Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 58/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlphaMissenseR 1.4.3 (landing page) Martin Morgan
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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
AlphaMissenseR.Rcheck/AlphaMissenseR-Ex.timings
name | user | system | elapsed | |
AlphaFold | 5.789 | 0.682 | 8.346 | |
AlphaMissense | 1.349 | 0.166 | 1.521 | |
ClinVar | 4.977 | 0.401 | 5.434 | |
GenomicRanges | 4.707 | 0.229 | 5.627 | |
Gosling | 2.146 | 0.281 | 1.669 | |
am_aa | 2.286 | 0.088 | 1.442 | |
db | 6.819 | 0.740 | 3.054 | |