Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1280/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
miRSM 2.2.0 (landing page) Junpeng Zhang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the miRSM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRSM.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: miRSM |
Version: 2.2.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRSM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miRSM_2.2.0.tar.gz |
StartedAt: 2024-12-20 03:32:19 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:40:01 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 461.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: miRSM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miRSM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miRSM_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/miRSM.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'miRSM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'miRSM' version '2.2.0' * 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 'miRSM' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * 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 whether startup messages can be suppressed ... 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 ... NOTE checkRd: (-1) module_GFA.Rd:47: Lost braces 47 | Bunte K, Lepp\'{a}aho E, Saarinen I, Kaski S. | ^ checkRd: (-1) module_GFA.Rd:50: Lost braces 50 | Lepp\'{a}aho E, Ammad-ud-din M, Kaski S. GFA: | ^ checkRd: (-1) module_biclust.Rd:54: Lost braces 54 | Preli\'{c} A, Bleuler S, Zimmermann P, Wille A, | ^ checkRd: (-1) module_biclust.Rd:55: Lost braces 55 | B\'{u}hlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E. | ^ checkRd: (-1) module_biclust.Rd:80: Lost braces 80 | Talloen W, Bijnens L, G\'{o}hlmann HW, Shkedy Z, Clevert DA. | ^ * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/miRSM/libs/x64/miRSM.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 diff_module 8.70 0.09 8.80 miRSM_SS 6.99 0.05 7.03 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test_miRSM.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/miRSM.Rcheck/00check.log' for details.
miRSM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL miRSM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'miRSM' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -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/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc -shared -s -static-libgcc -o miRSM.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-miRSM/00new/miRSM/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (miRSM)
miRSM.Rcheck/tests/test_miRSM.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 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. > suppressPackageStartupMessages(library(testthat)) > suppressPackageStartupMessages(library(GSEABase)) > suppressPackageStartupMessages(library(miRSM)) > > # Load datasets > data(BRCASampleData) > > # Identify gene co-expression modules using igraph method > modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)], + mRExp[, seq_len(10)]) > > > test_that("Test miRSM", { + expect_equal(geneIds(module_igraph(ceRExp[, seq_len(10)], + mRExp[, seq_len(10)])), geneIds(modulegenes_igraph)) + }) Test passed 🎉 > > proc.time() user system elapsed 16.39 1.53 17.84
miRSM.Rcheck/miRSM-Ex.timings
name | user | system | elapsed | |
cor_binary | 0.14 | 0.05 | 0.19 | |
diff_module | 8.70 | 0.09 | 8.80 | |
miRSM | 0.15 | 0.03 | 0.19 | |
miRSM_SS | 6.99 | 0.05 | 7.03 | |
module_CEA | 3.09 | 0.08 | 3.17 | |
module_Coexpress | 2.94 | 0.05 | 2.98 | |
module_FA | 0 | 0 | 0 | |
module_GFA | 4.27 | 0.13 | 4.39 | |
module_NMF | 3.11 | 0.06 | 3.17 | |
module_ProNet | 0.17 | 0.01 | 0.19 | |
module_Validate | 2.78 | 0.14 | 2.92 | |
module_WGCNA | 2.15 | 0.00 | 2.16 | |
module_biclust | 0.49 | 0.04 | 0.51 | |
module_clust | 0.12 | 0.01 | 0.14 | |
module_group_sim | 3.41 | 0.05 | 3.46 | |
module_igraph | 0.15 | 0.00 | 0.16 | |
module_miRdistribute | 3.19 | 0.03 | 3.22 | |
module_miRsponge | 2.94 | 0.08 | 3.01 | |
module_miRtarget | 3.15 | 0.01 | 3.18 | |
share_miRs | 2.93 | 0.03 | 2.95 | |