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 12:05 -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 7/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ABarray 1.74.0 (landing page) Yongming Andrew Sun
| 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 ABarray package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ABarray.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: ABarray |
Version: 1.74.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ABarray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ABarray_1.74.0.tar.gz |
StartedAt: 2024-12-19 23:30:11 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:32:25 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 134.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ABarray.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ABarray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ABarray_1.74.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ABarray.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ABarray/DESCRIPTION’ ... OK * this is package ‘ABarray’ version ‘1.74.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘ABarray’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 ... NOTE ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow = 5000, colClasses = colRead): partial argument match of 'nrow' to 'nrows' ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow = 36000, colClasses = colRead, as.is = TRUE, check.names = FALSE, comment.char = "", na.string = c("NA", "MultipleValues", "Multiple Values")): partial argument match of 'na.string' to 'na.strings' ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow = 36000, colClasses = colRead, as.is = TRUE, check.names = FALSE, comment.char = "", na.string = c("NA", "MultipleValues", "Multiple Values")): partial argument match of 'nrow' to 'nrows' ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow = 36000, colClasses = colRead, check.names = FALSE, comment.char = "", na.string = c("NA", "MultipleValues", "Multiple Values")): partial argument match of 'na.string' to 'na.strings' ABarray: warning in read.table(dataFile, header = TRUE, sep = sep, nrow = 36000, colClasses = colRead, check.names = FALSE, comment.char = "", na.string = c("NA", "MultipleValues", "Multiple Values")): partial argument match of 'nrow' to 'nrows' ABarray: warning in dir.create(dataDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' ABarray: warning in dir.create(pdfDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' ABarray: warning in dir.create(jpgDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' doLPE: warning in dir.create(dataDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' doPlotEset: warning in dir.create(dataDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' doPlotEset: warning in dir.create(pdfDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' doPlotEset: warning in dir.create(jpgDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' doPlotFCT: warning in dir.create(dataDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' doPlotFCT: warning in dir.create(pdfDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' doPlotFCT: warning in dir.create(jpgDir, showWarning = FALSE): partial argument match of 'showWarning' to 'showWarnings' icpPlot: warning in jpeg(file = paste(jpgDir, fname, "_Heatmap.jpg", sep = ""), width = fWidth, height = fHeight): partial argument match of 'file' to 'filename' ABarray: no visible binding for global variable ‘colSn’ ABarrayGUI : getImputeFunc: no visible binding for global variable ‘knnRbtn’ doLPE: no visible global function definition for ‘baseOlig.error’ doLPE: no visible global function definition for ‘lpe’ doVennDiagram: no visible global function definition for ‘vennCounts’ drawVennDiagram: no visible global function definition for ‘vennCounts’ getPantherMap: no visible binding for global variable ‘panther’ Undefined global functions or variables: baseOlig.error colSn knnRbtn lpe panther vennCounts * checking Rd files ... NOTE prepare_Rd: ABarrayGUI.Rd:12-13: Dropping empty section \arguments prepare_Rd: calcsn.Rd:26-28: Dropping empty section \examples prepare_Rd: cvv.Rd:22-24: Dropping empty section \examples prepare_Rd: cvvPlot.Rd:24-26: Dropping empty section \examples prepare_Rd: doVennDiagram.Rd:33-36: Dropping empty section \examples prepare_Rd: getMemberEset.Rd:23-25: Dropping empty section \examples prepare_Rd: getPantherMap.Rd:24-26: Dropping empty section \examples prepare_Rd: hclusterPlot.Rd:27-29: Dropping empty section \examples prepare_Rd: matrixPlot.Rd:32-34: Dropping empty section \examples prepare_Rd: qnNormalize.Rd:52-54: Dropping empty section \examples prepare_Rd: savejpg.Rd:26-28: Dropping empty section \examples prepare_Rd: snSummary.Rd:22-25: Dropping empty section \examples * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ABarray.Rcheck/00check.log’ for details.
ABarray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ABarray ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ABarray’ ... ** using staged installation ** R ** 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 (ABarray)
ABarray.Rcheck/ABarray-Ex.timings
name | user | system | elapsed | |
ABarray | 0.001 | 0.000 | 0.000 | |
ABarrayGUI | 0.000 | 0.001 | 0.000 | |
concord | 0.000 | 0.000 | 0.001 | |
doANOVA | 0.001 | 0.001 | 0.001 | |
doLPE | 0 | 0 | 0 | |
doPlotEset | 0 | 0 | 0 | |
doPlotFCT | 0.000 | 0.000 | 0.001 | |
drawVennDiagram | 0.000 | 0.001 | 0.000 | |
icpPlot | 0.001 | 0.001 | 0.000 | |
imputeFlag | 0.000 | 0.000 | 0.001 | |
lpe.fdr.BH | 0.000 | 0.001 | 0.001 | |
mamaplot | 0 | 0 | 0 | |
mvaPair2 | 0.000 | 0.001 | 0.001 | |
panel.cor | 0.000 | 0.001 | 0.000 | |
panel.scatter | 0.001 | 0.001 | 0.000 | |
rgcolorsfunc | 0.002 | 0.001 | 0.002 | |
scaleColorBar | 0.000 | 0.000 | 0.001 | |