##############################################################################
##############################################################################
###
### 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/library --timings netZooR_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/netZooR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.3.1’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
degreeAdjust: possible error in dim(A, 1): unused argument (1)
degreeAdjust: possible error in dim(A, 2): unused argument (2)
runEgret: no visible binding for global variable ‘NA12878’
spider: no visible global function definition for ‘normalizeNetwork’
spider: no visible global function definition for ‘tanimoto’
spider: no visible global function definition for ‘update.diagonal’
spider: no visible global function definition for ‘prepResult’
Undefined global functions or variables:
  NA12878 normalizeNetwork prepResult tanimoto update.diagonal
* 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 ... WARNING
Undocumented arguments in documentation object 'pandaPy'
  ‘with_header’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: pandaDiffEdges
> ### Title: Identify differential edges in two PANDA networks
> ### Aliases: pandaDiffEdges
> 
> ### ** Examples
> 
> # refer to four input datasets files in inst/extdat
> treated_expression_file_path <- system.file("extdata", "expr4_matched.txt", 
+ package = "netZooR", mustWork = TRUE)
> control_expression_file_path <- system.file("extdata", "expr10_matched.txt", 
+ package = "netZooR", mustWork = TRUE)
> motif_file_path <- system.file("extdata", "chip_matched.txt", package = "netZooR", mustWork = TRUE)
> ppi_file_path <- system.file("extdata", "ppi_matched.txt", package = "netZooR", mustWork = TRUE)
> 
> 
> # Run PANDA for treated and control network
> treated_all_panda_result <- pandaPy(expr_file = treated_expression_file_path, 
+ motif_file= motif_file_path, ppi_file = ppi_file_path, modeProcess="legacy", remove_missing = TRUE )
Use the legacy mode to pre-process the input dataset and keep only the matched TFs or Genes
Loading motif data ...
  Elapsed time: 0.04 sec.
Loading expression data ...
  Elapsed time: 0.05 sec.
Loading PPI data ...
Number of PPIs: 864
  Elapsed time: 0.01 sec.
Remove expression not in motif:
   0 rows removed from the initial 2501
Remove motif not in expression data:
   0 rows removed from the initial 6517
Remove ppi not in motif:
   0 rows removed from the initial 864
new case
Calculating coexpression network ...
  Elapsed time: 0.52 sec.
Creating motif network ...
  Elapsed time: 0.01 sec.
Creating PPI network ...
  Elapsed time: 0.00 sec.
legacy /home/biocbuild/bbs-3.17-bioc/R/library/netZooR/extdata/chip_matched.txt /home/biocbuild/bbs-3.17-bioc/R/library/netZooR/extdata/expr4_matched.txt /home/biocbuild/bbs-3.17-bioc/R/library/netZooR/extdata/ppi_matched.txt False True False
Normalizing networks ...
  Elapsed time: 1.02 sec.
Saving expression matrix and normalized networks ...
  Elapsed time: 0.01 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.6053860619186334
step: 1, hamming: 0.2768074074257472
step: 2, hamming: 0.1842826148018828
step: 3, hamming: 0.13809031835591642
step: 4, hamming: 0.10901383004024633
step: 5, hamming: 0.08855267912448243
step: 6, hamming: 0.07316734803528885
step: 7, hamming: 0.06107513055321894
step: 8, hamming: 0.051278890896493165
step: 9, hamming: 0.0431865281425748
step: 10, hamming: 0.03641682550464566
step: 11, hamming: 0.03071053026348646
step: 12, hamming: 0.025880776329931136
step: 13, hamming: 0.021785907204273
step: 14, hamming: 0.018313027819496168
step: 15, hamming: 0.015369848478199444
step: 16, hamming: 0.012878836764994505
step: 17, hamming: 0.010774089974126216
step: 18, hamming: 0.008998981832519974
step: 19, hamming: 0.007504869482335955
step: 20, hamming: 0.006249742108663955
step: 21, hamming: 0.005197387578293079
step: 22, hamming: 0.004316683483008586
step: 23, hamming: 0.00358091580890214
step: 24, hamming: 0.0029672377674210874
step: 25, hamming: 0.0024561817866209012
step: 26, hamming: 0.0020312026017894956
step: 27, hamming: 0.0016782737075565705
step: 28, hamming: 0.0013855418116878297
step: 29, hamming: 0.001143015387416966
step: 30, hamming: 0.000942295160851393
Running panda took: 29.22 seconds!
Rename the content of first two columns with prefix 'reg_' and 'tar_' as there are some duplicate node names between the first two columns
...Finish PANDA...
> control_all_panda_result <- pandaPy(expr_file = control_expression_file_path, 
+ motif_file= motif_file_path, ppi_file= ppi_file_path, modeProcess="legacy", remove_missing = TRUE )
Use the legacy mode to pre-process the input dataset and keep only the matched TFs or Genes
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      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)
  
  
  > 
  > #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)
  =========================Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CONDOR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/netZooR.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/bbs-3.17-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)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)


> 
> #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)
=========================Killed