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CHECK report for miRsponge on malbec2

This page was generated on 2018-10-17 08:30:34 -0400 (Wed, 17 Oct 2018).

Package 922/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRsponge 1.6.1
Junpeng Zhang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/miRsponge
Branch: RELEASE_3_7
Last Commit: f92ec6a
Last Changed Date: 2018-08-24 21:48:12 -0400 (Fri, 24 Aug 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: miRsponge
Version: 1.6.1
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:miRsponge.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings miRsponge_1.6.1.tar.gz
StartedAt: 2018-10-16 02:05:05 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:06:52 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 107.1 seconds
RetCode: 0
Status:  OK 
CheckDir: miRsponge.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:miRsponge.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings miRsponge_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/miRsponge.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 ‘miRsponge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRsponge’ version ‘1.6.1’
* package encoding: UTF-8
* 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 ‘miRsponge’ 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_miRsponge.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/miRsponge.Rcheck/00check.log’
for details.



Installation output

miRsponge.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL miRsponge
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘miRsponge’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c complex.c -o complex.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o miRsponge.so complex.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/miRsponge/libs
** R
** 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 (miRsponge)

Tests output

miRsponge.Rcheck/tests/test_miRsponge.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.

> library(testthat)
> library(miRsponge)

> 
> miR2Target <- system.file("extdata", "miR2Target.csv", package="miRsponge")
> miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")
> ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRsponge")
> ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",")
> 
> # miRHomology method
> miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology")
> 
> # pc method
> pcceRInt <- spongeMethod(miRTarget, ExpData, method = "pc")
> 
> # sppc method
> sppcceRInt <- spongeMethod(miRTarget, ExpData, senscorcutoff = 0.1, method = "sppc")
> 
> 
> test_that("Test spongeMethod", {
+     expect_equal(spongeMethod(miRTarget, method = "miRHomology"), miRHomologyceRInt)
+     expect_equal(spongeMethod(miRTarget, ExpData, method = "pc"), pcceRInt)
+     expect_equal(spongeMethod(miRTarget, ExpData, senscorcutoff = 0.1, method = "sppc"), sppcceRInt)    
+ })
> 
> proc.time()
   user  system elapsed 
  5.716   0.164   5.878 

Example timings

miRsponge.Rcheck/miRsponge-Ex.timings

nameusersystemelapsed
integrateMethod1.0920.0241.129
moduleDEA3.7560.0723.910
moduleFEA0.0000.0000.001
moduleSurvival0.5920.0000.597
netModule0.0200.0040.025
querymiRTargetbinding0.0920.0040.099
spongeMethod0.6600.0040.667
spongeValidate0.0200.0000.028