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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.6.0’
* 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 ‘SpliceWiz’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether 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 shell scripts ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SpliceWiz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Build-Reference-methods
> ### Title: Builds reference files used by SpliceWiz
> ### Aliases: Build-Reference-methods getResources buildRef buildFullRef
> ###   getNonPolyARef getAvailableGO
> 
> ### ** Examples
> 
> # Quick runnable example: generate a reference using SpliceWiz's example genome
> 
> example_ref <- file.path(tempdir(), "Reference")
> getResources(
+     reference_path = example_ref,
+     fasta = chrZ_genome(),
+     gtf = chrZ_gtf()
+ )
Jun 20 12:23:29 Converting FASTA to local TwoBitFile...done
Jun 20 12:23:30 Connecting to genome TwoBitFile...done
Jun 20 12:23:30 Making local copy of GTF file...done
> buildRef(
+     reference_path = example_ref
+ )
Jun 20 12:23:30 Reference generated without non-polyA reference
Jun 20 12:23:30 Reference generated without Mappability reference
Jun 20 12:23:30 Reference generated without Blacklist exclusion
Jun 20 12:23:30 Connecting to genome TwoBitFile...done
Jun 20 12:23:30 Reading source GTF file...done
Jun 20 12:23:31 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Jun 20 12:23:33 Gene ontology not prepared for this reference
Jun 20 12:23:36 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Jun 20 12:23:43 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Jun 20 12:23:55 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
done
Jun 20 12:23:58 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Jun 20 12:24:00 Splice Annotations Filtered
Jun 20 12:24:01 Translating Alternate Splice Peptides...done
Jun 20 12:24:02 Splice Annotations finished

Reference build finished
> 
> # NB: the above is equivalent to:
> 
> example_ref <- file.path(tempdir(), "Reference")
> buildRef(
+     reference_path = example_ref,
+     fasta = chrZ_genome(),
+     gtf = chrZ_gtf()
+ )
Jun 20 12:24:03 SpliceWiz reference already exists in given directory
NULL
> 
> # Get the path to the Non-PolyA BED file for hg19
> 
> getNonPolyARef("hg19")
[1] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/SpliceWiz/extra-input-files/Human_hg19_nonPolyA_ROI.bed"
> 
> # View available species for AnnotationHub's Ensembl/orgDB-based GO resources
> 
> availSpecies <- getAvailableGO()
> 
> # Build example reference with `Homo sapiens` Ens/orgDB gene ontology
> 
> ont_ref <- file.path(tempdir(), "Reference_withGO")
> buildRef(
+     reference_path = ont_ref,
+     fasta = chrZ_genome(),
+     gtf = chrZ_gtf(),
+     ontologySpecies = "Homo sapiens"
+ )
Jun 20 12:24:09 Reference generated without non-polyA reference
Jun 20 12:24:09 Reference generated without Mappability reference
Jun 20 12:24:09 Reference generated without Blacklist exclusion
Jun 20 12:24:09 Converting FASTA to local TwoBitFile...done
Jun 20 12:24:11 Connecting to genome TwoBitFile...done
Jun 20 12:24:11 Making local copy of GTF file...done
Jun 20 12:24:11 Reading source GTF file...done
Jun 20 12:24:12 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Jun 20 12:24:19 Retrieving gene GO-term pairings
Warning: Couldn't set synchronous mode: file is not a database
Use `synchronous` = NULL to turn off this warning.
Error: file is not a database
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.