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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpliceWiz_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   4.9Mb
* 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 loading without being on the library search path ... 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 04:18:44 Converting FASTA to local TwoBitFile...done
Jun 20 04:18:45 Connecting to genome TwoBitFile...done
Jun 20 04:18:45 Making local copy of GTF file...done
> buildRef(
+     reference_path = example_ref
+ )
Jun 20 04:18:45 Reference generated without non-polyA reference
Jun 20 04:18:45 Reference generated without Mappability reference
Jun 20 04:18:45 Reference generated without Blacklist exclusion
Jun 20 04:18:45 Connecting to genome TwoBitFile...done
Jun 20 04:18:45 Reading source GTF file...done
Jun 20 04:18:46 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Jun 20 04:18:47 Gene ontology not prepared for this reference
Jun 20 04:18:50 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Jun 20 04:18:54 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 04:19:01 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
done
Jun 20 04:19:04 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 04:19:05 Splice Annotations Filtered
Jun 20 04:19:06 Translating Alternate Splice Peptides...done
Jun 20 04:19:06 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 04:19:07 SpliceWiz reference already exists in given directory
NULL
> 
> # Get the path to the Non-PolyA BED file for hg19
> 
> getNonPolyARef("hg19")
[1] "/home/biocbuild/bbs-3.19-bioc/R/site-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 04:19:10 Reference generated without non-polyA reference
Jun 20 04:19:10 Reference generated without Mappability reference
Jun 20 04:19:10 Reference generated without Blacklist exclusion
Jun 20 04:19:10 Converting FASTA to local TwoBitFile...done
Jun 20 04:19:12 Connecting to genome TwoBitFile...done
Jun 20 04:19:12 Making local copy of GTF file...done
Jun 20 04:19:12 Reading source GTF file...done
Jun 20 04:19:12 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Jun 20 04:19:15 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘SW_Cookbook.Rmd’ using rmarkdown
--- finished re-building ‘SW_Cookbook.Rmd’

--- re-building ‘SW_QuickStart.Rmd’ using rmarkdown

Quitting from lines 340-347 [unnamed-chunk-16] (SW_QuickStart.Rmd)
Error: processing vignette 'SW_QuickStart.Rmd' failed with diagnostics:
file is not a database
--- failed re-building ‘SW_QuickStart.Rmd’

SUMMARY: processing the following file failed:
  ‘SW_QuickStart.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.