Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:37:12 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 1134/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MBASED 1.34.0 (landing page) Oleg Mayba
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the MBASED package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MBASED.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: MBASED |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MBASED.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MBASED_1.34.0.tar.gz |
StartedAt: 2023-10-16 03:28:58 -0400 (Mon, 16 Oct 2023) |
EndedAt: 2023-10-16 03:36:50 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 471.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MBASED.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MBASED.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MBASED_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MBASED.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MBASED/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MBASED’ version ‘1.34.0’ * 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 ‘MBASED’ 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 R 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 MBASEDMetaAnalysis: no visible global function definition for ‘pchisq’ MBASEDMetaAnalysis: no visible global function definition for ‘pnorm’ maxLogLikelihoodCalculator1s: no visible global function definition for ‘optimize’ maxLogLikelihoodCalculator2s: no visible global function definition for ‘optimize’ runMBASED: no visible global function definition for ‘is’ runMBASED1s: no visible global function definition for ‘is’ runMBASED2s: no visible global function definition for ‘is’ vectorizedRbetabinomAB: no visible global function definition for ‘rbeta’ vectorizedRbetabinomAB: no visible global function definition for ‘rbinom’ vectorizedRbetabinomMR: no visible global function definition for ‘rbeta’ vectorizedRbetabinomMR: no visible global function definition for ‘rbinom’ Undefined global functions or variables: is optimize pchisq pnorm rbeta rbinom Consider adding importFrom("methods", "is") importFrom("stats", "optimize", "pchisq", "pnorm", "rbeta", "rbinom") 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 ... 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 ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 ‘/Users/biocbuild/bbs-3.17-bioc/meat/MBASED.Rcheck/00check.log’ for details.
MBASED.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MBASED ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘MBASED’ ... ** 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 (MBASED)
MBASED.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (64-bit) 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. > BiocGenerics:::testPackage("MBASED") 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians RUNIT TEST PROTOCOL -- Mon Oct 16 03:36:28 2023 *********************************************** Number of test functions: 21 Number of errors: 0 Number of failures: 0 1 Test Suite : MBASED RUnit Tests - 21 test functions, 0 errors, 0 failures Number of test functions: 21 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 96.220 1.797 125.257
MBASED.Rcheck/MBASED-Ex.timings
name | user | system | elapsed | |
FreemanTukeyFunctions | 1.515 | 0.152 | 2.194 | |
MBASEDMetaAnalysis | 0.003 | 0.001 | 0.005 | |
MBASEDMetaAnalysisGetMeansAndSEs | 0.001 | 0.001 | 0.004 | |
MBASEDVectorizedMetaprop | 0.008 | 0.003 | 0.016 | |
MBASEDVectorizedPropDiffTest | 0.005 | 0.002 | 0.011 | |
betaParametrizationConverters | 0.001 | 0.001 | 0.002 | |
estimateMAF1s | 0.011 | 0.001 | 0.017 | |
estimateMAF2s | 0.012 | 0.001 | 0.016 | |
generatingBetaBinomialCounts | 0.001 | 0.001 | 0.002 | |
getPFinal | 0.002 | 0.001 | 0.003 | |
getSimulationPvalue | 0.001 | 0.000 | 0.001 | |
logLikelihoodCalculator1s | 0.001 | 0.000 | 0.001 | |
logLikelihoodCalculator2s | 0.001 | 0.001 | 0.002 | |
maxLogLikelihoodCalculator1s | 0.001 | 0.000 | 0.002 | |
maxLogLikelihoodCalculator2s | 0.002 | 0.000 | 0.007 | |
runMBASED | 0 | 0 | 0 | |
runMBASED1s | 0.000 | 0.001 | 0.001 | |
runMBASED1s1aseID | 0.000 | 0.001 | 0.001 | |
runMBASED2s | 0.000 | 0.000 | 0.001 | |
runMBASED2s1aseID | 0.000 | 0.000 | 0.001 | |
shiftAndAttenuateProportions | 0.002 | 0.001 | 0.003 | |