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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlphaMissenseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlphaMissenseR_1.5.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/AlphaMissenseR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlphaMissenseR/DESCRIPTION’ ... OK
* this is package ‘AlphaMissenseR’ version ‘1.5.4’
* 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 ‘AlphaMissenseR’ 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 whether 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 ... 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
db            7.283  0.922   2.471
AlphaFold     6.731  0.982  16.263
ClinVar       5.049  0.459   5.432
GenomicRanges 5.010  0.358   4.838
* 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:
  > 
  > test_check("AlphaMissenseR")
  * [19:30:03][info] disconnecting all registered connections
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-AlphaFold.R:13:5'): AlphaFold endpoints exist ────────────────
  httr::status_code(httr::HEAD(url)) (`actual`) not identical to 200L (`expected`).
  
    `actual`: 404
  `expected`: 200
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/AlphaMissenseR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlphaMissenseR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘AlphaMissenseR’ ...
** this is package ‘AlphaMissenseR’ version ‘1.5.4’
** 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 (AlphaMissenseR)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(AlphaMissenseR)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("AlphaMissenseR")
* [19:30:03][info] disconnecting all registered connections
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-AlphaFold.R:13:5'): AlphaFold endpoints exist ────────────────
httr::status_code(httr::HEAD(url)) (`actual`) not identical to 200L (`expected`).

  `actual`: 404
`expected`: 200

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
Error: Test failures
Execution halted