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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:OmaDB.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings OmaDB_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/OmaDB.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘OmaDB/DESCRIPTION’ ... OK
* this is package ‘OmaDB’ version ‘2.18.0’
* 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 ‘OmaDB’ 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 R 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmaDB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGenomePairs
> ### Title: Retrieves the pairwise relations among two genomes
> ### Aliases: getGenomePairs
> 
> ### ** Examples
> 
> getGenomePairs(genome_id1='YEAST',genome_id2='ASHGO')
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  : 
  arguments imply differing number of rows: 1, 0
Calls: getGenomePairs ... as.data.frame -> as.data.frame.list -> do.call -> <Anonymous>
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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘OmaDB.Rmd’ using ‘UTF-8’... failed
  ‘exploring_hogs.Rmd’ using ‘UTF-8’... failed
  ‘sequence_mapping.Rmd’ using ‘UTF-8’... failed
  ‘tree_visualisation.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘OmaDB.Rmd’
  ...
Loading required package: plyr


> xref = load("../data/xref.rda")
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '../data/xref.rda', probable reason 'No such file or directory'

  When sourcing ‘OmaDB.R’:
Error: cannot open the connection
Execution halted
when running code in ‘exploring_hogs.Rmd’
  ...
Loading required package: plyr


> load("../data/hog.rda")
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '../data/hog.rda', probable reason 'No such file or directory'

  When sourcing ‘exploring_hogs.R’:
Error: cannot open the connection
Execution halted
when running code in ‘sequence_mapping.Rmd’
  ...
Loading required package: plyr


> load("../data/sequence_map.rda")
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '../data/sequence_map.rda', probable reason 'No such file or directory'

  When sourcing ‘sequence_mapping.R’:
Error: cannot open the connection
Execution halted
when running code in ‘tree_visualisation.Rmd’
  ...
Loading required package: plyr


> load("../data/taxonomy.rda")
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '../data/taxonomy.rda', probable reason 'No such file or directory'

  When sourcing ‘tree_visualisation.R’:
Error: cannot open the connection
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/OmaDB.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL OmaDB
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘OmaDB’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (OmaDB)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> 
> test_that("Testing the URL validity", {
+   expect_equal(httr::status_code(httr::GET("https://omabrowser.org/api")), 200 ) #checking that the server is live and accesible
+ 
+ })
Test passed 😀
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  1.987   0.071   4.114