| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:39 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the miRspongeR package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1207/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miRspongeR 2.3.0 (landing page) Junpeng Zhang
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: miRspongeR |
| Version: 2.3.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRspongeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings miRspongeR_2.3.0.tar.gz |
| StartedAt: 2022-12-29 01:27:27 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 01:31:42 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 254.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miRspongeR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRspongeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings miRspongeR_2.3.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/miRspongeR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'miRspongeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miRspongeR' version '2.3.0'
* 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 whether package 'miRspongeR' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cernia_parallel: no visible binding for global variable 'i'
hermes_parallel: no visible binding for global variable 'i'
miRHomology_parallel: no visible binding for global variable 'i'
muTaME_parallel: no visible binding for global variable 'i'
pc_parallel: no visible binding for global variable 'i'
ppc_parallel: no visible binding for global variable 'i'
sample_cor_network: no visible binding for global variable 'i'
sponge_parallel: no visible binding for global variable 'i'
sponge_sample_specific: no visible binding for global variable 'i'
sppc_parallel: no visible binding for global variable 'i'
Undefined global functions or variables:
i
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.17-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 nor [v]sprintf. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
moduleDEA 6.11 0.53 6.80
sample_cor_network 3.76 0.72 37.36
sponge_sample_specific 0.70 0.03 18.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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: 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/miRspongeR.Rcheck/00check.log'
for details.
miRspongeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL miRspongeR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'miRspongeR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c complex.c -o complex.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o /bin/sh: -c: line 1: unexpected EOF while looking for matching `"' /bin/sh: -c: line 1: unexpected EOF while looking for matching `"' /bin/sh: -c: line 1: unexpected EOF while looking for matching `"' /bin/sh: -c: line 1: unexpected EOF while looking for matching `"' gcc -shared -s -static-libgcc -o miRspongeR.dll tmp.def complex.o registerDynamicSymbol.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-miRspongeR/00new/miRspongeR/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE' Warning: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' Warning: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE' Warning: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE' Warning: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE' Warning: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE' Warning: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE' Warning: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' Warning: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE' Warning: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE' Warning: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE' Warning: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE' Warning: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE' ** testing if installed package can be loaded from final location Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE' Warning: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' Warning: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE' Warning: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE' Warning: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE' Warning: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE' Warning: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE' ** testing if installed package keeps a record of temporary installation path * DONE (miRspongeR)
miRspongeR.Rcheck/tests/test_miRspongeR.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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)
Warning messages:
1: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE'
2: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE'
3: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE'
4: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE'
5: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE'
6: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE'
7: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE'
>
> 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=TRUE, 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)
+ })
Test passed 🥇
>
> proc.time()
user system elapsed
8.75 0.93 9.68
miRspongeR.Rcheck/miRspongeR-Ex.timings
| name | user | system | elapsed | |
| integrateMethod | 0.25 | 0.00 | 0.27 | |
| moduleDEA | 6.11 | 0.53 | 6.80 | |
| moduleFEA | 0 | 0 | 0 | |
| moduleSurvival | 0.15 | 0.01 | 0.17 | |
| netModule | 0.02 | 0.00 | 0.02 | |
| querymiRTargetbinding | 0.08 | 0.00 | 0.08 | |
| sample_cor_network | 3.76 | 0.72 | 37.36 | |
| spongeMethod | 0.16 | 0.02 | 0.17 | |
| spongeValidate | 0.01 | 0.00 | 0.01 | |
| sponge_sample_specific | 0.70 | 0.03 | 18.08 | |