Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the biobroom package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 155/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biobroom 1.24.0 (landing page) John D. Storey
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: biobroom |
Version: 1.24.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biobroom.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings biobroom_1.24.0.tar.gz |
StartedAt: 2021-10-14 20:08:05 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:10:48 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 163.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: biobroom.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biobroom.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings biobroom_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/biobroom.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'biobroom/DESCRIPTION' ... OK * this is package 'biobroom' version '1.24.0' * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DESeq2_tidiers 12.54 0.78 16.22 edgeR_tidiers 5.17 0.15 5.33 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DESeq2_tidiers 13.35 0.23 13.59 edgeR_tidiers 6.15 0.06 6.22 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/biobroom.Rcheck/00check.log' for details.
biobroom.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/biobroom_1.24.0.tar.gz && rm -rf biobroom.buildbin-libdir && mkdir biobroom.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biobroom.buildbin-libdir biobroom_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL biobroom_1.24.0.zip && rm biobroom_1.24.0.tar.gz biobroom_1.24.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 217k 100 217k 0 0 720k 0 --:--:-- --:--:-- --:--:-- 722k install for i386 * 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 converting help for package 'biobroom' finding HTML links ... done DESeq2_tidiers html ExpressionSet_tidiers html GRanges_tidiers html MSnSet_tidiers html SummarizedExperiment_tidiers html biobroom html edgeR_tidiers html edge_tidiers html hammer html limma_tidiers html list_tidiers html qvalue_tidiers html sva_tidiers html ** 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 install for x64 * installing *source* package 'biobroom' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'biobroom' as biobroom_1.24.0.zip * DONE (biobroom) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'biobroom' successfully unpacked and MD5 sums checked
biobroom.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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("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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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 objects are masked from 'package:dplyr': first, rename 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 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 15 | SKIP 0 | PASS 52 ] > > > proc.time() user system elapsed 17.62 1.37 18.98 |
biobroom.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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("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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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 objects are masked from 'package:dplyr': first, rename 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 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 15 | SKIP 0 | PASS 52 ] > > > proc.time() user system elapsed 20.79 0.59 21.37 |
biobroom.Rcheck/examples_i386/biobroom-Ex.timings
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biobroom.Rcheck/examples_x64/biobroom-Ex.timings
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