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###
### 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_1.3.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/netZooR.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.3.14’
* 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 ... ERROR
Running examples in ‘netZooR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spider
> ### Title: Seeding PANDA Interactions to Derive Epigenetic Regulation
> ### Aliases: spider
> ### Keywords: keywords
> 
> ### ** Examples
> 
> data(pandaToyData)
> spiderRes <- spider(pandaToyData$motif, pandaToyData$epifilter,
+            pandaToyData$expression,pandaToyData$ppi,hamming=.1,progress=TRUE)
[1] "Initializing and validating"
Error in Ops.data.frame(epifilter[, c(1, 2)], motif[, c(1, 2)]) : 
  ‘!=’ only defined for equally-sized data frames
Calls: spider -> Ops.data.frame
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL netZooR
###
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* 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)

R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
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 0.0236842105263158"
[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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100 1438k  100 1438k    0     0   852k      0  0:00:01  0:00:01 --:--:--  851k
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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"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 27822  100 27822    0     0  66785      0 --:--:-- --:--:-- --:--:-- 66879
Loading expression data ...
  Elapsed time: 0.03 sec.
No PPI data given: ppi matrix will be an identity matrix of size 0
Calculating coexpression network ...
  Elapsed time: 0.00 sec.
Returning the correlation matrix of expression data in <Panda_obj>.correlation_matrix
union None ./expr4_200_L.txt None False False True
Loading input data ...
  Elapsed time: 0.00 sec.
Number of total samples: 11
Number of computed samples: 1
Number of parallel cores: 1
Running LIONESS for sample 1:
Computing coexpression network:
  Elapsed time: 0.00 sec.
Normalizing networks:
  Elapsed time: 0.00 sec.
Inferring LIONESS network:
  Elapsed time: 0.00 sec.
Saving LIONESS network 0 (1) to lioness_output using no format:
lioness_output/lioness.1.0.no
Unknown format no! Use npy format instead.
  Elapsed time: 0.00 sec.
Trying to save lioness output. Format lioness_output/lioness.no not recognised
/usr/lib/python3/dist-packages/numpy/lib/function_base.py:2691: RuntimeWarning: invalid value encountered in true_divide
  c /= stddev[:, None]
/usr/lib/python3/dist-packages/numpy/lib/function_base.py:2692: RuntimeWarning: invalid value encountered in true_divide
  c /= stddev[None, :]
Loading motif data ...
  Elapsed time: 0.00 sec.
Loading expression data ...
  Elapsed time: 0.00 sec.
No PPI data given: ppi matrix will be an identity matrix of size 5
Calculating coexpression network ...
  Elapsed time: 0.01 sec.
Creating motif network ...
  Elapsed time: 0.00 sec.
union /home/biocbuild/bbs-3.17-bioc/R/site-library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt None False False True
Normalizing networks ...
  Elapsed time: 0.02 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.3008717441926663
step: 1, hamming: 0.32577840239393524
step: 2, hamming: 0.36046547993298494
step: 3, hamming: 0.3605852685089479
step: 4, hamming: 0.3466240823512551
step: 5, hamming: 0.3245626944300514
step: 6, hamming: 0.29894345984218623
step: 7, hamming: 0.27060190935086614
step: 8, hamming: 0.24146225569326207
step: 9, hamming: 0.21301541796450377
step: 10, hamming: 0.18618747428128798
step: 11, hamming: 0.16147381450104767
step: 12, hamming: 0.13913324895882448
step: 13, hamming: 0.11926159237252348
step: 14, hamming: 0.10185246481285497
step: 15, hamming: 0.08669455519421893
step: 16, hamming: 0.07353017763220263
step: 17, hamming: 0.06215000422873446
step: 18, hamming: 0.05239618178480321
step: 19, hamming: 0.044094874782060645
step: 20, hamming: 0.03701196105540176
step: 21, hamming: 0.03099423061137628
step: 22, hamming: 0.025900515663655664
step: 23, hamming: 0.021602975736466412
step: 24, hamming: 0.017987639137724457
step: 25, hamming: 0.014954147174028196
step: 26, hamming: 0.012414749356074952
step: 27, hamming: 0.010293476645031722
step: 28, hamming: 0.008524772832534418
step: 29, hamming: 0.007052536065331515
step: 30, hamming: 0.005828962967549885
step: 31, hamming: 0.004813469251228496
step: 32, hamming: 0.003971733841541573
step: 33, hamming: 0.0032748237354778796
step: 34, hamming: 0.0026984218422190184
step: 35, hamming: 0.0022221411979154518
step: 36, hamming: 0.0018289290757056958
step: 37, hamming: 0.001504551789099307
step: 38, hamming: 0.0012371486338304866
step: 39, hamming: 0.001016854768177505
step: 40, hamming: 0.0008354772054774319
Running panda took: 0.65 seconds!
Loading input data ...
  Elapsed time: 0.00 sec.
Number of total samples: 11
Number of computed samples: 1
Number of parallel cores: 1
Running LIONESS for sample 1:
Computing coexpression network:
  Elapsed time: 0.01 sec.
Normalizing networks:
  Elapsed time: 0.01 sec.
Inferring LIONESS network:
step: 0, hamming: 0.3015932422799911
step: 1, hamming: 0.3267447823984005
step: 2, hamming: 0.3610924818697022
step: 3, hamming: 0.36080894284507314
step: 4, hamming: 0.34665241776678835
step: 5, hamming: 0.324593971329214
step: 6, hamming: 0.2989655066138033
step: 7, hamming: 0.27062058204102296
step: 8, hamming: 0.24148327279879586
step: 9, hamming: 0.21304028351555687
step: 10, hamming: 0.1862048412948367
step: 11, hamming: 0.16148366668825018
step: 12, hamming: 0.1391392577665098
step: 13, hamming: 0.11927055262102533
step: 14, hamming: 0.10186083999388791
step: 15, hamming: 0.08670615581742021
step: 16, hamming: 0.0735398859822872
step: 17, hamming: 0.06215811356512222
step: 18, hamming: 0.05241372809810288
step: 19, hamming: 0.04410977556767968
step: 20, hamming: 0.037024570333260766
step: 21, hamming: 0.031005003311004406
step: 22, hamming: 0.025909572963571097
step: 23, hamming: 0.021610559908640598
step: 24, hamming: 0.017993951127131952
step: 25, hamming: 0.014959350583483993
step: 26, hamming: 0.012419036091496789
step: 27, hamming: 0.010296989659986962
step: 28, hamming: 0.008527684145049124
step: 29, hamming: 0.0070549628825015325
step: 30, hamming: 0.005830983737417977
step: 31, hamming: 0.0048151512025861225
step: 32, hamming: 0.00397313048419674
step: 33, hamming: 0.0032759823203912354
step: 34, hamming: 0.0026993820286102263
step: 35, hamming: 0.002222936231546897
step: 36, hamming: 0.0018295867892866278
step: 37, hamming: 0.0015050947585664959
step: 38, hamming: 0.0012375965038719326
step: 39, hamming: 0.00101722396992638
step: 40, hamming: 0.0008357813833833919
  Elapsed time: 0.66 sec.
Saving LIONESS network 0 (1) to lioness_output using no format:
lioness_output/lioness.1.0.no
Unknown format no! Use npy format instead.
  Elapsed time: 0.00 sec.
Trying to save lioness output. Format lioness_output/lioness.no not recognised
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: 0.01 sec.
Creating motif network ...
  Elapsed time: 0.01 sec.
Creating PPI network ...
  Elapsed time: 0.11 sec.
union /home/biocbuild/bbs-3.17-bioc/R/site-library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False True
Normalizing networks ...
  Elapsed time: 2.30 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.17 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.0874866187495562
step: 1, hamming: 0.0688871436586134
step: 2, hamming: 0.062114312778413824
step: 3, hamming: 0.05713353090446697
step: 4, hamming: 0.0530401692245583
step: 5, hamming: 0.0491011380228949
step: 6, hamming: 0.045074438192725476
step: 7, hamming: 0.04095526634659027
step: 8, hamming: 0.03683033393753415
step: 9, hamming: 0.03280131999197773
step: 10, hamming: 0.028958002291888458
step: 11, hamming: 0.025365652761878337
step: 12, hamming: 0.022066636023677578
step: 13, hamming: 0.019078836711277764
step: 14, hamming: 0.016405313028879688
step: 15, hamming: 0.014037779400693099
step: 16, hamming: 0.011959828418380588
step: 17, hamming: 0.010150090707741312
step: 18, hamming: 0.008584499851559678
step: 19, hamming: 0.007238007589517714
step: 20, hamming: 0.00608586224867505
step: 21, hamming: 0.00510441113870038
step: 22, hamming: 0.00427166159171862
step: 23, hamming: 0.0035675611746851135
step: 24, hamming: 0.0029740848850790787
step: 25, hamming: 0.0024752438901140448
step: 26, hamming: 0.0020569891001135303
step: 27, hamming: 0.0017070859535523093
step: 28, hamming: 0.0014149533300699788
step: 29, hamming: 0.0011714963862095064
step: 30, hamming: 0.0009689369122934255
Running panda took: 1016.77 seconds!