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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MouseFM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MouseFM_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/MouseFM.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MouseFM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MouseFM’ version ‘1.12.0’
* 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 ‘MouseFM’ 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 R 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 startup messages can be suppressed ... 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 ... NOTE
File ‘MouseFM/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("\n  ---------\n  \n  For example usage please run: vignette('MouseFM')\n  \n  Github Repo: https://github.com/matmu/MouseFM\n  MouseFM Backend: https://github.com/matmu/MouseFM-Backend  \n\n  Citation appreciated:\n  Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I (2021) In silico candidate variant and gene identification using inbred mouse strains. PeerJ. doi:10.7717/peerj.11017\n                        \n  ---------",     domain = NULL, appendLF = TRUE)

See section ‘Good practice’ in '?.onAttach'.
* 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 ‘MouseFM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GRanges2df
> ### Title: GenomicRanges::GRanges object to data frame
> ### Aliases: GRanges2df
> 
> ### ** Examples
> 
> geno.granges = finemap("chr1",
+     start = 5000000, end = 6000000,
+     strain1 = c("C57BL_6J"), strain2 = c("AKR_J", "A_J", "BALB_cJ"),
+     return_obj = "granges"
+ )
Query chr1:5,000,000-6,000,000
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [mousefm.genehopper.de] Resolving timed out after 10140 milliseconds
Calls: finemap ... request_fetch -> request_fetch.write_memory -> <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:
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─MouseFM::prio(...)
    5.   └─base::lapply(...)
    6.     └─MouseFM (local) FUN(X[[i]], ...)
    7.       └─MouseFM:::backend_request(q)
    8.         └─httr::GET(q)
    9.           └─httr:::request_perform(req, hu$handle$handle)
   10.             ├─httr:::request_fetch(req$output, req$url, handle)
   11.             └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   12.               └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/MouseFM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MouseFM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘MouseFM’ ...
** 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 (MouseFM)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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(MouseFM)

  ---------
  
  For example usage please run: vignette('MouseFM')
  
  Github Repo: https://github.com/matmu/MouseFM
  MouseFM Backend: https://github.com/matmu/MouseFM-Backend  

  Citation appreciated:
  Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I (2021) In silico candidate variant and gene identification using inbred mouse strains. PeerJ. doi:10.7717/peerj.11017
                        
  ---------
> 
> test_check("MouseFM")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_package.R:13:3'): Package works properly ───────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [mousefm.genehopper.de] Resolving timed out after 10128 milliseconds
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test_package.R:13:3
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─MouseFM::prio(...)
  5.   └─base::lapply(...)
  6.     └─MouseFM (local) FUN(X[[i]], ...)
  7.       └─MouseFM:::backend_request(q)
  8.         └─httr::GET(q)
  9.           └─httr:::request_perform(req, hu$handle$handle)
 10.             ├─httr:::request_fetch(req$output, req$url, handle)
 11.             └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 12.               └─curl::curl_fetch_memory(url, handle = handle)

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