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CHECK report for miRsponge on celaya2

This page was generated on 2019-10-16 13:00:43 -0400 (Wed, 16 Oct 2019).

Package 1017/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRsponge 1.10.0
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)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: miRsponge
Version: 1.10.0
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

Command output

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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.



Installation output

miRsponge.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL miRsponge
###
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* 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)

Tests output

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 

Example timings

miRsponge.Rcheck/miRsponge-Ex.timings

nameusersystemelapsed
integrateMethod2.0410.1042.146
moduleDEA6.1040.8046.919
moduleFEA0.0010.0010.001
moduleSurvival1.4080.1251.533
netModule0.0800.0090.089
querymiRTargetbinding0.1890.0030.192
spongeMethod1.5210.0721.593
spongeValidate0.0260.0050.031