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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TCGAutils_1.30.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/TCGAutils.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 ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.30.2’
* 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 ‘TCGAutils’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘GenomicRanges:::.normarg_field’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
simplifyTCGA            36.354  1.304  38.215
trimColData             14.864  0.474  15.969
TCGAprimaryTumors       14.677  0.513  15.915
imputeAssay             12.358  0.335  13.263
oncoPrintTCGA           12.198  0.307  12.897
curatedTCGAData-helpers 11.662  0.467  12.747
ID-translation           2.000  0.065   5.242
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 ‘TCGAutils.Rmd’ using rmarkdown

Quitting from TCGAutils.Rmd:213-223 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.12_NCBI36/GCF_000001405.12_NCBI36_assembly_report.txt'
---
Backtrace:
     ▆
  1. ├─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = `<chr>`)
  2. └─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = `<chr>`)
  3.   ├─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = value)
  4.   └─GenomeInfoDb::`seqlevelsStyle<-`(`*tmp*`, value = value)
  5.     └─BiocGenerics::mapply(...)
  6.       ├─BiocGenerics (local) standardGeneric("mapply")
  7.       │ ├─BiocGenerics::eval(mc, env)
  8.       │ └─base::eval(mc, env)
  9.       │   └─base::eval(mc, env)
 10.       └─base::mapply(...)
 11.         └─GenomeInfoDb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]], "UCSC")
 12.           └─GenomeInfoDb:::.map_NCBI_or_RefSeq_seqlevels_to_UCSC(...)
 13.             └─GenomeInfoDb::getChromInfoFromUCSC(new_genome, map.NCBI = TRUE)
 14.               └─GenomeInfoDb:::.get_chrom_info_for_registered_UCSC_genome(...)
 15.                 ├─BiocGenerics::do.call(...)
 16.                 ├─base::do.call(...)
 17.                 └─GenomeInfoDb (local) `<fn>`(...)
 18.                   └─GenomeInfoDb::getChromInfoFromNCBI(assembly_accession, assembly.units = AssemblyUnits)
 19.                     └─GenomeInfoDb:::.get_NCBI_chrom_info_from_accession(...)
 20.                       └─GenomeInfoDb:::.get_full_NCBI_chrom_info_from_accession(...)
 21.                         └─GenomeInfoDb::fetch_assembly_report(accession, assembly_name = assembly_name)
 22.                           └─GenomeInfoDb:::.fetch_assembly_report_from_url(report_url)
 23.                             └─GenomeInfoDb:::fetch_table_from_url(...)
 24.                               ├─base::suppressWarnings(download.file(url, destfile, quiet = TRUE))
 25.                               │ └─base::withCallingHandlers(...)
 26.                               └─utils::download.file(url, destfile, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'TCGAutils.Rmd' failed with diagnostics:
cannot open URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.12_NCBI36/GCF_000001405.12_NCBI36_assembly_report.txt'
--- failed re-building ‘TCGAutils.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL TCGAutils
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘TCGAutils’ ...
** this is package ‘TCGAutils’ version ‘1.30.2’
** 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 (TCGAutils)

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(TCGAutils)
> 
> test_check("TCGAutils")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
 14.951   0.721  20.097