Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miRSM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miRSM_2.2.0.tar.gz |
StartedAt: 2024-12-21 01:34:36 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 01:42:05 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 449.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: miRSM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miRSM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miRSM_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/miRSM.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * 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 for sufficient/correct file permissions ... OK * checking whether package ‘miRSM’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed diff_module 9.808 0.152 9.96 miRSM_SS 7.874 0.065 7.94 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/miRSM.Rcheck/00check.log’ for details.
miRSM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miRSM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘miRSM’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c complex.c -o complex.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o miRSM.so complex.o registerDynamicSymbol.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-miRSM/00new/miRSM/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 17.269 0.912 18.165
miRSM.Rcheck/miRSM-Ex.timings
name | user | system | elapsed | |
cor_binary | 0.328 | 0.012 | 0.340 | |
diff_module | 9.808 | 0.152 | 9.960 | |
miRSM | 0.268 | 0.005 | 0.274 | |
miRSM_SS | 7.874 | 0.065 | 7.940 | |
module_CEA | 3.328 | 0.066 | 3.392 | |
module_Coexpress | 3.355 | 0.064 | 3.418 | |
module_FA | 0 | 0 | 0 | |
module_GFA | 3.657 | 0.121 | 3.778 | |
module_NMF | 3.098 | 0.072 | 3.173 | |
module_ProNet | 0.181 | 0.003 | 0.185 | |
module_Validate | 3.359 | 0.079 | 3.441 | |
module_WGCNA | 2.453 | 0.013 | 2.468 | |
module_biclust | 0.491 | 0.008 | 0.502 | |
module_clust | 0.162 | 0.003 | 0.164 | |
module_group_sim | 3.537 | 0.113 | 3.720 | |
module_igraph | 0.162 | 0.003 | 0.165 | |
module_miRdistribute | 3.340 | 0.091 | 3.436 | |
module_miRsponge | 3.548 | 0.070 | 3.617 | |
module_miRtarget | 3.432 | 0.064 | 3.495 | |
share_miRs | 3.399 | 0.065 | 3.463 | |