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CHECK report for coexnet on malbec2

This page was generated on 2020-10-17 11:54:36 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE coexnet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 346/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coexnet 1.10.3
Juan David Henao
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/coexnet
Branch: RELEASE_3_11
Last Commit: 4f33ce7
Last Changed Date: 2020-06-15 17:31:12 -0400 (Mon, 15 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: coexnet
Version: 1.10.3
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:coexnet.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings coexnet_1.10.3.tar.gz
StartedAt: 2020-10-17 00:05:57 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:09:11 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 193.6 seconds
RetCode: 0
Status:  OK 
CheckDir: coexnet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:coexnet.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings coexnet_1.10.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/coexnet.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coexnet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coexnet’ version ‘1.10.3’
* 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 ‘coexnet’ 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
findThreshold 8.08  0.036   8.128
* 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

coexnet.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL coexnet
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘coexnet’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (coexnet)

Tests output

coexnet.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("coexnet")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Achieved FDR: 0.0979166666666667Achieved FDR: 0.0463636363636364Warning: 4 parsing failures.
row col   expected     actual         file
118  -- 16 columns 15 columns literal data
119  -- 16 columns 13 columns literal data
121  -- 16 columns 15 columns literal data
122  -- 16 columns 15 columns literal data



RUNIT TEST PROTOCOL -- Sat Oct 17 00:09:08 2020 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
coexnet RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 13.533   0.327  13.866 

Example timings

coexnet.Rcheck/coexnet-Ex.timings

nameusersystemelapsed
CCP0.0260.0000.025
cofVar0.0450.0040.048
createNet0.9890.0081.005
difExprs1.0850.0081.094
exprMat0.0010.0000.000
findThreshold8.0800.0368.128
geneSymbol0.0470.0040.064
getAffy0.3790.0000.402
getInfo000
ppiNet0.0050.0000.032
sharedComponents0.0060.0000.006