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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings EnrichmentBrowser_2.29.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.29.2’
* package encoding: UTF-8
* 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 ‘EnrichmentBrowser’ 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2'
  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
.getGOFromBiomart: no visible binding for global variable
  ‘go_linkage_type’
Undefined global functions or variables:
  go_linkage_type
* 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 ... ERROR
Running examples in ‘EnrichmentBrowser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: import
> ### Title: Import results from differential expression (DE) analysis
> ### Aliases: import
> 
> ### ** Examples
> 
> 
>   # Setup
>   ## i) Generate count data
>   nsamples <- 4
>   ngenes <- 1000
>   dispers <- 1 / rchisq(ngenes, df = 10)
>   rdesign <- model.matrix(~factor(rep(c(1, 2), each = 2)))
>     
>   counts <- rnbinom(ngenes * nsamples, mu = 20, size = 1 / dispers)
>   counts <- matrix(counts, nrow = ngenes, ncol = nsamples)
>   
>   ## ii) Generate intensity data
>   sd <- 0.3 * sqrt(4 / rchisq(100, df = 4))
>   intens <- matrix(rnorm(100 * 6, sd = sd), nrow = 100, ncol = 6)
>   rownames(intens) <- paste0("Gene", 1:100)
>   intens[1:2, 4:6] <- intens[1:2, 4:6] + 2
>   mdesign <- cbind(Grp1 = 1, Grp2vs1 = rep(c(0,1), each = 3))
> 
>   # (1) import from edgeR (RNA-seq count data)
>   # (1a) create the expression data object
>   library(edgeR)
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

>   d <- DGEList(counts)
>   d <- calcNormFactors(d)
>   d <- estimateDisp(d, rdesign)
>   
>   # (1b) obtain differential expression results 
>   fit <- glmQLFit(d, rdesign)
>   qlf <- glmQLFTest(fit)
>   res <- topTags(qlf, n = nrow(d), sort.by = "none")
> 
>   # (1c) import
>   se <- import(d, res)
> 
>   # (2) import from DESeq2 (RNA-seq count data)
>   # (2a) create the expression data object
>   library(DESeq2)
>   condition <- factor(rep(c("A", "B"), each = 2))
>   dds <- DESeqDataSetFromMatrix(counts, 
+                                 colData = DataFrame(condition = condition),
+                                 design = ~ condition)
converting counts to integer mode
> 
>   # (2b) obtain differential expression results 
>   dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
>   res <- results(dds)
> 
>   # (2c) import
>   se <- import(dds, res)
> 
>   # (3) import from voom/limma (RNA-seq count data)
>   # (3a) create the expression data object
>   library(limma)
>   keep <- filterByExpr(counts, rdesign)
>   el <- voom(counts[keep,], rdesign)
>   
>   # (3b) obtain differential expression results 
>   fit <- lmFit(el, rdesign)
>   fit <- eBayes(fit, robust = TRUE) 
Error in fitFDistRobustly(var, df1 = df, covariate = covariate, winsor.tail.p = winsor.tail.p) : 
  statmod package required but is not installed
Calls: eBayes -> .ebayes -> squeezeVar -> fitFDistRobustly
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘EnrichmentBrowser.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘EnrichmentBrowser.Rnw’ using knitr
Quitting from lines 371-373 (EnrichmentBrowser.Rnw) 
Error: processing vignette 'EnrichmentBrowser.Rnw' failed with diagnostics:
statmod package required but is not installed
--- failed re-building ‘EnrichmentBrowser.Rnw’

SUMMARY: processing the following file failed:
  ‘EnrichmentBrowser.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.