Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-15 11:42 -0400 (Thu, 15 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 |
Package 1266/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
miRspongeR 2.9.0 (landing page) Junpeng Zhang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the miRspongeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRspongeR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: miRspongeR |
Version: 2.9.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRspongeR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miRspongeR_2.9.0.tar.gz |
StartedAt: 2024-08-15 02:37:07 -0400 (Thu, 15 Aug 2024) |
EndedAt: 2024-08-15 02:43:15 -0400 (Thu, 15 Aug 2024) |
EllapsedTime: 368.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: miRspongeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRspongeR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miRspongeR_2.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/miRspongeR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 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 '2.9.0' * 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) 13.2.0' * 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 code 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-3.20-bioc/R/library/miRspongeR/libs/x64/miRspongeR.dll': Found '_exit', possibly from '_exit' (C) 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 9.00 0.83 10.05 sample_cor_network 5.20 1.06 67.09 sponge_sample_specific 0.86 0.08 26.29 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test_miRspongeR.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc/meat/miRspongeR.Rcheck/00check.log' for details.
miRspongeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL miRspongeR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'miRspongeR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c complex.c -o complex.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-miRspongeR/00new/miRspongeR/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' 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 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' 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 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' 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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' 2: replacing previous import 'Biobase::combine' by 'dplyr::combine' 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 11.75 1.34 13.34
miRspongeR.Rcheck/miRspongeR-Ex.timings
name | user | system | elapsed | |
integrateMethod | 1.00 | 0.01 | 1.05 | |
moduleDEA | 9.00 | 0.83 | 10.05 | |
moduleFEA | 0 | 0 | 0 | |
moduleSurvival | 0.22 | 0.02 | 0.27 | |
netModule | 0.02 | 0.00 | 0.02 | |
querymiRTargetbinding | 0.08 | 0.01 | 0.09 | |
sample_cor_network | 5.20 | 1.06 | 67.09 | |
spongeMethod | 0.31 | 0.04 | 0.36 | |
spongeValidate | 0.02 | 0.00 | 0.04 | |
sponge_sample_specific | 0.86 | 0.08 | 26.29 | |