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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings NetSAM_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/NetSAM.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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 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: MatSAM
> ### Title: Correlation network construction, seriation and modularization
> ###   from a matrix
> ### Aliases: MatSAM
> ### Keywords: methods
> 
> ### ** Examples
> 
> 	inputMatDir <- system.file("extdata","exampleExpressionData.cct",package="NetSAM")
> 	cat(inputMatDir)
/home/biocbuild/R/R-4.3.1/site-library/NetSAM/extdata/exampleExpressionData.cct> 	sampleAnnDir <- system.file("extdata","sampleAnnotation.tsi",package="NetSAM")
> 	cat(sampleAnnDir)
/home/biocbuild/R/R-4.3.1/site-library/NetSAM/extdata/sampleAnnotation.tsi> 	outputFileName <- paste(getwd(),"/MatSAM",sep="")
> 	matModule <- MatSAM(inputMat=inputMatDir, sampleAnn=sampleAnnDir, outputFileName=outputFileName, outputFormat="msm", organism="hsapiens", map_to_symbol=FALSE, idType="auto", collapse_mode="maxSD", naPer=0.7, meanPer=0.8, varPer=0.8, corrType="spearman", matNetMethod="rank", valueThr=0.6, rankBest=0.003, networkType="signed", netFDRMethod="BH", netFDRThr=0.05, minModule=0.003, stepIte=FALSE, maxStep=4, moduleSigMethod="cutoff", modularityThr=0.2, ZRanNum=10, PerRanNum=100, ranSig=0.05, idNumThr=(-1), nThreads=3)
The input data contain 3899 ids and 90 samples. No missing values in the data.
After removing ids based on parameters 'naPer', 'meanPer' and 'varPer', 2495 ids are remained!
Allowing multi-threading with up to 3 threads.
Calculating spearman correlation for each pair of ids...
Base on rank-based method, an undirected network with 1993 nodes and 3048 edges was identified when selecting most similar 7 nodes.
Allowing multi-threading with up to 3 threads.

Identifying the hierarchical modules of the network...
Starting to analysis connected component 1!
Evaluating networks in Level 1 ...
Network modularity: 0.8002244

Evaluating networks in Level 2 ...
Modularity of network 1: 0.7213026

Modularity of network 2: 0.5231162

Modularity of network 3: 0.566358

Modularity of network 4: 0.6766937

Modularity of network 5: 0.505102

Modularity of network 6: 0.4201183

Modularity of network 7: 0.3163265

Modularity of network 8: 0.465374

Modularity of network 9: 0.5625

Modularity of network 10: 0.2956104

Modularity of network 11: 0.6538086

Modularity of network 12: 0.4965278

Modularity of network 13: 0.4756944

Modularity of network 14: 0.6963684

Modularity of network 15: 0.5321181

Modularity of network 16: 0.5478316

Modularity of network 17: 0.6276706

Modularity of network 18: 0.5371094

Modularity of network 19: 0.355

Modularity of network 20: 0.4669421

Modularity of network 21: 0.3417609

Modularity of network 22: 0.4002268

Modularity of network 23: 0.2205679

Modularity of network 24: 0.4244444

Modularity of network 25: 0.4387755

Modularity of network 26: 0.3571429

Modularity of network 27: 0.5117188

Modularity of network 28: 0.3671875

Modularity of network 29: 0.4584775

Modularity of network 30: 0.3571429

Modularity of network 31: 0.3571429

Modularity of network 32: 0.2578125

Modularity of network 33: 0.4012346

Modularity of network 34: 0.504017

Modularity of network 35: 0.4171598

Modularity of network 36: 0.4822485

Modularity of network 37: 0.06568878

Modularity of network 38: 0.26

Modularity of network 39: 0.3

Modularity of network 40: 0.500651

Modularity of network 41: 0.26

Modularity of network 42: 0.26

Modularity of network 43: 0.165

Modularity of network 44: 0.4380165

Modularity of network 45: 0.3571429

Modularity of network 46: 0.26

Modularity of network 47: 0.2109375

Modularity of network 48: 0.26

Modularity of network 49: 0.2083333

Modularity of network 50: 0.2916667

Modularity of network 51: 0.26

Modularity of network 52: 0.3671875

Modularity of network 53: 0.4467456

Modularity of network 54: 0.3571429

Modularity of network 55: 0.2916667

Modularity of network 56: 0.3571429

Modularity of network 57: 0.3264463

Modularity of network 58: 0.3671875

Modularity of network 59: 0.257716

Modularity of network 60: 0.3644444

Modularity of network 61: 0.3828125

Modularity of network 62: 0.4723183

Modularity of network 63: 0.2844444

Modularity of network 64: 0.26

Modularity of network 65: 0.3571429

Modularity of network 66: 0.2301587

Modularity of network 67: 0.3571429

Modularity of network 68: 0.2901235

Modularity of network 69: 0.1938776

Modularity of network 70: 0.3194444

Modularity of network 71: 0.2083333

Modularity of network 72: 0.2959184

Modularity of network 73: 0.3194444

Modularity of network 74: 0.3194444

Modularity of network 75: 0.3

Modularity of network 76: 0.1938776

Modularity of network 77: 0.3194444

Modularity of network 78: 0.1122449

Modularity of network 79: 0.15625

Modularity of network 80: 0.1694215

Modularity of network 81: 0.0672

Modularity of network 82: 0.1234568

Modularity of network 83: 0.2541091

Modularity of network 84: 0.09259259

Evaluating networks in Level 3 ...
Modularity of network 1: 0.2916667

Modularity of network 2: 0.3222656

Modularity of network 3: 0.4157986

Modularity of network 4: 0.4158951

Modularity of network 5: 0.2142857

Modularity of network 6: 0.1631944

Modularity of network 7: 0.002835539

Modularity of network 8: 0

Modularity of network 9: 0

Modularity of network 10: 0.1770833

Modularity of network 11: 0.125

Modularity of network 12: 0.1626276

Modularity of network 13: 0.3298611

Modularity of network 14: 0.5918913

Modularity of network 15: 0.395

Modularity of network 16: 0.5145682

Modularity of network 17: 0.5367461

Modularity of network 18: 0.26

Modularity of network 19: 0.2530864

* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/NetSAM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL NetSAM
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
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.

> 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 !         *

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


Allowing multi-threading with up to 3 threads.

Identifying the hierarchical modules of the network...
Starting to analysis connected component 1!
Evaluating networks in Level 1 ...
Network modularity: 0.5512183

Evaluating networks in Level 2 ...
Modularity of network 1: 0.2083333

Modularity of network 2: 0.2915519

Modularity of network 3: 0.377551

Modularity of network 4: 0.4114896

Modularity of network 5: 0.3669114

Modularity of network 6: 0.4228597

Modularity of network 7: 0.25

Modularity of network 8: 0.1985731

Modularity of network 9: 0.21875

Modularity of network 10: 0.07986111

Modularity of network 11: 0

Evaluating networks in Level 3 ...
Modularity of network 1: 0

Modularity of network 2: 0.2040816

Modularity of network 3: 0.1417769

Modularity of network 4: 0.3047337

Modularity of network 5: 0.3584807

Modularity of network 6: 0.1725207

Modularity of network 7: 0.1982249

Modularity of network 8: 0

Modularity of network 9: 0

Modularity of network 10: 0.1942149

Modularity of network 11: 0.2904

Modularity of network 12: 0.2366864

Modularity of network 13: 0.3010204

Modularity of network 14: 0.02664399

Modularity of network 15: 0.1938776

Modularity of network 16: 0.1064815

Modularity of network 17: 0.21875

Evaluating networks in Level 4 ...
Modularity of network 1: 0.03061224

Modularity of network 2: 0.1577778

Modularity of network 3: 0.1342593

Modularity of network 4: 0.08

Modularity of network 5: 0.2167969

Modularity of network 6: 0.21875

Modularity of network 7: 2.379049e-17

Modularity of network 8: 0

Modularity of network 9: 0.08

Evaluating networks in Level 5 ...
Modularity of network 1: 0



Reordering the genes in the one dimentional layout...
NetSAM identified 39 modules in 5 levels!
Processing completed!



RUNIT TEST PROTOCOL -- Thu Nov  2 12:59:22 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
NetSAM RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
160.837   4.679 186.359