Junpeng Zhang
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/miRspongeR |
| Branch: RELEASE_3_12 |
| Last Commit: ca92261 |
| Last Changed Date: 2020-11-17 08:38:57 -0400 (Tue, 17 Nov 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:18 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the miRspongeR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1117/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miRspongeR 1.16.2 (landing page) Junpeng Zhang
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: miRspongeR |
| Version: 1.16.2 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRspongeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings miRspongeR_1.16.2.tar.gz |
| StartedAt: 2021-05-06 04:43:20 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:47:31 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 251.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miRspongeR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRspongeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings miRspongeR_1.16.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/miRspongeR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'miRspongeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miRspongeR' version '1.16.2'
* 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 whether package 'miRspongeR' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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-3.12-bioc/R/library/miRspongeR/libs/i386/miRspongeR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/miRspongeR/libs/x64/miRspongeR.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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
moduleDEA 8.06 0.19 8.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
moduleDEA 8.35 0.19 8.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test_miRspongeR.R'
OK
** running tests for arch 'x64' ...
Running 'test_miRspongeR.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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/miRspongeR.Rcheck/00check.log'
for details.
miRspongeR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/miRspongeR_1.16.2.tar.gz && rm -rf miRspongeR.buildbin-libdir && mkdir miRspongeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=miRspongeR.buildbin-libdir miRspongeR_1.16.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL miRspongeR_1.16.2.zip && rm miRspongeR_1.16.2.tar.gz miRspongeR_1.16.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 343k 100 343k 0 0 12.7M 0 --:--:-- --:--:-- --:--:-- 13.4M
install for i386
* installing *source* package 'miRspongeR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c complex.c -o complex.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o
sh: -c: line 0: unexpected EOF while looking for matching `"'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching `"'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching `"'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching `"'
sh: -c: line 1: syntax error: unexpected end of file
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o miRspongeR.dll tmp.def complex.o registerDynamicSymbol.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/miRspongeR.buildbin-libdir/00LOCK-miRspongeR/00new/miRspongeR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'miRspongeR'
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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'miRspongeR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c complex.c -o complex.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o
sh: -c: line 0: unexpected EOF while looking for matching `"'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching `"'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching `"'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching `"'
sh: -c: line 1: syntax error: unexpected end of file
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o miRspongeR.dll tmp.def complex.o registerDynamicSymbol.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/miRspongeR.buildbin-libdir/miRspongeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'miRspongeR' as miRspongeR_1.16.2.zip
* DONE (miRspongeR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'miRspongeR' successfully unpacked and MD5 sums checked
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miRspongeR.Rcheck/tests_i386/test_miRspongeR.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(miRspongeR)
>
> miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR")
> miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")
> ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR")
> ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE)
>
> # 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)
+ })
Test passed
>
> proc.time()
user system elapsed
10.68 0.82 11.54
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miRspongeR.Rcheck/tests_x64/test_miRspongeR.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(miRspongeR)
>
> miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR")
> miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")
> ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR")
> ExpData <- read.csv(ExpDatacsv, header=FALSE, sep=",", stringsAsFactors = TRUE)
>
> # 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)
+ })
Test passed
>
> proc.time()
user system elapsed
8.12 0.35 8.56
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miRspongeR.Rcheck/examples_i386/miRspongeR-Ex.timings
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miRspongeR.Rcheck/examples_x64/miRspongeR-Ex.timings
|