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This page was generated on 2022-01-24 13:05:21 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for miRspongeR on nebbiolo2


To the developers/maintainers of the miRspongeR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRspongeR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1171/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRspongeR 1.20.0  (landing page)
Junpeng Zhang
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/miRspongeR
git_branch: RELEASE_3_14
git_last_commit: 2e59690
git_last_commit_date: 2021-10-26 12:37:14 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: miRspongeR
Version: 1.20.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:miRspongeR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings miRspongeR_1.20.0.tar.gz
StartedAt: 2022-01-23 08:37:12 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 08:40:17 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 185.0 seconds
RetCode: 0
Status:   OK  
CheckDir: miRspongeR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:miRspongeR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings miRspongeR_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/miRspongeR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miRspongeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRspongeR’ version ‘1.20.0’
* 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 ‘miRspongeR’ 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
moduleDEA 7.316  0.452   7.768
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_miRspongeR.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-3.14-bioc/meat/miRspongeR.Rcheck/00check.log’
for details.



Installation output

miRspongeR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL miRspongeR
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘miRspongeR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include   -fpic  -g -O2  -Wall -c complex.c -o complex.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include   -fpic  -g -O2  -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o miRspongeR.so complex.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-miRspongeR/00new/miRspongeR/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miRspongeR)

Tests output

miRspongeR.Rcheck/tests/test_miRspongeR.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(miRspongeR)


> 
> miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR")
> miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")
> ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR")
> ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE)
> 
> # 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)    
+ })
Test passed 🌈
> 
> proc.time()
   user  system elapsed 
  9.550   0.374   9.908 

Example timings

miRspongeR.Rcheck/miRspongeR-Ex.timings

nameusersystemelapsed
integrateMethod1.3810.1121.493
moduleDEA7.3160.4527.768
moduleFEA0.0000.0000.001
moduleSurvival0.5120.0200.532
netModule0.0110.0080.020
querymiRTargetbinding0.1450.0040.149
spongeMethod0.6330.0040.636
spongeValidate0.0140.0000.015