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This page was generated on 2021-09-15 15:05:09 -0400 (Wed, 15 Sep 2021).

CHECK results for NetSAM on nebbiolo1

To the developers/maintainers of the NetSAM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NetSAM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1268/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetSAM 1.32.0  (landing page)
Zhiao Shi
Snapshot Date: 2021-09-14 04:50:06 -0400 (Tue, 14 Sep 2021)
git_url: https://git.bioconductor.org/packages/NetSAM
git_branch: RELEASE_3_13
git_last_commit: f04aab5
git_last_commit_date: 2021-05-19 11:59:14 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NetSAM
Version: 1.32.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings NetSAM_1.32.0.tar.gz
StartedAt: 2021-09-14 10:49:54 -0400 (Tue, 14 Sep 2021)
EndedAt: 2021-09-14 11:10:51 -0400 (Tue, 14 Sep 2021)
EllapsedTime: 1257.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: NetSAM.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings NetSAM_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/NetSAM.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetSAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NetSAM’ version ‘1.32.0’
* 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 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: mapToSymbol
> ### Title: Map other ids to gene symbols
> ### Aliases: mapToSymbol
> ### Keywords: methods
> 
> ### ** Examples
> 
> 	
> 	###transform ids from a gene list to gene symbols###
> 	geneListDir <- system.file("extdata","exampleGeneList.txt",package="NetSAM")
> 	geneList <- read.table(geneListDir,header=FALSE,sep="\t",stringsAsFactors=FALSE)
> 	geneList <- as.vector(as.matrix(geneList))
> 	geneList_symbol <- mapToSymbol(inputData=geneList, organism="hsapiens", inputType="genelist",idType="affy_hg_u133_plus_2")
Ensembl site unresponsive, trying uswest mirror
Error in .GeneToSymbol(geneList = inputData, organism = organism, idType = idType,  : 
  The function can not connect to Biomart. Please try again!
Calls: mapToSymbol -> .GeneToSymbol
Execution halted
* 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-3.13-bioc/meat/NetSAM.Rcheck/00check.log’
for details.


Installation output

NetSAM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL NetSAM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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)

Tests output

NetSAM.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> 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 parallel execution with up to 71 working processes.

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: 0.0798611

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: 0.3584808

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: 0.04195011

Modularity of network 15: 0.1938775

Modularity of network 16: 0.1064815

Modularity of network 17: 0.21875

Evaluating networks in Level 4 ...
Modularity of network 1: 0.03061226

Modularity of network 2: 0.1577778

Modularity of network 3: 0.1342593

Modularity of network 4: 0.08000001

Modularity of network 5: 0.2167969

Modularity of network 6: 0.21875

Modularity of network 7: 0

Modularity of network 8: 0

Modularity of network 9: 0.08000001

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 -- Tue Sep 14 11:10:49 2021 
*********************************************** 
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 
115.057   0.815 115.879 

Example timings

NetSAM.Rcheck/NetSAM-Ex.timings

nameusersystemelapsed
GOAssociation60.892 1.91262.811
MatNet10.538 0.88411.442
MatSAM675.175 4.177719.663
NetAnalyzer0.1660.0040.171
NetSAM109.720 0.075109.820
consensusNet 0.414 0.00059.248
featureAssociation12.047 0.31212.362