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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetSAM_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/NetSAM.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetSAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NetSAM’ version ‘1.42.0’
* 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 ‘NetSAM’ 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 startup messages can be suppressed ... 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘NetSAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NetAnalyzer
> ### Title: Network analyzer
> ### Aliases: NetAnalyzer
> ### Keywords: methods
> 
> ### ** Examples
> 
> 	inputNetworkDir <- system.file("extdata","exampleNetwork.net",package="NetSAM")
> 	outputFileName <- paste(getwd(),"/NetSAM",sep="")
> 	NetAnalyzer(inputNetworkDir,outputFileName,"unweighted")
Error in read.graph.ncol(file, ...) : 
  INTEGER() can only be applied to a 'integer', not a 'double'
Calls: NetAnalyzer -> read.graph -> read_graph -> read.graph.ncol
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
   
  1 Test Suite : 
  NetSAM RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in test_NetSAM: Error in read.graph.ncol(file, ...) : 
    INTEGER() can only be applied to a 'integer', not a 'double'
  
  Test files with failing tests
  
     test_NetSAM.R 
       test_NetSAM 
  
  
  Error in BiocGenerics:::testPackage("NetSAM") : 
    unit tests failed for package NetSAM
  Execution halted
* 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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/NetSAM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NetSAM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘NetSAM’ ...
** 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 (NetSAM)

R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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.

> BiocGenerics:::testPackage("NetSAM")

Attaching package: 'igraph'

The following object is masked from 'package:seriation':

    permute

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

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust



Attaching package: 'WGCNA'

The following object is masked from 'package:stats':

    cor

******************************************

*            Welcome to NetSAM !         *

******************************************

Timing stopped at: 0.011 0.001 0.011
Error in read.graph.ncol(file, ...) : 
  INTEGER() can only be applied to a 'integer', not a 'double'


RUNIT TEST PROTOCOL -- Sun Mar  3 22:29:12 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
NetSAM RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test_NetSAM: Error in read.graph.ncol(file, ...) : 
  INTEGER() can only be applied to a 'integer', not a 'double'

Test files with failing tests

   test_NetSAM.R 
     test_NetSAM 


Error in BiocGenerics:::testPackage("NetSAM") : 
  unit tests failed for package NetSAM
Execution halted