Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -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 53/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ALDEx2 1.38.0 (landing page) Greg Gloor
| 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 ALDEx2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ALDEx2.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: ALDEx2 |
Version: 1.38.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ALDEx2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ALDEx2_1.38.0.tar.gz |
StartedAt: 2024-12-19 22:49:56 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 22:55:00 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 304.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ALDEx2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ALDEx2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ALDEx2_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ALDEx2.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 'ALDEx2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ALDEx2' version '1.38.0' * 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 'ALDEx2' 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 ... NOTE Invalid package aliases in Rd file 'ALDEx2m-package.Rd': 'ALDEx2m-package' * 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 aldex.glm 4.97 0.09 5.07 * 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: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/ALDEx2.Rcheck/00check.log' for details.
ALDEx2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ALDEx2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'ALDEx2' ... ** using staged installation ** 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 (ALDEx2)
ALDEx2.Rcheck/tests/testthat.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. > library(testthat) > library(ALDEx2) Loading required package: zCompositions Loading required package: MASS Loading required package: NADA Loading required package: survival Attaching package: 'NADA' The following object is masked from 'package:stats': cor Loading required package: truncnorm Loading required package: lattice Loading required package: latticeExtra > > test_check("ALDEx2") [ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ] [ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 91.48 5.59 97.14
ALDEx2.Rcheck/ALDEx2-Ex.timings
name | user | system | elapsed | |
ALDEx2m-package | 0 | 0 | 0 | |
aldex | 3.27 | 1.73 | 5.00 | |
aldex.clr-class | 0.11 | 0.00 | 0.11 | |
aldex.corr | 1.64 | 0.02 | 1.65 | |
aldex.effect | 0.32 | 0.02 | 0.33 | |
aldex.expectedDistance | 1.23 | 0.03 | 1.27 | |
aldex.glm | 4.97 | 0.09 | 5.07 | |
aldex.glm.effect | 0.61 | 0.02 | 0.63 | |
aldex.glm.plot | 0 | 0 | 0 | |
aldex.kw | 2.30 | 0.06 | 2.36 | |
aldex.makeScaleMatrix | 0.01 | 0.01 | 0.03 | |
aldex.plot | 0 | 0 | 0 | |
aldex.plotFeature | 0.15 | 0.00 | 0.15 | |
aldex.set.mode | 0.1 | 0.0 | 0.1 | |
aldex.ttest | 0.15 | 0.02 | 0.17 | |
getConditions-method | 0.08 | 0.02 | 0.09 | |
getDenom-method | 0.10 | 0.00 | 0.09 | |
getDirichletInstances-method | 0.06 | 0.01 | 0.08 | |
getDirichletReplicate-method | 0.09 | 0.00 | 0.10 | |
getDirichletSample-method | 0.08 | 0.02 | 0.09 | |
getFeatureNames-method | 0.06 | 0.00 | 0.06 | |
getFeatures-method | 0.1 | 0.0 | 0.1 | |
getMonteCarloInstances-method | 0.07 | 0.01 | 0.09 | |
getMonteCarloReplicate-method | 0.08 | 0.02 | 0.09 | |
getMonteCarloSample-method | 0.06 | 0.01 | 0.08 | |
getReads-method | 0.11 | 0.00 | 0.11 | |
getSampleIDs-method | 0.10 | 0.02 | 0.11 | |
getScaleSamples-method | 0.09 | 0.00 | 0.09 | |
numConditions-method | 0.06 | 0.00 | 0.07 | |
numFeatures-method | 0.07 | 0.00 | 0.07 | |
numMCInstances-method | 0.04 | 0.01 | 0.06 | |