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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:megadepth.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings megadepth_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/megadepth.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 ‘megadepth/DESCRIPTION’ ... OK
* this is package ‘megadepth’ version ‘1.20.0’
* 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 ‘megadepth’ 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 ... ERROR
Running examples in ‘megadepth-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_bigwig
> ### Title: Convert a BAM file to a BigWig
> ### Aliases: bam_to_bigwig
> 
> ### ** Examples
> 
> 
> ## Install the latest version if necessary
> install_megadepth(force = TRUE)
The latest megadepth version is 1.2.0
Warning in utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb") :
  downloaded length 0 != reported length 55124
Warning in utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb") :
  cannot open URL 'https://github.com/ChristopherWilks/megadepth/releases/download/1.2.0/megadepth': HTTP status was '502 Bad Gateway'
Error in utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb") : 
  cannot open URL 'https://github.com/ChristopherWilks/megadepth/releases/download/1.2.0/megadepth'
Calls: install_megadepth -> <Anonymous>
Execution halted
* 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:
  > library(testthat)
  > library(megadepth)
  > 
  > ## Install the latest version if necessary
  > install_megadepth(force = TRUE)
  The latest megadepth version is 1.2.0
  Error in utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb") : 
    cannot open URL 'https://github.com/ChristopherWilks/megadepth/releases/download/1.2.0/megadepth'
  Calls: install_megadepth -> <Anonymous>
  In addition: Warning messages:
  1: In utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb") :
    downloaded length 0 != reported length 55124
  2: In utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb") :
    cannot open URL 'https://github.com/ChristopherWilks/megadepth/releases/download/1.2.0/megadepth': HTTP status was '502 Bad Gateway'
  Execution halted
* 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 ‘megadepth.Rmd’ using rmarkdown

Quitting from megadepth.Rmd:127-130 [install_software]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `utils::download.file()`:
! cannot open URL 'https://github.com/ChristopherWilks/megadepth/releases/download/1.2.0/megadepth'
---
Backtrace:
    ▆
 1. └─megadepth::install_megadepth(force = TRUE)
 2.   └─utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'megadepth.Rmd' failed with diagnostics:
cannot open URL 'https://github.com/ChristopherWilks/megadepth/releases/download/1.2.0/megadepth'
--- failed re-building ‘megadepth.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/megadepth.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL megadepth
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘megadepth’ ...
** this is package ‘megadepth’ version ‘1.20.0’
** 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 (megadepth)

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(megadepth)
> 
> ## Install the latest version if necessary
> install_megadepth(force = TRUE)
The latest megadepth version is 1.2.0
Error in utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb") : 
  cannot open URL 'https://github.com/ChristopherWilks/megadepth/releases/download/1.2.0/megadepth'
Calls: install_megadepth -> <Anonymous>
In addition: Warning messages:
1: In utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb") :
  downloaded length 0 != reported length 55124
2: In utils::download.file(url, destfile = exec, quiet = TRUE, mode = "wb") :
  cannot open URL 'https://github.com/ChristopherWilks/megadepth/releases/download/1.2.0/megadepth': HTTP status was '502 Bad Gateway'
Execution halted