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 11:36:43 -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 2039/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SummarizedBenchmark 2.18.0 (landing page) Patrick Kimes
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SummarizedBenchmark package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SummarizedBenchmark.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: SummarizedBenchmark |
Version: 2.18.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SummarizedBenchmark.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SummarizedBenchmark_2.18.0.tar.gz |
StartedAt: 2023-10-16 07:26:24 -0400 (Mon, 16 Oct 2023) |
EndedAt: 2023-10-16 07:29:56 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 212.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SummarizedBenchmark.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SummarizedBenchmark.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SummarizedBenchmark_2.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/SummarizedBenchmark.Rcheck' * using R version 4.3.1 (2023-06-16 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.2.0 GNU Fortran (GCC) 12.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SummarizedBenchmark/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SummarizedBenchmark' version '2.18.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'tidyr', 'SummarizedExperiment', 'S4Vectors', 'BiocGenerics', 'UpSetR', 'rlang', 'stringr', 'BiocParallel', 'ggplot2', 'mclust', 'dplyr', 'digest', 'sessioninfo', 'crayon', 'tibble' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 whether package 'SummarizedBenchmark' can be installed ... OK * checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: data 6.4Mb * 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 ... NOTE Unexported object imported by a ':::' call: 'BiocGenerics:::replaceSlots' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .combineSummarizedBenchmarks: no visible binding for global variable 'colid' .combineSummarizedBenchmarks: no visible binding for global variable 'label' .compare.meta: no visible binding for global variable 'label' .compare.meta : <anonymous>: no visible binding for global variable 'label' .compare.meta: no visible binding for global variable 'value' .compare.meta: no visible binding for global variable 'comparison' .list2mat: no visible binding for global variable '.id' .list2mat: no visible binding for global variable '.val' .list2mat: no visible binding for global variable '.method' .printUpdateBench: no visible binding for global variable 'f' .printUpdateBench: no visible binding for global variable 'meta' .printUpdateBench: no visible binding for global variable 'post' .printUpdateBench: no visible binding for global variable 'rerun' .printUpdateBench: no visible binding for global variable 'overlap' plotROC: no visible binding for global variable 'FDR' plotROC: no visible binding for global variable 'TPR' plotROC: no visible binding for global variable 'method' tidyUpMetrics: no visible binding for global variable 'key' tidyUpMetrics: no visible binding for global variable 'value' updateBench: no visible binding for global variable 'overlap' updateBench: no visible binding for global variable 'f' updateBench: no visible binding for global variable 'meta' updateBench: no visible binding for global variable 'post' Undefined global functions or variables: .id .method .val FDR TPR colid comparison f key label meta method overlap post rerun value * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... WARNING LazyData DB of 6.4 MB without LazyDataCompression set See ยง1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.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 WARNING, 4 NOTEs See 'F:/biocbuild/bbs-3.17-bioc/meat/SummarizedBenchmark.Rcheck/00check.log' for details.
SummarizedBenchmark.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SummarizedBenchmark ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'SummarizedBenchmark' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (SummarizedBenchmark)
SummarizedBenchmark.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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. > library("testthat") > library("SummarizedBenchmark") Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:testthat': matches Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats 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 Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics 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 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:tidyr': expand 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: Biobase 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 Loading required package: UpSetR Loading required package: rlang Attaching package: 'rlang' The following object is masked from 'package:Biobase': exprs The following objects are masked from 'package:testthat': is_false, is_null, is_true Loading required package: stringr Loading required package: BiocParallel Loading required package: ggplot2 Loading required package: mclust Package 'mclust' version 6.0.0 Type 'citation("mclust")' for citing this R package in publications. Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:GenomicRanges': intersect, setdiff, union The following object is masked from 'package:GenomeInfoDb': intersect The following objects are masked from 'package:IRanges': collapse, desc, intersect, setdiff, slice, union The following objects are masked from 'package:S4Vectors': first, intersect, rename, setdiff, setequal, union The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, union The following object is masked from 'package:matrixStats': count The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: digest Loading required package: sessioninfo Loading required package: crayon Attaching package: 'crayon' The following object is masked from 'package:ggplot2': %+% The following object is masked from 'package:rlang': chr Loading required package: tibble > > test_check("SummarizedBenchmark") Attaching package: 'iCOBRA' The following objects are masked from 'package:GenomicRanges': score, score<- The following objects are masked from 'package:BiocGenerics': score, score<- Option rerun is set to `FALSE`: Rerunning performance metrics only for the following methods: BH2 Found already estimated performance metrics, replacing these Found already estimated performance metrics, replacing these Found already estimated performance metrics, replacing these Found already estimated performance metrics, replacing these [ FAIL 0 | WARN 108 | SKIP 0 | PASS 224 ] [ FAIL 0 | WARN 108 | SKIP 0 | PASS 224 ] > > proc.time() user system elapsed 30.71 4.50 41.68
SummarizedBenchmark.Rcheck/SummarizedBenchmark-Ex.timings
name | user | system | elapsed | |
BDData-setter | 0.03 | 0.00 | 0.03 | |
BDData | 0 | 0 | 0 | |
BDMethod-setter | 0.03 | 0.00 | 0.03 | |
BDMethod | 0.02 | 0.00 | 0.01 | |
BDMethodList-setter | 0 | 0 | 0 | |
BDMethodList | 0.02 | 0.00 | 0.01 | |
BenchDesign | 0.01 | 0.00 | 0.02 | |
SummarizedBenchmark-class | 1.16 | 0.14 | 1.45 | |
SummarizedBenchmark | 0.15 | 0.01 | 0.18 | |
addMethod | 0.02 | 0.00 | 0.04 | |
addPerformanceMetric | 0.03 | 0.04 | 0.06 | |
allSB | 0.00 | 0.01 | 0.02 | |
assayNames-setter | 0.05 | 0.05 | 0.09 | |
availableMetrics | 0 | 0 | 0 | |
buildBench | 1.81 | 0.36 | 2.80 | |
compareBDData | 0 | 0 | 0 | |
compareBDMethod | 0.17 | 0.00 | 0.17 | |
compareBenchDesigns | 0.36 | 0.01 | 0.37 | |
dropMethod | 0.03 | 0.00 | 0.03 | |
estimateMetrics | 0.51 | 0.05 | 0.57 | |
expandMethod | 0.05 | 0.00 | 0.04 | |
modifyMethod | 0.03 | 0.02 | 0.05 | |
performanceMetrics-setter | 0.03 | 0.01 | 0.05 | |
performanceMetrics | 0.05 | 0.02 | 0.06 | |
plotMethodsOverlap | 0.00 | 0.01 | 0.02 | |
plotROC | 0.00 | 0.02 | 0.01 | |
printMethod | 0.02 | 0.00 | 0.02 | |
sb | 0.00 | 0.01 | 0.01 | |
tdat | 0 | 0 | 0 | |
tidyUpMetrics | 0.19 | 0.00 | 0.19 | |
updateBench | 1.00 | 0.03 | 1.08 | |