Package: coexnet

Version: 1.4.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:coexnet.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings coexnet_1.4.0.tar.gz

StartedAt: 2019-04-15 23:03:51 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:06:44 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 173.1 seconds

RetCode: 0

Status:  OK

CheckDir: coexnet.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:coexnet.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings coexnet_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/coexnet.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
findThreshold 7.748  0.096   7.856
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL coexnet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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-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: 0.0975Achieved 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 23:06:42 2019 
*********************************************** 
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 
 12.280   0.324  12.663 

name	user	system	elapsed
CCP	0.156	0.000	0.156
cofVar	0.072	0.000	0.073
createNet	1.624	0.008	1.663
difExprs	0.552	0.004	0.553
exprMat	0	0	0
findThreshold	7.748	0.096	7.856
geneSymbol	0.052	0.012	0.078
getAffy	0.464	0.000	0.476
getInfo	0	0	0
ppiNet	0.008	0.000	0.015
sharedComponents	0.004	0.004	0.008