022
monsterCalculateTmStats	0.023	0.000	0.023
monsterCheckDataType	0.132	0.108	0.240
monsterGetTm	0.004	0.000	0.004
monsterHclHeatmapPlot	0.661	0.043	0.741
monsterMonsterNI	42.425	0.070	43.786
monsterPlotMonsterAnalysis	0.030	0.000	0.029
monsterPrintMonsterAnalysis	0.026	0.003	0.030
monsterTransformationMatrix	6.298	0.028	6.387
monsterTransitionNetworkPlot	0.375	0.012	0.393
monsterTransitionPCAPlot	0.210	0.024	0.236
monsterdTFIPlot	0.477	0.012	0.490
normalizeTissueAware	19.199	0.155	20.004
otter	0.004	0.000	0.003
pandaDiffEdges	0.004	0.000	0.004
pandaPy	0.004	0.000	0.004
pandaToAlpaca	0.000	0.005	0.004
pandaToCondorObject	0.001	0.003	0.003
plotCMDS	0.309	0.000	0.309
plotDensity	0.684	0.004	0.710
plotHeatmap	1.218	0.016	1.237
puma	13.417	0.091	13.661
qsmooth	17.145	0.025	17.888
runEgret	0.022	0.000	0.056
sambar	2.393	0.036	2.991
skin	0	0	0
sourcePPI	0.010	0.000	0.029
spider	11.753	0.032	12.324