Package: coexnet

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:coexnet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings coexnet_1.4.0.tar.gz

StartedAt: 2019-04-15 23:08:31 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:11:53 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 201.6 seconds

RetCode: 0

Status:  OK

CheckDir: coexnet.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:coexnet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings coexnet_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/coexnet.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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 ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
findThreshold 8.109  0.886    9.09
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL coexnet
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘coexnet’ ...
** 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
* DONE (coexnet)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 0.0975Achieved FDR: 0.0478571428571429Warning: 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 -- Mon Apr 15 23:11:48 2019 
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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 
 13.570   0.750  14.375 

name	user	system	elapsed
CCP	0.145	0.004	0.149
cofVar	0.070	0.001	0.072
createNet	1.572	0.030	1.617
difExprs	0.559	0.041	0.604
exprMat	0.001	0.000	0.001
findThreshold	8.109	0.886	9.090
geneSymbol	0.041	0.006	0.047
getAffy	0.435	0.013	0.453
getInfo	0.000	0.000	0.001
ppiNet	0.006	0.001	0.006
sharedComponents	0.008	0.002	0.011