Junpeng Zhang
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/miRsponge |
| Branch: RELEASE_3_8 |
| Last Commit: 7f424e3 |
| Last Changed Date: 2019-03-12 22:46:07 -0400 (Tue, 12 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:57 -0400 (Tue, 16 Apr 2019).
| Package 975/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| miRsponge 1.8.2 Junpeng Zhang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: miRsponge |
| Version: 1.8.2 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:miRsponge.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings miRsponge_1.8.2.tar.gz |
| StartedAt: 2019-04-16 01:30:23 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:32:51 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 148.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miRsponge.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:miRsponge.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings miRsponge_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/miRsponge.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 ‘miRsponge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRsponge’ version ‘1.8.2’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘org.Hs.eg.db’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘miRsponge/R/zzz.R’:
.onLoad calls:
packageStartupMessage("|---------------------------------------------------------------------------------------------------- |\n", "| |\n", "| Note: The name of the 'miRsponge' package has been changed into 'miRspongeR', please download |\n", "| miRspongeR package and obtain the source from Github: https://github.com/zhangjunpeng411/miRspongeR.|\n", "| |\n", "|-------------------------------------------------------------------------------------------------------|\n")
See section ‘Good practice’ in '?.onAttach'.
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/miRsponge.Rcheck/00check.log’
for details.
miRsponge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL miRsponge ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘miRsponge’ ... ** libs gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c complex.c -o complex.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o miRsponge.so complex.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-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)
miRsponge.Rcheck/tests/test_miRsponge.Rout
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.
> library(testthat)
> library(miRsponge)
|---------------------------------------------------------------------------------------------------- |
| |
| Note: The name of the 'miRsponge' package has been changed into 'miRspongeR', please download |
| miRspongeR package and obtain the source from Github: https://github.com/zhangjunpeng411/miRspongeR.|
| |
|-------------------------------------------------------------------------------------------------------|
>
> 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
8.320 0.144 8.476
miRsponge.Rcheck/miRsponge-Ex.timings
| name | user | system | elapsed | |
| integrateMethod | 0.852 | 0.036 | 0.901 | |
| moduleDEA | 4.120 | 0.048 | 4.461 | |
| moduleFEA | 0.000 | 0.000 | 0.001 | |
| moduleSurvival | 1.028 | 0.000 | 1.028 | |
| netModule | 0.024 | 0.000 | 0.025 | |
| querymiRTargetbinding | 0.1 | 0.0 | 0.1 | |
| spongeMethod | 0.912 | 0.032 | 0.950 | |
| spongeValidate | 0.020 | 0.000 | 0.022 | |