Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:42 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 1356/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSPrep 1.14.0 (landing page) Max McGrath
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | 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 | ERROR | OK | |||||||||
To the developers/maintainers of the MSPrep package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSPrep.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: MSPrep |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSPrep.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSPrep_1.14.0.tar.gz |
StartedAt: 2024-08-12 08:07:04 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 08:27:10 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 1206.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSPrep.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSPrep.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSPrep_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSPrep.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSPrep/DESCRIPTION’ ... OK * this is package ‘MSPrep’ version ‘1.14.0’ * 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 ‘MSPrep’ 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 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MSPrep 47.508 1.123 57.903 msImpute 46.726 0.790 56.383 msNormalize 41.098 0.622 50.586 msFilter 39.405 0.670 50.446 msPrepare 38.625 0.588 47.202 msSummarize 36.838 0.449 45.200 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: OK
MSPrep.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSPrep ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MSPrep’ ... ** using staged installation ** R ** data ** 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 (MSPrep)
MSPrep.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > Sys.setenv(R_TESTS="") > library(testthat) > library(MSPrep) > > test_check("MSPrep") Number of significant surrogate variables is: 4 Iteration (out of 5 ):1 2 3 4 5 Found 7 genes with uniform expression within a single batch (all zeros); these will not be adjusted for batch. Number of significant surrogate variables is: 4 Iteration (out of 5 ):1 2 3 4 5 Number of significant surrogate variables is: 4 Iteration (out of 5 ):1 2 3 4 5 Found 7 genes with uniform expression within a single batch (all zeros); these will not be adjusted for batch. Number of significant surrogate variables is: 4 Iteration (out of 5 ):1 2 3 4 5 [ FAIL 0 | WARN 12 | SKIP 0 | PASS 84 ] [ FAIL 0 | WARN 12 | SKIP 0 | PASS 84 ] > > > proc.time() user system elapsed 357.672 6.548 422.551
MSPrep.Rcheck/MSPrep-Ex.timings
name | user | system | elapsed | |
COPD_131 | 0.322 | 0.016 | 0.382 | |
MSPrep | 47.508 | 1.123 | 57.903 | |
msFilter | 39.405 | 0.670 | 50.446 | |
msImpute | 46.726 | 0.790 | 56.383 | |
msNormalize | 41.098 | 0.622 | 50.586 | |
msPrepare | 38.625 | 0.588 | 47.202 | |
msSummarize | 36.838 | 0.449 | 45.200 | |
msquant | 0.132 | 0.008 | 0.165 | |