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 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 511/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ddCt 1.62.0 (landing page) Jitao David Zhang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the ddCt package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ddCt.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: ddCt |
Version: 1.62.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ddCt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ddCt_1.62.0.tar.gz |
StartedAt: 2024-12-20 17:00:22 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 17:01:05 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 42.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ddCt.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ddCt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ddCt_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ddCt.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 ‘ddCt/DESCRIPTION’ ... OK * this is package ‘ddCt’ version ‘1.62.0’ * 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 ‘ddCt’ 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 ... NOTE barploterrbar: no visible global function definition for ‘par’ barploterrbar: no visible global function definition for ‘layout’ barploterrbar: no visible global function definition for ‘barplot’ barploterrbar: no visible global function definition for ‘segments’ ddCtErrBarchart: no visible global function definition for ‘as.formula’ ddCtReport: no visible global function definition for ‘write.table’ na.mad: no visible global function definition for ‘mad’ na.median: no visible global function definition for ‘median’ na.sd: no visible global function definition for ‘sd’ replaceNames: no visible global function definition for ‘na.omit’ ddCtWithEExec,InputFrame: no visible global function definition for ‘deriv’ ddCtWithEExec,InputFrame: no visible global function definition for ‘as.formula’ elistWrite,ddCtExpression-character: no visible global function definition for ‘write.table’ readRawData,QuantStudioReader-character: no visible global function definition for ‘read.table’ readRawData,SDMReader-character: no visible global function definition for ‘read.table’ readRawData,TSVReader-character: no visible global function definition for ‘read.table’ Undefined global functions or variables: as.formula barplot deriv layout mad median na.omit par read.table sd segments write.table Consider adding importFrom("graphics", "barplot", "layout", "par", "segments") importFrom("stats", "as.formula", "deriv", "mad", "median", "na.omit", "sd") importFrom("utils", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... WARNING checkRd: (7) InputFrame.Rd:18: Invalid URL: mailto: jitao_david.zhang@roche.com checkRd: (-1) SDMFrame-class.Rd:83: Escaped LaTeX specials: \$ checkRd: (7) SDMFrame-class.Rd:172: Invalid email address: mailto:r.biczok@dkfz.de checkRd: (7) SDMFrame-class.Rd:173: Invalid email address: mailto:jitao_david.zhang@roche.com checkRd: (-1) ddCtAbsolute.Rd:30: Escaped LaTeX specials: \_ checkRd: (-1) ddCtExpression-class.Rd:97: Lost braces; missing escapes or markup? 97 | "character")}: {writes ddCtExpression object into a file} | ^ checkRd: (7) ddCtExpression-class.Rd:101: Invalid email address: mailto:r.biczok@dkfz.de checkRd: (7) ddCtExpression-methods.Rd:59: Invalid email address: mailto:r.biczok@dkfz.de * 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’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ Running ‘unit.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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ddCt.Rcheck/00check.log’ for details.
ddCt.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ddCt ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘ddCt’ ... ** using staged installation ** R ** 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 (ddCt)
ddCt.Rcheck/tests/testthat.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. > library(testthat) > library(ddCt) > > test_check("ddCt") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 1.100 0.111 1.200
ddCt.Rcheck/tests/unit.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. > ################################################################################ > ## > ## This software is created by Molecular Genom Analysis Group > ## Department of German Cancer Research Center in Heidelberg > ## > ## > ## unit.R > ## Created on: Oct 23, 2008 > ## Author: Rudolf Biczok <r.biczok@dkfz-heidelberg.de> > ## Description: RUnit test suit for ddCt classes > ## > ################################################################################ > > pkg <- "ddCt" > unit.path <- file.path(getwd(), "units") > > unitMode <- function() { + if(Sys.getenv("R_DEVELOP_MODE") == "TRUE") + return("unit") + else + return("normal") + } > > normalTest <- function() { + testFile <- system.file("./extdata/Experiment2.txt", package=pkg) + + ## Basic SDMFrame + sdm <- SDMFrame(testFile) + + ## ddCt + x <- ddCtExpression(sdm, + calibrationSample="Sample3", + housekeepingGenes="Gene2") + + ## coerece as data frame + y1 <- as(x, "data.frame") + y2 <- elist(x) + stopifnot(all.equal(y1,y2)) + + ## visualization + errBarchart(x) + } > > > ## --- Setup --- > > library(package=pkg, character.only=TRUE) > > # put this in an enclosure so we can return early > (function() { + if(unitMode() != "unit") { + normalTest() + return() + } + + if(!require("RUnit", quietly=TRUE)) { + stop("cannot run unit tests -- package RUnit is not available") + } + + ## --- Testing --- + cat("------------------- BEGIN UNIT TESTS ----------------------\n\n") + + ## --- Setup test suit --- + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=unit.path) + tests <- runTestSuite(testSuite) + + ## --- Setup report directory --- + pathReport <- file.path(getwd(),"report") + if (!file.exists(pathReport)) { + dir.create(pathReport) + } + + ## --- Reporting --- + cat("------------------- UNIT TEST SUMMARY ---------------------\n\n") + + printTextProtocol(tests, showDetails=FALSE) + printTextProtocol(tests, showDetails=FALSE, + fileName=file.path(pathReport, "summary.txt")) + printTextProtocol(tests, showDetails=TRUE, + fileName=file.path(pathReport, "summary-detail.txt")) + printHTMLProtocol(tests, + fileName=file.path(pathReport, "summary.html")) + + errors <- getErrors(tests) + if(errors$nFail > 0 | errors$nErr > 0) { + warning(paste("\n\nunit testing failed (#unit failures: ", errors$nFail, + ", #R errors: ", errors$nErr, ")\n\n", sep="")) + } + + cat("------------------- END OF UNIT TESTING -------------------\n\n") + })() NULL > > proc.time() user system elapsed 0.910 0.088 0.990
ddCt.Rcheck/ddCt-Ex.timings
name | user | system | elapsed | |
InputFrame | 0.004 | 0.000 | 0.005 | |
InputReader-class | 0.002 | 0.001 | 0.001 | |
QuantStudioFrame | 0.119 | 0.037 | 0.157 | |
SDMFrame-class | 0.018 | 0.004 | 0.022 | |
SDMFrame | 0.006 | 0.001 | 0.007 | |
barploterrbar | 0.005 | 0.001 | 0.005 | |
ddCtExpression-class | 0.071 | 0.002 | 0.073 | |
ddCtExpression-methods | 0.067 | 0.001 | 0.068 | |
elistWrite-methods | 0.031 | 0.001 | 0.033 | |
errBarchartParameter-class | 0 | 0 | 0 | |
getDir | 0.001 | 0.001 | 0.000 | |
replaceVectorByEquality | 0 | 0 | 0 | |