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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:28:09 -0400 (Sat, 13 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 | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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### 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
###
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* 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.
miRsponge.Rcheck/00install.out
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###
### 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
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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
|
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
|
|
miRsponge.Rcheck/examples_i386/miRsponge-Ex.timings
|
miRsponge.Rcheck/examples_x64/miRsponge-Ex.timings
|