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CHECK report for coexnet on malbec2

This page was generated on 2018-10-17 08:30:22 -0400 (Wed, 17 Oct 2018).

Package 286/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coexnet 1.2.0
Juan David Henao
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/coexnet
Branch: RELEASE_3_7
Last Commit: 89d4e16
Last Changed Date: 2018-04-30 10:35:47 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: coexnet
Version: 1.2.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:coexnet.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings coexnet_1.2.0.tar.gz
StartedAt: 2018-10-15 23:24:21 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:26:50 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 148.8 seconds
RetCode: 0
Status:  OK 
CheckDir: coexnet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:coexnet.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings coexnet_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/coexnet.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.0’
* 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 5.76  0.052   5.825
* 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:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL coexnet
###
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* installing to library ‘/home/biocbuild/bbs-3.7-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)

Tests output

coexnet.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 # A tibble: 4 x 5 col     row col   expected   actual     file         expected   <int> <chr> <chr>      <chr>      <chr>        actual 1   118 <NA>  16 columns 15 columns literal data file 2   119 <NA>  16 columns 13 columns literal data row 3   121 <NA>  16 columns 15 columns literal data col 4   122 <NA>  16 columns 15 columns literal data



RUNIT TEST PROTOCOL -- Mon Oct 15 23:26:47 2018 
*********************************************** 
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 
  9.476   0.280  10.546 

Example timings

coexnet.Rcheck/coexnet-Ex.timings

nameusersystemelapsed
CCP0.0200.0000.019
cofVar0.0440.0000.043
createNet1.5840.0121.615
difExprs0.3320.0000.334
exprMat0.0040.0000.001
findThreshold5.7600.0525.825
geneSymbol0.1440.0040.275
getAffy0.4880.0000.500
getInfo000
ppiNet0.0040.0000.016
sharedComponents0.0040.0040.008