Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 798/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
geneRxCluster 1.43.0 (landing page) Charles Berry
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the geneRxCluster package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geneRxCluster.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: geneRxCluster |
Version: 1.43.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geneRxCluster.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geneRxCluster_1.43.0.tar.gz |
StartedAt: 2024-12-23 19:25:30 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 19:26:01 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 30.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: geneRxCluster.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geneRxCluster.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geneRxCluster_1.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/geneRxCluster.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 ‘geneRxCluster/DESCRIPTION’ ... OK * this is package ‘geneRxCluster’ version ‘1.43.0’ * 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 ‘geneRxCluster’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 .gRxCluster: no visible global function definition for ‘tail’ .gRxCluster: no visible global function definition for ‘head’ .gRxCluster: no visible global function definition for ‘metadata’ .gRxCluster: no visible global function definition for ‘metadata<-’ critVal.alpha : <anonymous>: no visible global function definition for ‘pbinom’ critVal.alpha : <anonymous>: no visible global function definition for ‘tail’ critVal.alpha : <anonymous>: no visible global function definition for ‘head’ critVal.power: no visible global function definition for ‘plogis’ critVal.power: no visible global function definition for ‘qlogis’ critVal.power : <anonymous>: no visible global function definition for ‘qbinom’ critVal.power : <anonymous>: no visible global function definition for ‘dbinom’ critVal.power : <anonymous>: no visible global function definition for ‘pbinom’ critVal.target : <anonymous>: no visible global function definition for ‘pbinom’ critVal.target : <anonymous>: no visible global function definition for ‘tail’ critVal.target : <anonymous>: no visible global function definition for ‘head’ gRxCluster: no visible global function definition for ‘as’ gRxCluster: no visible global function definition for ‘runValue’ gRxCluster: no visible global function definition for ‘metadata’ gRxCluster: no visible global function definition for ‘metadata<-’ gRxPlot: no visible global function definition for ‘qlogis’ gRxPlot: no visible global function definition for ‘hist’ gRxPlot: no visible global function definition for ‘metadata’ gRxPlotClumps: no visible global function definition for ‘metadata’ gRxPlotClumps: no visible global function definition for ‘seqlengths’ gRxPlotClumps: no visible global function definition for ‘runValue’ gRxPlotClumps: no visible global function definition for ‘seqlengths<-’ gRxPlotClumps: no visible global function definition for ‘queryHits’ gRxPlotClumps: no visible global function definition for ‘subjectHits’ gRxPlotClumps: no visible global function definition for ‘par’ gRxPlotClumps: no visible global function definition for ‘box’ gRxPlotClumps: no visible global function definition for ‘segments’ gRxPlotClumps: no visible global function definition for ‘text’ gRxSummary: no visible global function definition for ‘metadata’ plot.cutpoints: no visible global function definition for ‘barplot’ plot.cutpoints: no visible global function definition for ‘points’ prune.loglik : x.max: no visible global function definition for ‘subjectHits’ Undefined global functions or variables: as barplot box dbinom head hist metadata metadata<- par pbinom plogis points qbinom qlogis queryHits runValue segments seqlengths seqlengths<- subjectHits tail text Consider adding importFrom("graphics", "barplot", "box", "hist", "par", "points", "segments", "text") importFrom("methods", "as") importFrom("stats", "dbinom", "pbinom", "plogis", "qbinom", "qlogis") importFrom("utils", "head", "tail") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: gRxCluster-object.Rd: GRanges 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * 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 ‘doRunit.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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/geneRxCluster.Rcheck/00check.log’ for details.
geneRxCluster.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL geneRxCluster ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘geneRxCluster’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cluster.c -o cluster.o cluster.c:83:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if (*pvj==HITAIL) ^ 1 warning generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o geneRxCluster.so cluster.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-geneRxCluster/00new/geneRxCluster/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (geneRxCluster)
geneRxCluster.Rcheck/tests/doRunit.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 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. > ## unit tests will not be done if RUnit is not available > if(require("RUnit", quietly=TRUE)) { + + ## --- Setup --- + + pkg <- "geneRxCluster" # <-- Change to package name! + if(Sys.getenv("RCMDCHECK") == "FALSE") { + ## Path to unit tests for standalone running under Makefile (not R CMD check) + ## PKG/tests/../inst/unitTests + path <- file.path(getwd(), "..", "inst", "unitTests") + } else { + ## Path to unit tests for R CMD check + ## PKG.Rcheck/tests/../PKG/unitTests + path <- system.file(package=pkg, "unitTests") + } + cat("\nRunning unit tests\n") + print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path)) + + library(package=pkg, character.only=TRUE) + + ## If desired, load the name space to allow testing of private functions + ## if (is.element(pkg, loadedNamespaces())) + ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3) + ## + ## or simply call PKG:::myPrivateFunction() in tests + + ## --- Testing --- + + ## Define tests + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), + dirs=path) + ## Run + tests <- runTestSuite(testSuite) + + ## Default report name + pathReport <- file.path(path, "report") + + ## Report to stdout and text files + cat("------------------- UNIT TEST SUMMARY ---------------------\n\n") + printTextProtocol(tests, showDetails=FALSE) + printTextProtocol(tests, showDetails=FALSE, + fileName=paste(pathReport, "Summary.txt", sep="")) + printTextProtocol(tests, showDetails=TRUE, + fileName=paste(pathReport, ".txt", sep="")) + + ## Report to HTML file + printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep="")) + + ## Return stop() to cause R CMD check stop in case of + ## - failures i.e. FALSE to unit tests or + ## - errors i.e. R errors + tmp <- getErrors(tests) + if(tmp$nFail > 0 | tmp$nErr > 0) { + stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail, + ", #R errors: ", tmp$nErr, ")\n\n", sep="")) + } + } else { + warning("cannot run unit tests -- package RUnit is not available") + } Running unit tests $pkg [1] "geneRxCluster" $getwd [1] "/Users/biocbuild/bbs-3.21-bioc/meat/geneRxCluster.Rcheck/tests" $pathToUnitTests [1] "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpvTW6eW/RLIBS_17934d847255/geneRxCluster/unitTests" Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Executing test function test_bad_args_gRxCluster ... Error in gRxCluster(rep("a", 100), 0:100L, c(rep(TRUE, 5), rep(c(FALSE, : object, starts, and group must have same lengths In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry done successfully. Executing test function test_crossover_gRxCluster ... done successfully. Executing test function test_permutation_both_ways_gRxCluster ... done successfully. Executing test function test_prune_gRxCluster ... done successfully. Executing test function test_simply_grx_clust_Call ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Mon Dec 23 19:25:57 2024 *********************************************** Number of test functions: 5 Number of errors: 0 Number of failures: 0 1 Test Suite : geneRxCluster unit testing - 5 test functions, 0 errors, 0 failures > > proc.time() user system elapsed 1.328 0.086 1.411
geneRxCluster.Rcheck/geneRxCluster-Ex.timings
name | user | system | elapsed | |
critVal.alpha | 0.058 | 0.001 | 0.059 | |
critVal.power | 0.102 | 0.001 | 0.103 | |
critVal.target | 0.006 | 0.001 | 0.007 | |
gRxPlot | 0.299 | 0.010 | 0.309 | |
gRxPlotClumps | 0.117 | 0.001 | 0.117 | |
gRxSummary | 0.108 | 0.001 | 0.108 | |