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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 58/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaMissenseR 1.4.3  (landing page)
Martin Morgan
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/AlphaMissenseR
git_branch: RELEASE_3_21
git_last_commit: 25fd9ae
git_last_commit_date: 2025-10-11 18:12:16 -0400 (Sat, 11 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.6 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for AlphaMissenseR on kjohnson1

To the developers/maintainers of the AlphaMissenseR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AlphaMissenseR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: AlphaMissenseR
Version: 1.4.3
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_1.4.3.tar.gz
StartedAt: 2025-10-14 12:36:35 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 12:38:41 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 126.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: AlphaMissenseR.Rcheck
Warnings: NA

Command output

##############################################################################
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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_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/AlphaMissenseR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlphaMissenseR/DESCRIPTION’ ... OK
* this is package ‘AlphaMissenseR’ version ‘1.4.3’
* 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            6.819  0.740   3.054
AlphaFold     5.789  0.682   8.346
ClinVar       4.977  0.401   5.434
GenomicRanges 4.707  0.229   5.627
* 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")
  * [12:38:25][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-3.21-bioc/meat/AlphaMissenseR.Rcheck/00check.log’
for details.


Installation output

AlphaMissenseR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlphaMissenseR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘AlphaMissenseR’ ...
** this is package ‘AlphaMissenseR’ version ‘1.4.3’
** 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)

Tests output

AlphaMissenseR.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
* [12:38:25][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

Example timings

AlphaMissenseR.Rcheck/AlphaMissenseR-Ex.timings

nameusersystemelapsed
AlphaFold5.7890.6828.346
AlphaMissense1.3490.1661.521
ClinVar4.9770.4015.434
GenomicRanges4.7070.2295.627
Gosling2.1460.2811.669
am_aa2.2860.0881.442
db6.8190.7403.054