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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ASpli_2.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ASpli.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘2.10.0’
* 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 ‘ASpli’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
See ‘/home/biocbuild/bbs-3.17-bioc/meat/ASpli.Rcheck/00install.out’ for details.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ASpli-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ASpli-package
> ### Title: Analysis of Alternative Splicing Using RNAseq
> ### Aliases: ASpli-package ASpli
> ### Keywords: RNA-seq alternative splicing analysis using bin coverage and
> ###   junctions
> 
> ### ** Examples
>  
> library(GenomicFeatures)
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
> gtfFileName <- aspliExampleGTF()
> genomeTxDb <- makeTxDbFromGFF( gtfFileName )
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> features <- binGenome( genomeTxDb )
* Number of extracted Genes = 10
* Number of extracted Exon Bins = 38
* Number of extracted intron bins = 34
* Number of extracted trascripts = 25
* Number of extracted junctions = 23
* Number of AS bins (not include external) = 17
* Number of AS bins (include external) = 17
* Classified as: 
	ES bins = 1	(6%)
	IR bins = 3	(18%)
	Alt5'ss bins = 2	(12%)
	Alt3'ss bins = 2	(12%)
	Multiple AS bins = 9	(53%)
	classified as:
			ES bins = 1	(11%)
			IR bins = 4	(44%)
			Alt5'ss bins = 2	(22%)
			Alt3'ss bins = 1	(11%)

Correcting Io ends, this might take a while...
Genome binning completed
> BAMFiles <- aspliExampleBamList()
> targets <- data.frame( 
+   row.names = paste0('Sample',c(1:12)),
+   bam = BAMFiles,
+   f1 = c( 'A','A','A','A','A','A',
+           'B','B','B','B','B','B'),
+   f2 = c( 'C','C','C','D','D','D',
+           'C','C','C','D','D','D'),
+   stringsAsFactors = FALSE)
>   getConditions(targets)
[1] "A_C" "A_D" "B_C" "B_D"
>   mBAMs <- data.frame(bam      = sub("_[02]","",targets$bam[c(1,4,7,10)]),
+                       condition= c("A_C","A_D","B_C","B_D"))
> 
> gbcounts  <- gbCounts( features = features, 
+                            targets = targets, 
+                            minReadLength = 100, maxISize = 50000,
+                            libType="SE", 
+                            strandMode=0)
Summarizing Sample1
ETA: 2 min
Summarizing Sample2
ETA: 2 min
Summarizing Sample3
ETA: 1 min
Summarizing Sample4
ETA: 1 min
Summarizing Sample5
ETA: 1 min
Summarizing Sample6
ETA: 1 min
Summarizing Sample7
ETA: 1 min
Summarizing Sample8
ETA: 1 min
Summarizing Sample9
ETA: 0 min
Summarizing Sample10
ETA: 0 min
Summarizing Sample11
ETA: 0 min
Summarizing Sample12
ETA: 0 min
> asd   <- jCounts(counts = gbcounts, 
+                      features = features, 
+                      minReadLength = 100,
+                      libType="SE", 
+                      strandMode=0)
Junctions PJU completed
Junctions PIR completed
Junctions IR PIR completed
Junctions AltSS PSI completed
Junctions ES PSI completed
>                      
>    
> gb      <- gbDUreport(counts=gbcounts,
+ contrast = c( 1, -1, -1, 1 ) )
Filtering genes:
  Filtering by reads.
  Filtering using A_C,A_D,B_C,B_D conditions
  Filtering any condition with mean minimum value 10
  Filtering by read density.
  Filtering using A_C,A_D,B_C,B_D conditions
  Filtering any condition with mean minimum value 0.05
Filtering genes done
Genes differential expression:
  Contrast:1A_C  -1A_D  -1B_C  1B_D  
  Running GLM LRT
Error in fitFDistRobustly(var, df1 = df, covariate = covariate, winsor.tail.p = winsor.tail.p) : 
  statmod package required but is not installed
Calls: gbDUreport ... 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 ...
  ‘ASpli.Rnw’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘ASpli.Rnw’
  ...
  Filtering using control,treatment conditions
  Filtering any condition with mean minimum value 0.05
Filtering genes done
Genes differential expression:
  Contrast:-1control  1treatment  
  Running GLM LRT

  When sourcing 'ASpli.R':
Error: statmod package required but is not installed
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘ASpli.Rnw’ using Sweave
Loading required package: parallel
Loading required package: edgeR
Loading required package: limma
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object is masked from ‘package:limma’:

    plotMA

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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
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

Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
* Number of extracted Genes = 10
* Number of extracted Exon Bins = 38
* Number of extracted intron bins = 34
* Number of extracted trascripts = 25
* Number of extracted junctions = 23
* Number of AS bins (not include external) = 17
* Number of AS bins (include external) = 17
* Classified as: 
	ES bins = 1	(6%)
	IR bins = 3	(18%)
	Alt5'ss bins = 2	(12%)
	Alt3'ss bins = 2	(12%)
	Multiple AS bins = 9	(53%)
	classified as:
			ES bins = 1	(11%)
			IR bins = 4	(44%)
			Alt5'ss bins = 2	(22%)
			Alt3'ss bins = 1	(11%)

Correcting Io ends, this might take a while...
Genome binning completed
Summarizing Sample1
ETA: 1 min
Summarizing Sample2
ETA: 1 min
Summarizing Sample3
ETA: 0 min
Summarizing Sample4
ETA: 0 min
Summarizing Sample5
ETA: 0 min
Summarizing Sample6
ETA: 0 min
Junctions PJU completed
Junctions PIR completed
Junctions IR PIR completed
Junctions AltSS PSI completed
Junctions ES PSI completed
Filtering genes:
  Filtering by reads.
  Filtering using control,treatment conditions
  Filtering any condition with mean minimum value 10
  Filtering by read density.
  Filtering using control,treatment conditions
  Filtering any condition with mean minimum value 0.05
Filtering genes done
Genes differential expression:
  Contrast:-1control  1treatment  
  Running GLM LRT

Error: processing vignette 'ASpli.Rnw' failed with diagnostics:
 chunk 5 (label = quickStart3) 
Error in fitFDistRobustly(var, df1 = df, covariate = covariate, winsor.tail.p = winsor.tail.p) : 
  statmod package required but is not installed

--- failed re-building 'ASpli.Rnw'

SUMMARY: processing the following file failed:
  'ASpli.Rnw'

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ASpli.Rcheck/00check.log’
for details.