Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 171/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biobroom 1.37.0 (landing page) John D. Storey
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the biobroom package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biobroom.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: biobroom |
Version: 1.37.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biobroom.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings biobroom_1.37.0.tar.gz |
StartedAt: 2024-08-20 22:39:22 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 22:41:06 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 103.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: biobroom.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biobroom.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings biobroom_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/biobroom.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'biobroom/DESCRIPTION' ... OK * this is package 'biobroom' version '1.37.0' * 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 whether package 'biobroom' 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 ... WARNING 'library' or 'require' call to 'DESeq2' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing or unexported object: 'dplyr::tbl_dt' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE finish: no visible global function definition for 'tbl_dt' glance.DGEExact: no visible global function definition for 'p.adjust' glance.GRanges: no visible binding for global variable 'gr' glance.GRangesList: no visible binding for global variable 'gr' makeExampleDataSet: no visible global function definition for 'estimateSizeFactors' makeExampleDataSet: no visible global function definition for 'counts' makeExampleDataSet: no visible global function definition for 'colData' makeExampleDataSet: no visible global function definition for 'seqnames' makeExampleDataSet: no visible global function definition for 'rowRanges' makeExampleDataSet: no visible global function definition for 'start' makeExampleDataSet: no visible global function definition for 'end' makeExampleDataSet: no visible global function definition for 'DGEList' makeExampleDataSet: no visible global function definition for 'calcNormFactors' makeExampleDataSet: no visible global function definition for 'model.matrix' makeExampleDataSet: no visible global function definition for 'design' makeExampleDataSet: no visible global function definition for 'voomWithQualityWeights' makeExampleDataSet: no visible global function definition for 'voom' makeExampleDataSet: no visible global function definition for 'pData<-' makeExampleDataSet: no visible global function definition for 'fData<-' makeExampleDataSet: no visible global function definition for 'is' tidy.DESeqDataSet: no visible binding for global variable 'term' tidy.DESeqDataSet: no visible binding for global variable '.' tidy.DESeqDataSet: no visible global function definition for 'counts' tidy.DESeqDataSet: no visible binding for global variable 'gene' tidy.DGEList: no visible binding for global variable 'gene' tidy.EList: no visible global function definition for 'setNames' tidy.ExpressionSet: no visible binding for global variable 'value' tidy.ExpressionSet: no visible binding for global variable 'gene' tidy.ExpressionSet: no visible global function definition for 'pData' tidy.MArrayLM: no visible binding for global variable 'term' tidy.MArrayLM: no visible binding for global variable 'estimate' tidy.MArrayLM: no visible binding for global variable 'gene' tidy.MSnSet: no visible binding for global variable 'sample.id' tidy.MSnSet: no visible binding for global variable 'value' tidy.MSnSet: no visible binding for global variable 'protein' tidy.MSnSet: no visible global function definition for 'pData' tidy.RangedSummarizedExperiment: no visible binding for global variable 'value' tidy.RangedSummarizedExperiment: no visible binding for global variable 'gene' tidy.RangedSummarizedExperiment: no visible global function definition for 'colData' tidy.deSet: no visible global function definition for 'exprs<-' tidy.deSet: no visible binding for global variable 'value' tidy.deSet: no visible binding for global variable 'gene' tidy.deSet: no visible global function definition for 'pData' tidy.qvalue: no visible binding for global variable 'smoothed' tidy.qvalue: no visible binding for global variable 'pi0' tidy.qvalue: no visible binding for global variable 'lambda' tidy_matrix: no visible binding for global variable 'value' tidy_matrix: no visible binding for global variable 'gene' Undefined global functions or variables: . DGEList calcNormFactors colData counts design end estimate estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames setNames smoothed start tbl_dt term value voom voomWithQualityWeights Consider adding importFrom("methods", "is") importFrom("stats", "end", "model.matrix", "p.adjust", "setNames", "start") 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DESeq2_tidiers 10.96 0.71 11.72 edgeR_tidiers 5.13 0.14 5.28 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.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 'F:/biocbuild/bbs-3.20-bioc/meat/biobroom.Rcheck/00check.log' for details.
biobroom.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL biobroom ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'biobroom' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (biobroom)
biobroom.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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("magrittr") Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not > library("dplyr") Attaching package: 'dplyr' 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 > library("DESeq2") Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:dplyr': combine, intersect, setdiff, union 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, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following objects are masked from 'package:dplyr': first, rename 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 objects are masked from 'package:dplyr': collapse, desc, slice The following object is masked from 'package:grDevices': windows Loading required package: GenomicRanges Loading required package: GenomeInfoDb Attaching package: 'GenomicRanges' The following object is masked from 'package:magrittr': subtract Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following object is masked from 'package:dplyr': count 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: 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 > library("edgeR") Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:DESeq2': plotMA The following object is masked from 'package:BiocGenerics': plotMA > library("Biobase") > library("biobroom") Loading required package: broom Registered S3 methods overwritten by 'biobroom': method from glance.list broom tidy.list broom > > test_check("biobroom") [ FAIL 0 | WARN 20 | SKIP 0 | PASS 52 ] [ FAIL 0 | WARN 20 | SKIP 0 | PASS 52 ] > > > proc.time() user system elapsed 17.75 0.67 18.46
biobroom.Rcheck/biobroom-Ex.timings
name | user | system | elapsed | |
DESeq2_tidiers | 10.96 | 0.71 | 11.72 | |
ExpressionSet_tidiers | 1.55 | 0.00 | 1.54 | |
GRanges_tidiers | 0 | 0 | 0 | |
MSnSet_tidiers | 4.14 | 0.24 | 4.42 | |
SummarizedExperiment_tidiers | 0 | 0 | 0 | |
edgeR_tidiers | 5.13 | 0.14 | 5.28 | |
limma_tidiers | 0.36 | 0.04 | 0.40 | |
qvalue_tidiers | 0.67 | 0.00 | 0.67 | |