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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AssessORF.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AssessORF_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/AssessORF.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-06 22:54:05 UTC
* using option ‘--no-vignettes’
* checking for file ‘AssessORF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AssessORF’ version ‘1.30.0’
* 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 ‘AssessORF’ 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 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 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 ... NOTE
checkRd: (-1) CompareAssessmentResults.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:77-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:79-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CompareAssessmentResults.Rd:81-83: Lost braces in \itemize; meant \describe ?
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 98762 Bus error: 10           LANGUAGE=en _R_CHECK_INTERNALS2_=1 R_LIBS=/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpiq5AG3/RLIBS_177467546a328 R_ENVIRON_USER='' R_LIBS_USER='NULL' R_LIBS_SITE='NULL' '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'AssessORF-Ex.Rout' 2>&1 < 'AssessORF-Ex.R'
 ERROR
Running examples in ‘AssessORF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MapAssessmentData
> ### Title: Map Evidence to a Genome
> ### Aliases: MapAssessmentData
> 
> ### ** Examples
> 
> 
> ## Example showing the minimum number of arguments that need to be specified
> ## to map both proteomics and evolutionary conservation data:
> 
> ## Not run: 
> ##D myMapObj <- MapAssessmentData(myDBFile, central_ID = "1",
> ##D                               related_IDs = as.character(2:1001),
> ##D                               protHits_Seqs = myProtSeqs)
> ## End(Not run)
> 
> 
> ## Runnable example that uses evolutionary conservation data only:
> ## Human adenovirus 1 is the strain of interest, and the set of Adenoviridae
> ## genomes will serve as the set of genome. The cenral genome, also known as
> ## the genome of human adenovirus 1, is at identifier 1. The related genomes
> ## are at identifiers 2 - 13.
> 
> myMapObj <- MapAssessmentData(system.file("extdata",
+                                           "Adenoviridae.sqlite",
+                                           package = "AssessORF"),
+                               central_ID = "1",
+                               related_IDs = as.character(2:13),
+                               speciesName = "Human adenovirus 1",
+                               useProt = FALSE)
================================================================================
Distance from related genomes to central genome (i.e. strain's genome) measured.

Most distant related genomes selected. Beginning evolutionary conservation mapping.

====================
 *** caught bus error ***
address 0x8ad7ffffc, cause 'invalid alignment'

Traceback:
 1: FindSynteny(genomes_DBFile, tblName = tblName, identifier = c(central_ID,     validRelated_IDs[rIdx]), processors = processors, verbose = FALSE)
 2: MapAssessmentData(system.file("extdata", "Adenoviridae.sqlite",     package = "AssessORF"), central_ID = "1", related_IDs = as.character(2:13),     speciesName = "Human adenovirus 1", useProt = FALSE)
An irrecoverable exception occurred. R is aborting now ...
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/AssessORF.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AssessORF
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘AssessORF’ ...
** this is package ‘AssessORF’ version ‘1.30.0’
** 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 (AssessORF)