##############################################################################
##############################################################################
###
### Running command:
###
###   /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/library --timings ASpli_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ASpli.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘2.9.0’
* 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 ... 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
Killed
* 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
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ASpli.Rnw’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘ASpli.Rnw’
  ...

> mBAMs <- data.frame(bam = sub("_[012]", "", targets$bam[c(1, 
+     4)]), condition = c("control", "treatment"))

> gbcounts <- gbCounts(features = features, targets = targets, 
+     minReadLength = 100, maxISize = 50000)
Summarizing Sample1
Killed

... incomplete output.  Crash?

* 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 objects are masked from ‘package:base’:

    I, expand.grid, unname

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
Killed

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

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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ASpli
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘ASpli’ ...
** 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 (ASpli)