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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:AlphaMissenseR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings AlphaMissenseR_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/AlphaMissenseR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlphaMissenseR/DESCRIPTION’ ... OK
* this is package ‘AlphaMissenseR’ version ‘1.3.0’
* 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 ‘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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘AlphaMissenseR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: af_predictions
> ### Title: AlphaFold Protein Structure Retrieval and Display
> ### Aliases: af_predictions af_prediction_view af_colorfunc_by_position
> 
> ### ** Examples
> 
> 
> ## af_predictions
> 
> uniprot_ids <-
+     am_data("aa_substitutions") |>
+     dplyr::filter(uniprot_id %like% "P3555%") |>
+     dplyr::distinct(uniprot_id) |>
+     pull(uniprot_id)
Warning in file(con, "r") :
  cannot open URL 'https://zenodo.org/api/records/10813168/versions/latest': HTTP status was '504 Gateway Timeout'
Error in file(con, "r") : 
  cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
Calls: pull ... withVisible -> eval -> eval -> <Anonymous> -> readLines -> file
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:
    1. ├─dplyr::filter(am_data("hg38"), uniprot_id == "P35557") at test-AlphaFold.R:89:5
    2. └─AlphaMissenseR::am_data("hg38")
    3.   └─AlphaMissenseR::am_available(record = record)
    4.     └─AlphaMissenseR:::am_available_from_internet(record, bfc)
    5.       ├─AlphaMissenseR:::am_record_json(record)
    6.       │ ├─base::withVisible(eval(mc, parent.frame()))
    7.       │ └─base::eval(mc, parent.frame())
    8.       │   └─base::eval(mc, parent.frame())
    9.       └─AlphaMissenseR (local) `<fn>`(record = record)
   10.         └─base::readLines(url, warn = FALSE)
   11.           └─base::file(con, "r")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 123 ]
  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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/AlphaMissenseR.Rcheck/00check.log’
for details.