Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for miRsponge on tokay1

This page was generated on 2019-04-13 11:28:09 -0400 (Sat, 13 Apr 2019).

Package 975/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRsponge 1.8.2
Junpeng Zhang
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: miRsponge
Version: 1.8.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRsponge.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings miRsponge_1.8.2.tar.gz
StartedAt: 2019-04-13 03:53:46 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:57:49 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 242.8 seconds
RetCode: 0
Status:  OK  
CheckDir: miRsponge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRsponge.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings miRsponge_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/miRsponge.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/miRsponge/libs/i386/miRsponge.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
moduleDEA 5.14   0.11    5.25
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test_miRsponge.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/miRsponge.Rcheck/00check.log'
for details.



Installation output

miRsponge.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/miRsponge_1.8.2.tar.gz && rm -rf miRsponge.buildbin-libdir && mkdir miRsponge.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=miRsponge.buildbin-libdir miRsponge_1.8.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL miRsponge_1.8.2.zip && rm miRsponge_1.8.2.tar.gz miRsponge_1.8.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  339k  100  339k    0     0  7860k      0 --:--:-- --:--:-- --:--:-- 8478k

install for i386

* installing *source* package 'miRsponge' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c complex.c -o complex.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o miRsponge.dll tmp.def complex.o registerDynamicSymbol.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/miRsponge.buildbin-libdir/miRsponge/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'miRsponge'
    finding HTML links ... done
    integrateMethod                         html  
    moduleDEA                               html  
    moduleFEA                               html  
    moduleSurvival                          html  
    netModule                               html  
    querymiRTargetbinding                   html  
    spongeMethod                            html  
    spongeValidate                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'miRsponge' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c complex.c -o complex.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o miRsponge.dll tmp.def complex.o registerDynamicSymbol.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/miRsponge.buildbin-libdir/miRsponge/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'miRsponge' as miRsponge_1.8.2.zip
* DONE (miRsponge)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'miRsponge' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

miRsponge.Rcheck/tests_i386/test_miRsponge.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   6.39    0.51    6.89 

miRsponge.Rcheck/tests_x64/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-w64-mingw32/x64 (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 
   6.90    0.23    7.12 

Example timings

miRsponge.Rcheck/examples_i386/miRsponge-Ex.timings

nameusersystemelapsed
integrateMethod0.830.021.00
moduleDEA3.300.233.53
moduleFEA000
moduleSurvival0.660.000.73
netModule0.030.000.04
querymiRTargetbinding0.140.000.14
spongeMethod0.750.070.81
spongeValidate0.020.000.04

miRsponge.Rcheck/examples_x64/miRsponge-Ex.timings

nameusersystemelapsed
integrateMethod1.160.021.17
moduleDEA5.140.115.25
moduleFEA000
moduleSurvival0.720.000.72
netModule0.020.000.01
querymiRTargetbinding0.120.000.13
spongeMethod0.860.000.86
spongeValidate0.000.010.01