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This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 1793/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RUVSeq 1.34.0 (landing page) Davide Risso
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the RUVSeq package: - 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: RUVSeq |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RUVSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RUVSeq_1.34.0.tar.gz |
StartedAt: 2023-10-18 21:09:52 -0400 (Wed, 18 Oct 2023) |
EndedAt: 2023-10-18 21:19:19 -0400 (Wed, 18 Oct 2023) |
EllapsedTime: 566.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RUVSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RUVSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RUVSeq_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RUVSeq.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RUVSeq/DESCRIPTION’ ... OK * this is package ‘RUVSeq’ 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 ‘RUVSeq’ 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 residuals.DGEGLM : <anonymous>: no visible global function definition for ‘poisson’ Undefined global functions or variables: poisson Consider adding importFrom("stats", "poisson") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘RUVg.R’ Running ‘RUVr.R’ Running ‘RUVs.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-mac-arm64/meat/RUVSeq.Rcheck/00check.log’ for details.
RUVSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RUVSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘RUVSeq’ ... ** 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 (RUVSeq)
RUVSeq.Rcheck/tests/RUVg.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-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. > library(RUVSeq) Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: EDASeq Loading required package: ShortRead Loading required package: BiocParallel Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 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: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: Rsamtools Loading required package: GenomicRanges Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians 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 The following object is masked from 'package:Biobase': rowMedians Loading required package: edgeR Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA > > mat <- matrix(data=rpois(100, lambda=10), ncol=10) > rownames(mat) <- paste("gene", 1:10, sep="") > > es <- newSeqExpressionSet(mat) > > ## dimension of W > ks <- 1:5 > > ## matrix > r1 <- lapply(ks, function(k) RUVg(mat, 1:10, k)) > > print(sapply(r1, function(x) dim(x$W))) [,1] [,2] [,3] [,4] [,5] [1,] 10 10 10 10 10 [2,] 1 2 3 4 5 > stopifnot(all(lapply(r1, function(x) dim(x$W)[2])==ks)) > > ## already logged data > r1b <- lapply(ks, function(k) RUVg(log(mat+1), 1:10, k)) Warning messages: 1: In RUVg(log(mat + 1), 1:10, k) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 2: In RUVg(log(mat + 1), 1:10, k) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 3: In RUVg(log(mat + 1), 1:10, k) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 4: In RUVg(log(mat + 1), 1:10, k) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 5: In RUVg(log(mat + 1), 1:10, k) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation > r1c <- lapply(ks, function(k) RUVg(log(mat+1), 1:10, k, isLog=TRUE)) > r1d <- lapply(ks, function(k) RUVg(mat, 1:10, k, round=FALSE)) > > stopifnot(all(sapply(ks, function(i) all(r1[[i]]$W==r1c[[i]]$W)))) > stopifnot(all(sapply(ks, function(i) all(r1d[[i]]$W==r1c[[i]]$W)))) > > stopifnot(all(sapply(ks, function(i) all(log(r1d[[i]]$normalizedCounts+1)-r1c[[i]]$normalizedCounts<1e-8)))) > > ## SeqExpressionSet > r2 <- lapply(ks, function(k) RUVg(es, rownames(es)[1:10], k)) > > print(sapply(r2, function(x) dim(pData(x)))) [,1] [,2] [,3] [,4] [,5] [1,] 10 10 10 10 10 [2,] 1 2 3 4 5 > stopifnot(all(lapply(r2, function(x) dim(pData(x))[2])==ks)) > > ## check handling of zeros > mat <- matrix(data=rpois(100, lambda=2), ncol=10) > rownames(mat) <- paste("gene", 1:10, sep="") > r3 <- RUVg(mat, 1:10, k=1) > print(table(mat==0)) FALSE TRUE 82 18 > print(table(r3$normalizedCounts==0)) FALSE TRUE 85 15 > > proc.time() user system elapsed 14.887 0.721 26.941
RUVSeq.Rcheck/tests/RUVr.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-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. > library(RUVSeq) Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: EDASeq Loading required package: ShortRead Loading required package: BiocParallel Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 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: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: Rsamtools Loading required package: GenomicRanges Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians 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 The following object is masked from 'package:Biobase': rowMedians Loading required package: edgeR Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA > library(edgeR) > > mat <- matrix(data=rpois(100, lambda=10), ncol=10) > rownames(mat) <- paste("gene", 1:10, sep="") > > es <- newSeqExpressionSet(mat) > > ## compute edgeR residuals > x <- as.factor(rep(c("Ctl", "Trt"), each=5)) > design <- model.matrix(~x) > y <- DGEList(counts=mat, group=x) > y <- calcNormFactors(y, method="upperquartile") > y <- estimateGLMCommonDisp(y, design) > y <- estimateGLMTagwiseDisp(y, design) > > fit <- glmFit(y, design) > res <- residuals(fit, type="deviance") > > ## dimension of W > ks <- 1:5 > > ## matrix > r1 <- lapply(ks, function(k) RUVr(mat, 1:10, k, res)) > > print(sapply(r1, function(x) dim(x$W))) [,1] [,2] [,3] [,4] [,5] [1,] 10 10 10 10 10 [2,] 1 2 3 4 5 > stopifnot(all(lapply(r1, function(x) dim(x$W)[2])==ks)) > > ## already logged data > r1b <- lapply(ks, function(k) RUVr(log(mat+1), 1:10, k, res)) Warning messages: 1: In RUVr(log(mat + 1), 1:10, k, res) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 2: In RUVr(log(mat + 1), 1:10, k, res) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 3: In RUVr(log(mat + 1), 1:10, k, res) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 4: In RUVr(log(mat + 1), 1:10, k, res) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 5: In RUVr(log(mat + 1), 1:10, k, res) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation > r1c <- lapply(ks, function(k) RUVr(log(mat+1), 1:10, k, res, isLog=TRUE)) > r1d <- lapply(ks, function(k) RUVr(mat, 1:10, k, res, round=FALSE)) > > stopifnot(all(sapply(ks, function(i) all(r1[[i]]$W==r1c[[i]]$W)))) > stopifnot(all(sapply(ks, function(i) all(r1d[[i]]$W==r1c[[i]]$W)))) > > stopifnot(all(sapply(ks, function(i) all(log(r1d[[i]]$normalizedCounts+1)-r1c[[i]]$normalizedCounts<1e-8)))) > > ## SeqExpressionSet > r2 <- lapply(ks, function(k) RUVr(es, rownames(es)[1:10], k, res)) > > print(sapply(r2, function(x) dim(pData(x)))) [,1] [,2] [,3] [,4] [,5] [1,] 10 10 10 10 10 [2,] 1 2 3 4 5 > stopifnot(all(lapply(r2, function(x) dim(pData(x))[2])==ks)) > > ## check handling of zeros > mat <- matrix(data=rpois(100, lambda=2), ncol=10) > rownames(mat) <- paste("gene", 1:10, sep="") > r3 <- RUVr(mat, 1:10, k=1, res) > print(table(mat==0)) FALSE TRUE 88 12 > print(table(r3$normalizedCounts==0)) FALSE TRUE 88 12 > > proc.time() user system elapsed 14.856 0.717 27.396
RUVSeq.Rcheck/tests/RUVs.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-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. > library(RUVSeq) Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: EDASeq Loading required package: ShortRead Loading required package: BiocParallel Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 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: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: Rsamtools Loading required package: GenomicRanges Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians 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 The following object is masked from 'package:Biobase': rowMedians Loading required package: edgeR Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA > > mat <- matrix(data=rpois(100, lambda=10), ncol=10) > rownames(mat) <- paste("gene", 1:10, sep="") > > differences <- matrix(data=c(1:3, 4:6), byrow=TRUE, nrow=2) > > es <- newSeqExpressionSet(mat) > > ## dimension of W > ks <- 1:4 > > ## matrix > r1 <- lapply(ks, function(k) RUVs(mat, 1:10, k, differences)) > > print(sapply(r1, function(x) dim(x$W))) [,1] [,2] [,3] [,4] [1,] 10 10 10 10 [2,] 1 2 3 4 > stopifnot(all(lapply(r1, function(x) dim(x$W)[2])==ks)) > > ## already logged data > r1b <- lapply(ks, function(k) RUVs(log(mat+1), 1:10, k, differences)) Warning messages: 1: In RUVs(log(mat + 1), 1:10, k, differences) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 2: In RUVs(log(mat + 1), 1:10, k, differences) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 3: In RUVs(log(mat + 1), 1:10, k, differences) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation 4: In RUVs(log(mat + 1), 1:10, k, differences) : The expression matrix does not contain counts. Please, pass a matrix of counts (not logged) or set isLog to TRUE to skip the log transformation > r1c <- lapply(ks, function(k) RUVs(log(mat+1), 1:10, k, differences, isLog=TRUE)) > r1d <- lapply(ks, function(k) RUVs(mat, 1:10, k, differences, round=FALSE)) > > stopifnot(all(sapply(ks, function(i) all(r1[[i]]$W==r1c[[i]]$W)))) > stopifnot(all(sapply(ks, function(i) all(r1d[[i]]$W==r1c[[i]]$W)))) > > stopifnot(all(sapply(ks, function(i) all(log(r1d[[i]]$normalizedCounts+1)-r1c[[i]]$normalizedCounts<1e-8)))) > > ## SeqExpressionSet > r2 <- lapply(ks, function(k) RUVs(es, rownames(es)[1:10], k, differences)) > > print(sapply(r2, function(x) dim(pData(x)))) [,1] [,2] [,3] [,4] [1,] 10 10 10 10 [2,] 1 2 3 4 > stopifnot(all(lapply(r2, function(x) dim(pData(x))[2])==ks)) > > ## check handling of zeros > mat <- matrix(data=rpois(100, lambda=2), ncol=10) > rownames(mat) <- paste("gene", 1:10, sep="") > r3 <- RUVs(mat, 1:10, k=1, differences) > print(table(mat==0)) FALSE TRUE 85 15 > print(table(r3$normalizedCounts==0)) FALSE TRUE 85 15 > > ## make groups > factor1 <- rep(c("a", "b", "c"), each=3) > factor2 <- c(rep("a", 4), rep("b", 2), rep("c", 3)) > factor3 <- rep(1:6, each=2) > > makeGroups(factor1) [,1] [,2] [,3] [1,] 1 2 3 [2,] 4 5 6 [3,] 7 8 9 > makeGroups(as.factor(factor1)) [,1] [,2] [,3] [1,] 1 2 3 [2,] 4 5 6 [3,] 7 8 9 > makeGroups(factor2) [,1] [,2] [,3] [,4] [1,] 1 2 3 4 [2,] 5 6 -1 -1 [3,] 7 8 9 -1 > makeGroups(as.factor(factor2)) [,1] [,2] [,3] [,4] [1,] 1 2 3 4 [2,] 5 6 -1 -1 [3,] 7 8 9 -1 > makeGroups(factor3) [,1] [,2] [1,] 1 2 [2,] 3 4 [3,] 5 6 [4,] 7 8 [5,] 9 10 [6,] 11 12 > makeGroups(as.factor(factor3)) [,1] [,2] [1,] 1 2 [2,] 3 4 [3,] 5 6 [4,] 7 8 [5,] 9 10 [6,] 11 12 > > > > proc.time() user system elapsed 14.734 0.700 26.470
RUVSeq.Rcheck/RUVSeq-Ex.timings
name | user | system | elapsed | |
RUVg | 0.482 | 0.050 | 0.854 | |
RUVr | 0.774 | 0.022 | 1.268 | |
RUVs | 0.172 | 0.009 | 0.275 | |
makeGroups | 0.001 | 0.000 | 0.002 | |
residuals.DGEGLM | 0.611 | 0.013 | 0.950 | |