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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1384/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetSAM 1.45.0  (landing page)
Zhiao Shi
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/NetSAM
git_branch: devel
git_last_commit: 643d2c4
git_last_commit_date: 2024-04-30 10:32:16 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for NetSAM on kjohnson1

To the developers/maintainers of the NetSAM package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: NetSAM
Version: 1.45.0
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_1.45.0.tar.gz
StartedAt: 2024-06-11 02:56:55 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 03:20:59 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 1444.0 seconds
RetCode: 0
Status:   OK  
CheckDir: NetSAM.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/NetSAM.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetSAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NetSAM’ version ‘1.45.0’
* 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 code 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 whether 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
MatSAM             784.388  7.142 792.508
NetSAM             151.576  0.377 152.106
GOAssociation       66.244  3.506  69.901
MatNet              12.492  1.138  13.638
featureAssociation  10.911  0.980  11.896
mapToSymbol          6.222  0.381  10.320
consensusNet         0.455  0.023  70.846
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

NetSAM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NetSAM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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)

Tests output

NetSAM.Rcheck/tests/runTests.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 -- Tue Jun 11 03:20:50 2024 
*********************************************** 
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 
156.031   0.772 156.925 

Example timings

NetSAM.Rcheck/NetSAM-Ex.timings

nameusersystemelapsed
GOAssociation66.244 3.50669.901
MatNet12.492 1.13813.638
MatSAM784.388 7.142792.508
NetAnalyzer0.1850.0120.201
NetSAM151.576 0.377152.106
consensusNet 0.455 0.02370.846
featureAssociation10.911 0.98011.896
mapToSymbol 6.222 0.38110.320
mergeDuplicate0.0960.0020.098
testFileFormat0.8310.0050.837