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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AssessORFData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AssessORFData_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/AssessORFData.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘AssessORFData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AssessORFData’ version ‘1.24.0’
* 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 ‘AssessORFData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 145.8Mb
  sub-directories of 1Mb or more:
    data     124.9Mb
    extdata   20.6Mb
* 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘AssessORFData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SaveGenomeToPath
> ### Title: Save a Strain's Genome to a Directory
> ### Aliases: SaveGenomeToPath
> 
> ### ** Examples
> 
> 
> tmpFile <- paste0(tempfile(), ".fasta")
> SaveGenomeToPath("MGAS5005", tmpFile)
Error in DB2Seqs(filePath, genomesFile, identifier = as.character(strainIdx),  : 
  Package 'RSQLite' must be installed.
Calls: SaveGenomeToPath -> DB2Seqs
Execution halted
* 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 ‘AssessORFDataGuide.Rmd’ using rmarkdown

Quitting from AssessORFDataGuide.Rmd:53-64 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `DB2Seqs()`:
! Package 'RSQLite' must be installed.
---
Backtrace:
    x
 1. \-AssessORFData::SaveGenomeToPath("MGAS5005", tmpFile)
 2.   \-DECIPHER::DB2Seqs(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'AssessORFDataGuide.Rmd' failed with diagnostics:
Package 'RSQLite' must be installed.
--- failed re-building ‘AssessORFDataGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/AssessORFData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL AssessORFData
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘AssessORFData’ ...
** using staged installation
** R
** data
** 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 (AssessORFData)