############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/AssessORFData.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 lines 54-64 [unnamed-chunk-4] (AssessORFDataGuide.Rmd) 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.