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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ASpli_2.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ASpli.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘2.17.0’
* 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: program compiled against libxml 212 using older 211
  Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
See ‘/home/biocbuild/bbs-3.21-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 code 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
Namespace in Imports field not imported from: 'txdbmaker'
  All declared Imports should be used.
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DUreport.Rd: edgeR
  DUreport.norm.Rd: edgeR
  DUreport.offset.Rd: edgeR
  DUreportBinSplice-method.Rd: edgeR
  gbDUreport-method.Rd: edgeR
  jDUreport.Rd: edgeR
  junctionDUreport.Rd: edgeR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: splicingReport
> ### Title: Splicing report
> ### Aliases: splicingReport
> 
> ### ** Examples
> 
> 
> # Create a transcript DB from gff/gtf annotation file.
> # Warnings in this examples can be ignored. 
> library(GenomicFeatures)
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
> genomeTxDb <- txdbmaker::makeTxDbFromGFF( system.file('extdata','genes.mini.gtf', 
+                                  package="ASpli") )
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
OK
>   
> # Create an ASpliFeatures object from TxDb
> 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
>   
> # Define bam files, sample names and experimental factors for targets.
> bamFileNames <- c( "A_C_0.bam", "A_C_1.bam", "A_C_2.bam", 
+                      "A_D_0.bam", "A_D_1.bam", "A_D_2.bam" )
> 
> targets <- data.frame( 
+                row.names = paste0('Sample_',c(1:6)),
+                bam = system.file( 'extdata', bamFileNames, package="ASpli" ),
+                factor1 = c( 'C','C','C','D','D','D'),
+                subject = c(0, 1, 2, 0, 1, 2))
>   
> # Read counts from bam files
> gbcounts  <- gbCounts( features = features, 
+                            targets = targets, 
+                            minReadLength = 100, maxISize = 50000,
+                            libType="SE", 
+                            strandMode=0)
Summarizing Sample_1
ETA: 2 min
Summarizing Sample_2
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
ASpli-package           165.738  0.523 166.667
exportIntegratedSignals  86.570  0.038  86.849
integrateSignals         85.816  0.064  87.598
exportSplicingReports    85.498  0.044  85.953
jDUreport                83.158  0.004  85.800
jCounts-methods          82.270  0.008  82.384
gbDUreport-method        74.573  0.011  76.151
gbCounts                 73.278  0.016  75.446
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ...