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### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:AssessORF.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings AssessORF_1.21.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AssessORF.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AssessORF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AssessORF’ version ‘1.21.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... 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)
Error in SearchDB(dbFile = genomes_DBFile, tblName = tblName, identifier = central_ID,  : 
  Package 'RSQLite' must be installed.
Calls: MapAssessmentData -> SearchDB
Execution halted
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/AssessORF.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL AssessORF
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘AssessORF’ ...
** 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)