Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-07 12:08 -0400 (Thu, 07 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 2/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
a4Base 1.57.0 (landing page) Laure Cougnaud
| nebbiolo2 | Linux (Ubuntu 24.04.2 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 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the a4Base package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/a4Base.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: a4Base |
Version: 1.57.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:a4Base.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings a4Base_1.57.0.tar.gz |
StartedAt: 2025-08-06 18:02:17 -0400 (Wed, 06 Aug 2025) |
EndedAt: 2025-08-06 18:03:36 -0400 (Wed, 06 Aug 2025) |
EllapsedTime: 79.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: a4Base.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:a4Base.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings a4Base_1.57.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/a4Base.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘a4Base/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘a4Base’ version ‘1.57.0’ * checking package namespace information ... OK * checking package dependencies ... INFO Package which this enhances but not available for checking: ‘JavaGD’ * 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 ‘a4Base’ can be installed ... OK * checking installed package size ... OK * checking package 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) computeLogRatio.Rd:49-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) computeLogRatio.Rd:52-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) filterVarInt.Rd:52: Escaped LaTeX specials: \& checkRd: (-1) histPvalue.Rd:50: Escaped LaTeX specials: \& checkRd: (-1) lassoReg.Rd:38: Escaped LaTeX specials: \& checkRd: (-1) plotLogRatio.Rd:166: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotLogRatio.Rd:167: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotLogRatio.Rd:168: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotLogRatio.Rd:169: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotLogRatio.Rd:170: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotLogRatio.Rd:183-185: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotLogRatio.Rd:186-191: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotLogRatio.Rd:192-200: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotLogRatio.Rd:201-203: Lost braces in \itemize; meant \describe ? checkRd: (-1) spectralMap.Rd:49: Escaped LaTeX specials: \& checkRd: (-1) topTable-methods.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) volcanoPlot.Rd:45: Escaped LaTeX specials: \& * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'a4palette.Rd': ‘[grDevices]{palettes}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: ExpressionSetWithComputation-class.Rd: ExpressionSet-class, eSet-class, VersionedBiobase-class, Versioned-class combineTwoExpressionSet.Rd: ExpressionSet-class createExpressionSet.Rd: ExpressionSet-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 examples ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/a4Base.Rcheck/00check.log’ for details.
a4Base.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL a4Base ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘a4Base’ ... ** this is package ‘a4Base’ version ‘1.57.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (a4Base)
a4Base.Rcheck/a4Base-Ex.timings
name | user | system | elapsed | |
a4palette | 0.015 | 0.001 | 0.015 | |
addQuantilesColors | 0.828 | 0.057 | 0.888 | |
boxPlot | 1.078 | 0.024 | 1.101 | |
combineTwoExpressionSet | 0 | 0 | 0 | |
computeLogRatio | 1.722 | 0.053 | 1.776 | |
createExpressionSet | 0.008 | 0.000 | 0.008 | |
filterVarInt | 0.966 | 0.039 | 1.006 | |
heatmap.expressionSet | 0 | 0 | 0 | |
histPvalue | 0.774 | 0.021 | 0.795 | |
histpvalueplotter | 0.764 | 0.019 | 0.785 | |
lassoReg | 0.782 | 0.018 | 0.801 | |
logReg | 0 | 0 | 0 | |
nlcvTT | 0.000 | 0.001 | 0.000 | |
plot1gene | 0.759 | 0.022 | 0.785 | |
plotComb2Samples | 0.807 | 0.024 | 0.831 | |
plotCombMultSamples | 1.293 | 0.046 | 1.347 | |
plotCombination2genes | 1.257 | 0.019 | 1.283 | |
plotLogRatio | 1.560 | 0.078 | 1.641 | |
probabilitiesPlot | 0.000 | 0.000 | 0.001 | |
probe2gene | 0.662 | 0.011 | 0.680 | |
profilesPlot | 0.751 | 0.020 | 0.773 | |
propdegenescalculation | 0.996 | 0.030 | 1.033 | |
replicates | 0.001 | 0.001 | 0.000 | |
spectralMap | 4.493 | 0.191 | 4.729 | |
tTest | 0.876 | 0.035 | 0.926 | |
volcanoPlot | 0.993 | 0.038 | 1.037 | |