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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:crupR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings crupR_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/crupR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘crupR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crupR’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘crupR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
normalize    105.603 18.860 125.193
getEnhancers  10.334  1.504  11.842
getDynamics   10.292  0.414  10.708
* 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:
   19.               └─GenomeInfoDb::getChromInfoFromUCSC(genome, map.NCBI = TRUE)
   20.                 └─GenomeInfoDb:::.get_chrom_info_for_registered_UCSC_genome(...)
   21.                   ├─BiocGenerics::do.call(...)
   22.                   ├─base::do.call(...)
   23.                   └─GenomeInfoDb (local) `<fn>`(`<df[,4]>`, assembly_accession = "GCF_000001635.26")
   24.                     └─GenomeInfoDb::getChromInfoFromNCBI(assembly_accession, assembly.units = AssemblyUnits)
   25.                       └─GenomeInfoDb:::.get_NCBI_chrom_info_from_accession(...)
   26.                         └─GenomeInfoDb:::.get_full_NCBI_chrom_info_from_accession(...)
   27.                           └─GenomeInfoDb::fetch_assembly_report(accession, assembly_name = assembly_name)
   28.                             └─GenomeInfoDb:::.form_assembly_report_url(...)
   29.                               └─GenomeInfoDb::find_NCBI_assembly_ftp_dir(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 40 ]
  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
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/crupR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL crupR
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘crupR’ ...
** this is package ‘crupR’ version ‘1.3.0’
** using staged installation
** R
** 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 (crupR)

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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(crupR)
> #setwd("/project/wig/persia/CRUP_package/CRUP/tests/")
> 
> test_check("crupR")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 40 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_normalization.R:50:3'): the error messages of normalize() work ──
`crupR::normalize(...)` threw an error with unexpected message.
Expected match: "Sequencing parameter is not valid.\n Choose one of:paired,single"
Actual message: "cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/'"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_normalization.R:50:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─crupR::normalize(...)
  7.   ├─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = GenomeInfoDb::seqlevelsStyle(si)[1])
  8.   └─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = GenomeInfoDb::seqlevelsStyle(si)[1])
  9.     ├─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = value)
 10.     └─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = value)
 11.       └─BiocGenerics::mapply(...)
 12.         ├─BiocGenerics (local) standardGeneric("mapply")
 13.         │ ├─BiocGenerics::eval(mc, env)
 14.         │ └─base::eval(mc, env)
 15.         │   └─base::eval(mc, env)
 16.         └─base::mapply(...)
 17.           └─GenomeInfoDb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]], "NCBI")
 18.             └─GenomeInfoDb:::.map_UCSC_seqlevels_to_NCBI_or_RefSeq(...)
 19.               └─GenomeInfoDb::getChromInfoFromUCSC(genome, map.NCBI = TRUE)
 20.                 └─GenomeInfoDb:::.get_chrom_info_for_registered_UCSC_genome(...)
 21.                   ├─BiocGenerics::do.call(...)
 22.                   ├─base::do.call(...)
 23.                   └─GenomeInfoDb (local) `<fn>`(`<df[,4]>`, assembly_accession = "GCF_000001635.26")
 24.                     └─GenomeInfoDb::getChromInfoFromNCBI(assembly_accession, assembly.units = AssemblyUnits)
 25.                       └─GenomeInfoDb:::.get_NCBI_chrom_info_from_accession(...)
 26.                         └─GenomeInfoDb:::.get_full_NCBI_chrom_info_from_accession(...)
 27.                           └─GenomeInfoDb::fetch_assembly_report(accession, assembly_name = assembly_name)
 28.                             └─GenomeInfoDb:::.form_assembly_report_url(...)
 29.                               └─GenomeInfoDb::find_NCBI_assembly_ftp_dir(...)

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 40 ]
Error: Test failures
Execution halted