Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-15 11:06:24 -0500 (Sat, 15 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4160
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4055
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3997
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4114
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

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 1284/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetSAM 1.35.0  (landing page)
Zhiao Shi
Snapshot Date: 2022-01-14 13:55:18 -0500 (Fri, 14 Jan 2022)
git_url: https://git.bioconductor.org/packages/NetSAM
git_branch: master
git_last_commit: 4f2b691
git_last_commit_date: 2021-10-26 12:08:28 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NetSAM
Version: 1.35.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings NetSAM_1.35.0.tar.gz
StartedAt: 2022-01-14 20:12:34 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 20:35:19 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 1365.1 seconds
RetCode: 0
Status:   OK  
CheckDir: NetSAM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings NetSAM_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/NetSAM.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.35.0’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
MatSAM             627.578  3.595 678.981
NetSAM             122.362  0.157 122.520
GOAssociation       56.238  0.800  57.057
featureAssociation  11.889  0.488  12.379
MatNet              10.605  0.864  11.488
mapToSymbol         10.362  0.796 159.698
consensusNet         0.405  0.046  66.681
* 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: OK


Installation output

NetSAM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL NetSAM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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 -- Fri Jan 14 20:35:16 2022 
*********************************************** 
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 
118.449   1.090 119.548 

Example timings

NetSAM.Rcheck/NetSAM-Ex.timings

nameusersystemelapsed
GOAssociation56.238 0.80057.057
MatNet10.605 0.86411.488
MatSAM627.578 3.595678.981
NetAnalyzer0.1810.0040.186
NetSAM122.362 0.157122.520
consensusNet 0.405 0.04666.681
featureAssociation11.889 0.48812.379
mapToSymbol 10.362 0.796159.698
mergeDuplicate0.1150.0040.120
testFileFormat0.7130.0120.725