##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:Rvisdiff.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings Rvisdiff_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Rvisdiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rvisdiff’ version ‘1.0.0’
* 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 ‘Rvisdiff’ 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 loading without being on the library search path ... 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 ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
DEreport 31.129   1.06  32.192
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘Rvisdiff-Tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Rvisdiff.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL Rvisdiff
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘Rvisdiff’ ...
** 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 (Rvisdiff)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(Rvisdiff)
> 
> ### Prapare input data
> 
> library("airway")
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:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
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

> data("airway")
> se <- airway
> se$dex <- relevel(se$dex, ref="untrt")
> countdata <- assay(se)
> coldata <- colData(se)
> 
> ### Produce interactive DE reports from DESeq2 results
> 
> library("DESeq2")
> dds <- DESeqDataSet(se, design = ~ cell + dex)
> dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> DEreport(dds, countdata)
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N052611_N061011" path.
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N052611_N080611" path.
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N052611_N61311" path.
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N061011_N080611" path.
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N061011_N61311" path.
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/cell_N080611_N61311" path.
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/dex_untrt_trt" path.
The index has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path.
> 
> ### Produce interactive DE reports from edgeR results
> 
> 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

> design <- model.matrix(~ cell + dex, data = coldata)
> dl <- DGEList(counts = countdata, group = coldata$dex)
> dl <- calcNormFactors(dl)
> dl <- estimateDisp(dl, design=design)
> DEreport(dl, countdata)
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path.
> de <- exactTest(dl,pair=1:2)
> DEreport(de, countdata, coldata$dex)
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path.
> 
> ### Produce interactive DE reports from limma results
> 
> library("limma")
> design <- model.matrix(~ 0 + dex + cell, data = coldata)
> contr <- makeContrasts(dextrt - dexuntrt,levels=colnames(design))
> limmaexprs <- voom(countdata, design)
> fit <- lmFit(limmaexprs, design)
> fit <- contrasts.fit(fit, contrasts=contr)
> fit <- eBayes(fit)
> DEreport(fit, countdata)
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport/dextrt - dexuntrt" path.
The index has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path.
> 
> ### Produce interactive DE reports from Differential test results
> 
> untrt <- countdata[,coldata$dex=="untrt"]
> trt <- countdata[,coldata$dex=="trt"]
> library(matrixTests)
> wilcox <- col_wilcoxon_twosample(t(untrt), t(trt))
Warning message:
col_wilcoxon_twosample: 50597 of the columns had ties: cannot compute exact p-values with ties.
First occurrence at column 2 
> stat <- wilcox$statistic
> p <- wilcox$pvalue
> log2FoldChange <- log2(rowMeans(trt)+1) - log2(rowMeans(untrt)+1)
> wilcox <- data.frame(genes = rownames(countdata), statistic = stat,
+     pValue = round(p, 6), pAdjust = p.adjust(wilcox[,2], method = "BH"),
+     expMean = rowMeans(countdata), log2FC = log2FoldChange)
> normalized <- edgeR::cpm(countdata)
> normalized <- as.data.frame(normalized)
> normalized$genes <- rownames(normalized)
> DEreport(wilcox, NULL, coldata$dex, normalized = normalized, genes="genes",
+ pvalue="pValue", padj = "pAdjust", stat = "statistic",
+ baseMean="expMean", log2FoldChange="log2FC")
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path.
> 
> ### Missing columns tests
> colnames(wilcox) <- c("genes","missing1","missing2","missing3","missing4","missing5")
> DEreport(wilcox, NULL, coldata$dex, normalized = normalized, genes="genes")
The report has been generated in the "/home/biocbuild/bbs-3.18-bioc/meat/Rvisdiff.Rcheck/tests/DEreport" path.
Warning messages:
1: In getColnamesJSON(colnames(DE)) :
  Missing pvalue in DE results. Valid names for pvalue are 'pvalue', 'P.Value',
'PValue' or you can especify a custom name in pvalue argument.
2: In getColnamesJSON(colnames(DE)) :
  Missing padj in DE results. Valid names for padj are 'padj', 'FDR',
'adj.P.Val' or you can especify a custom name in padj argument.
3: In getColnamesJSON(colnames(DE)) :
  Missing log2FoldChange in DE results. Valid names for log2FoldChange are
'log2FoldChange', 'logFC' or you can especify a custom name in log2FoldChange
argument.
4: In getColnamesJSON(colnames(DE)) :
  Missing baseMean in DE results. Valid names for baseMean are 'baseMean',
'AveExpr', 'logCPM' or you can especify a custom name in baseMean argument.
> 
> 
> proc.time()
   user  system elapsed 
 92.891   1.959  94.838