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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:AlphaMissenseR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings AlphaMissenseR_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/AlphaMissenseR.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 ‘AlphaMissenseR/DESCRIPTION’ ... OK
* this is package ‘AlphaMissenseR’ version ‘1.6.1’
* 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': 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’
 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 ‘alphafold.Rmd’ using rmarkdown

Quitting from alphafold.Rmd:50-52 [am_available]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
---
Backtrace:
    ▆
 1. └─AlphaMissenseR::am_available()
 2.   └─AlphaMissenseR:::am_available_from_internet(record, bfc)
 3.     ├─AlphaMissenseR:::am_record_is_latest(record)
 4.     │ ├─base::withVisible(eval(mc, parent.frame()))
 5.     │ └─base::eval(mc, parent.frame())
 6.     │   └─base::eval(mc, parent.frame())
 7.     └─AlphaMissenseR (local) `<fn>`(record = record)
 8.       └─base::readLines(latest_version_url, warn = FALSE)
 9.         └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'alphafold.Rmd' failed with diagnostics:
cannot open the connection to 'https://zenodo.org/api/records/10813168/versions/latest'
--- failed re-building ‘alphafold.Rmd’

--- re-building ‘benchmarking.Rmd’ using rmarkdown
--- finished re-building ‘benchmarking.Rmd’

--- re-building ‘clinvar.Rmd’ using rmarkdown
--- finished re-building ‘clinvar.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘issues.Rmd’ using rmarkdown
--- finished re-building ‘issues.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/AlphaMissenseR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL AlphaMissenseR
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘AlphaMissenseR’ ...
** this is package ‘AlphaMissenseR’ version ‘1.6.1’
** 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 4.5.2 (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.

> # 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 objects are masked from 'package:stats':

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> test_check("AlphaMissenseR")
* [21:04:33][info] disconnecting all registered connections
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 128 ]
> 
> proc.time()
   user  system elapsed 
 22.362   2.482  55.438