Junpeng Zhang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/miRsponge |
| Branch: RELEASE_3_9 |
| Last Commit: 7c8534c |
| Last Changed Date: 2019-05-02 11:54:08 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:00:43 -0400 (Wed, 16 Oct 2019).
| Package 1017/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Junpeng Zhang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: miRsponge |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:miRsponge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings miRsponge_1.10.0.tar.gz |
| StartedAt: 2019-10-16 04:42:48 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:46:44 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 236.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miRsponge.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:miRsponge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings miRsponge_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/miRsponge.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.0’
* 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 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
Examples with CPU or elapsed time > 5s
user system elapsed
moduleDEA 6.104 0.804 6.919
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/miRsponge.Rcheck/00check.log’
for details.
miRsponge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL miRsponge ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘miRsponge’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c complex.c -o complex.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o miRsponge.so complex.o registerDynamicSymbol.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-miRsponge/00new/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 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 (miRsponge)
miRsponge.Rcheck/tests/test_miRsponge.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
11.302 1.126 12.398
miRsponge.Rcheck/miRsponge-Ex.timings
| name | user | system | elapsed | |
| integrateMethod | 2.041 | 0.104 | 2.146 | |
| moduleDEA | 6.104 | 0.804 | 6.919 | |
| moduleFEA | 0.001 | 0.001 | 0.001 | |
| moduleSurvival | 1.408 | 0.125 | 1.533 | |
| netModule | 0.080 | 0.009 | 0.089 | |
| querymiRTargetbinding | 0.189 | 0.003 | 0.192 | |
| spongeMethod | 1.521 | 0.072 | 1.593 | |
| spongeValidate | 0.026 | 0.005 | 0.031 | |