##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MetaScope.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MetaScope_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/MetaScope.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MetaScope/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaScope’ version ‘1.10.0’
* 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 ‘MetaScope’ 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 ... NOTE
download_refseq_16S : download_from_url: no visible global function
  definition for ‘str_split’
download_refseq_16S : download_from_url: no visible global function
  definition for ‘getURL’
download_refseq_16S : download_from_url: no visible global function
  definition for ‘str_trim’
download_refseq_16S : download_from_url: no visible global function
  definition for ‘download.file’
download_refseq_16S: no visible global function definition for ‘gunzip’
Undefined global functions or variables:
  download.file getURL gunzip str_split str_trim
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MetaScope-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filter_host_bowtie
> ### Title: Use Rbowtie2 to align reads against one or more filter libraries
> ###   and subsequently remove mapped reads
> ### Aliases: filter_host_bowtie
> 
> ### ** Examples
> 
> #### Filter reads from bam file that align to any of the filter libraries
> 
> ## Assuming a bam file has already been created with align_target_bowtie()
> # Create temporary filter library
> filter_ref_temp <- tempfile()
> dir.create(filter_ref_temp)
> 
> ## Create temporary taxonomizr accession
> tmp_accession <- system.file("extdata", "example_accessions.sql", package = "MetaScope")
> 
> ## Download reference genome
> MetaScope::download_refseq("Orthoebolavirus zairense",
+                            reference = FALSE,
+                            representative = FALSE,
+                            compress = TRUE,
+                            out_dir = filter_ref_temp,
+                            caching = TRUE,
+                            accession_path = tmp_accession)
Warning in file(file, "rt") :
  URL 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt': status was 'SSL connect error'
Error in file(file, "rt") : 
  cannot open the connection to 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt'
Calls: <Anonymous> ... download_parentkingdom -> get_table -> <Anonymous> -> file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
convert_animalcules       11.051  0.685  11.737
convert_animalcules_silva  8.102  0.373   9.238
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
 OK
* 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 ‘MetaScope_vignette.Rmd’ using rmarkdown

Quitting from MetaScope_vignette.Rmd:142-155 [target_lib]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt'
---
Backtrace:
    ▆
 1. └─base::sapply(...)
 2.   └─base::lapply(X = X, FUN = FUN, ...)
 3.     └─MetaScope (local) FUN(X[[i]], ...)
 4.       └─MetaScope:::download_parentkingdom(parent_kingdom, quiet)
 5.         └─MetaScope:::get_table(parent_kingdom)
 6.           └─utils::read.table(...)
 7.             └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MetaScope_vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt'
--- failed re-building ‘MetaScope_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/MetaScope.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MetaScope
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MetaScope’ ...
** this is package ‘MetaScope’ version ‘1.10.0’
** 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 (MetaScope)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> if (requireNamespace("spelling", quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.147   0.037   0.171