Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:16:34 -0400 (Thu, 12 Apr 2018).
Package 872/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
miRsponge 1.2.0 Junpeng Zhang
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: miRsponge |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings miRsponge_1.2.0.tar.gz |
StartedAt: 2018-04-12 01:10:43 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 01:12:51 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 127.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: miRsponge.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings miRsponge_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/miRsponge.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.2.0’ * 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 ‘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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed moduleDEA 7.48 0.06 7.725 * 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: OK
miRsponge.Rcheck/00install.out
* installing *source* package ‘miRsponge’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (miRsponge)
miRsponge.Rcheck/tests/test_miRsponge.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" 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 6.320 0.116 6.435
miRsponge.Rcheck/miRsponge-Ex.timings
name | user | system | elapsed | |
integrateMethod | 1.108 | 0.016 | 1.124 | |
moduleDEA | 7.480 | 0.060 | 7.725 | |
moduleFEA | 0.000 | 0.000 | 0.001 | |
moduleSurvival | 1.820 | 0.016 | 1.850 | |
netModule | 0.024 | 0.000 | 0.027 | |
querymiRTargetbinding | 0.120 | 0.004 | 0.126 | |
spongeMethod | 0.808 | 0.004 | 0.810 | |
spongeValidate | 0.064 | 0.000 | 0.078 | |