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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:edgeR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings edgeR_3.41.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/edgeR.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 ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.41.8’
* 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 ‘edgeR’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.5Mb
* 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘edgeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glmQLFit
> ### Title: Genewise Negative Binomial Generalized Linear Models with
> ###   Quasi-likelihood Tests
> ### Aliases: glmQLFit glmQLFit.DGEList glmQLFit.SummarizedExperiment
> ###   glmQLFit.default glmQLFTest
> 
> ### ** Examples
> 
> nlibs <- 4
> ngenes <- 1000
> dispersion.true <- 1/rchisq(ngenes, df=10)
> design <- model.matrix(~factor(c(1,1,2,2)))
> 
> # Generate count data
> y <- rnbinom(ngenes*nlibs,mu=20,size=1/dispersion.true)
> y <- matrix(y,ngenes,nlibs)
> d <- DGEList(y)
> d <- normLibSizes(d)
> 
> # Fit the NB GLMs with QL methods
> d <- estimateDisp(d, design)
> fit <- glmQLFit(d, design)
> results <- glmQLFTest(fit)
> topTags(results)
Coefficient:  factor(c(1, 1, 2, 2))2 
        logFC    logCPM         F      PValue       FDR
742  1.918395 10.116882 10.018069 0.002241407 0.7277013
853 -1.880158 10.166377  9.909632 0.002360815 0.7277013
406  1.861304 10.151516  9.441564 0.002957299 0.7277013
871 -1.825113 10.396763  8.824292 0.003992925 0.7277013
606  1.768963 10.347209  8.491539 0.004701817 0.7277013
755 -1.725141 10.432081  7.982148 0.006051921 0.7277013
344 -2.308974  9.461463  7.860685 0.006430059 0.7277013
997  1.735521 10.326748  7.823119 0.006551943 0.7277013
294  1.750603 10.658947  7.155459 0.009172803 0.7277013
420  1.558797 10.259833  7.113880 0.009368706 0.7277013
> fit <- glmQLFit(d, design, robust=TRUE)
Error in fitFDistRobustly(var, df1 = df, covariate = covariate, winsor.tail.p = winsor.tail.p) : 
  statmod package required but is not installed
Calls: glmQLFit ... glmQLFit -> glmQLFit.default -> squeezeVar -> fitFDistRobustly
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’
 ERROR
Running the tests in ‘tests/edgeR-Tests.R’ failed.
Last 13 lines of output:
   0.1385  0.1792  0.1964  0.1935  0.2026  0.2709 
  > 
  > dglm2 <- estimateDisp(dglm, design)
  > summary(dglm2$tagwise.dispersion)
     Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   0.1652  0.1740  0.1821  0.1852  0.1909  0.2259 
  > dglm2 <- estimateDisp(dglm, design, prior.df=20)
  > summary(dglm2$tagwise.dispersion)
     Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   0.1527  0.1669  0.1814  0.1858  0.1951  0.2497 
  > dglm2 <- estimateDisp(dglm, design, robust=TRUE)
  Error in fitFDistRobustly(var, df1 = df, covariate = covariate, winsor.tail.p = winsor.tail.p) : 
    statmod package required but is not installed
  Calls: estimateDisp ... estimateDisp.default -> squeezeVar -> fitFDistRobustly
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘edgeR.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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