##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:UCSCRepeatMasker.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings UCSCRepeatMasker_3.17.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-annotation/meat/UCSCRepeatMasker.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘UCSCRepeatMasker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘UCSCRepeatMasker’ version ‘3.17.3’
* 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 ‘UCSCRepeatMasker’ 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 ... 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
* 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 ‘UCSCRepeatMasker.Rmd’ using rmarkdown

Quitting from UCSCRepeatMasker.Rmd:74-77 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: AH99003
  title: UCSC RepeatMasker annotations (Sep2021) for Human (hg38)
  reason: require("GenomicRanges") failed: use BiocManager::install() to install package?
---
Backtrace:
     ▆
  1. ├─ah[["AH99003"]]
  2. └─ah[["AH99003"]]
  3.   └─AnnotationHub (local) .local(x, i, j = j, ...)
  4.     └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  5.       └─base::tryCatch(...)
  6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8.             └─value[[3L]](cond)
  9.               └─base::tryCatch(...)
 10.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                     └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'UCSCRepeatMasker.Rmd' failed with diagnostics:
failed to load resource
  name: AH99003
  title: UCSC RepeatMasker annotations (Sep2021) for Human (hg38)
  reason: require("GenomicRanges") failed: use BiocManager::install() to install package?
--- failed re-building ‘UCSCRepeatMasker.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.21-data-annotation/meat/UCSCRepeatMasker.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL UCSCRepeatMasker
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘UCSCRepeatMasker’ ...
** this is package ‘UCSCRepeatMasker’ version ‘3.17.3’
** 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 (UCSCRepeatMasker)