##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BSgenomeForge.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BSgenomeForge_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BSgenomeForge.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘BSgenomeForge/DESCRIPTION’ ... OK
* this is package ‘BSgenomeForge’ version ‘1.10.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'BiocGenerics', 'IRanges', 'Seqinfo', 'GenomeInfoDb', 'Biostrings',
  'BSgenome'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘BSgenomeForge’ 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/extdata/seeds/BSgenome.Creinhardtii.JGI.v5.6-tools/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
AdvancedBSgenomeForge            5.236  0.078   5.322
downloadGenomicSequencesFromUCSC 0.324  0.079   9.035
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
            and unassembled molecules are specified ──
  Error in `download.file(url, destfile, method, quiet = TRUE)`: cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/782/755/'
  Backtrace:
      ▆
   1. └─GenomeInfoDb::getChromInfoFromNCBI("GCA_025782755.1") at test-get_circ_seqs_from_NCBI.R:94:5
   2.   └─GenomeInfoDb:::.get_NCBI_chrom_info_from_accession(...)
   3.     └─GenomeInfoDb:::.get_full_NCBI_chrom_info_from_accession(...)
   4.       └─GenomeInfoDb::fetch_assembly_report(accession, assembly_name = assembly_name)
   5.         └─GenomeInfoDb:::.form_assembly_report_url(...)
   6.           └─GenomeInfoDb::find_NCBI_assembly_ftp_dir(...)
  
  [ FAIL 2 | WARN 1 | SKIP 2 | PASS 36 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BSgenomeForge.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BSgenomeForge’ ...
** this is package ‘BSgenomeForge’ version ‘1.10.2’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘forgeBSgenomeDataPkg’ in package ‘BSgenomeForge’
Creating a new generic function for ‘forgeMaskedBSgenomeDataPkg’ in package ‘BSgenomeForge’
** 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 (BSgenomeForge)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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.

> library(testthat)
> library(BSgenomeForge)
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: Seqinfo
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'BSgenomeForge'

The following objects are masked from 'package:BSgenome':

    forgeBSgenomeDataPkg, forgeMaskedBSgenomeDataPkg, forgeMasksFiles,
    forgeSeqFiles, forgeSeqlengthsRdaFile, forgeSeqlengthsRdsFile

> 
> test_check("BSgenomeForge")
Creating package in /tmp/Rtmp6i6bs0/BSgenome.Tvirus1.NCBI.ViralProj15247 
Creating package in /tmp/Rtmp6i6bs0/BSgenome.Evirus.UCSC.eboVir3 
Saving _problems/test-get_circ_seqs_from_NCBI-70.R
Saving _problems/test-get_circ_seqs_from_NCBI-94.R
[ FAIL 2 | WARN 1 | SKIP 2 | PASS 36 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-utils.R:1:1', 'test-utils.R:5:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-get_circ_seqs_from_NCBI.R:70:5'): .get_circ_seqs_from_NCBI() works for an unregistered assembly
          with assembled molecules and NO circular sequences ──
Error in `download.file(url, destfile, quiet = TRUE)`: cannot open URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/692/155/GCA_003692155.1_ASM369215v1/GCA_003692155.1_ASM369215v1_assembly_report.txt'
Backtrace:
    ▆
 1. └─GenomeInfoDb::getChromInfoFromNCBI("GCA_003692155.1") at test-get_circ_seqs_from_NCBI.R:70:5
 2.   └─GenomeInfoDb:::.get_NCBI_chrom_info_from_accession(...)
 3.     └─GenomeInfoDb:::.get_full_NCBI_chrom_info_from_accession(...)
 4.       └─GenomeInfoDb::fetch_assembly_report(accession, assembly_name = assembly_name)
 5.         └─GenomeInfoDb:::.fetch_assembly_report_from_url(report_url)
 6.           └─GenomeInfoDb:::fetch_table_from_url(...)
 7.             ├─base::suppressWarnings(download.file(url, destfile, quiet = TRUE))
 8.             │ └─base::withCallingHandlers(...)
 9.             └─utils::download.file(url, destfile, quiet = TRUE)
── Error ('test-get_circ_seqs_from_NCBI.R:94:5'): .get_circ_seqs_from_NCBI() throws an error when both assembled
          and unassembled molecules are specified ──
Error in `download.file(url, destfile, method, quiet = TRUE)`: cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/782/755/'
Backtrace:
    ▆
 1. └─GenomeInfoDb::getChromInfoFromNCBI("GCA_025782755.1") at test-get_circ_seqs_from_NCBI.R:94:5
 2.   └─GenomeInfoDb:::.get_NCBI_chrom_info_from_accession(...)
 3.     └─GenomeInfoDb:::.get_full_NCBI_chrom_info_from_accession(...)
 4.       └─GenomeInfoDb::fetch_assembly_report(accession, assembly_name = assembly_name)
 5.         └─GenomeInfoDb:::.form_assembly_report_url(...)
 6.           └─GenomeInfoDb::find_NCBI_assembly_ftp_dir(...)

[ FAIL 2 | WARN 1 | SKIP 2 | PASS 36 ]
Error:
! Test failures.
Execution halted