Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-29 11:41 -0400 (Mon, 29 Sep 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" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4580 |
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 708/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
faers 1.4.0 (landing page) Yun Peng
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the faers package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/faers.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: faers |
Version: 1.4.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:faers.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings faers_1.4.0.tar.gz |
StartedAt: 2025-09-26 10:30:54 -0000 (Fri, 26 Sep 2025) |
EndedAt: 2025-09-26 10:31:55 -0000 (Fri, 26 Sep 2025) |
EllapsedTime: 61.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: faers.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:faers.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings faers_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/faers.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 ‘faers/DESCRIPTION’ ... OK * this is package ‘faers’ version ‘1.4.0’ * 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 ‘faers’ 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 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 faers_available 1.899 0.056 6.691 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
faers.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL faers ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘faers’ ... ** this is package ‘faers’ version ‘1.4.0’ ** 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 (faers)
faers.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(faers) > > test_check("faers") Starting 2 test processes [ FAIL 0 | WARN 0 | SKIP 16 | PASS 274 ] ══ Skipped tests (16) ══════════════════════════════════════════════════════════ • On CRAN (1): 'test_meta.R:2:5' • dir.exists("~/Data/MedDRA/MedDRA_26_1_English") is not TRUE (15): 'test_counts.R:2:5', 'test_dedup.R:2:5', 'test_combine.R:49:5', 'test_combine.R:78:5', 'test_meddra.R:6:5', 'test_merge.R:57:5', 'test_signal.R:2:5', 'test_signal.R:29:5', 'test_standardize.R:2:5', 'test_methods.R:103:5', 'test_methods.R:147:5', 'test_methods.R:195:5', 'test_methods.R:218:5', 'test_methods.R:241:5', 'test_methods.R:550:5' [ FAIL 0 | WARN 0 | SKIP 16 | PASS 274 ] > > proc.time() user system elapsed 11.176 0.767 7.353
faers.Rcheck/faers-Ex.timings
name | user | system | elapsed | |
FAERS-class | 0.540 | 0.027 | 0.571 | |
FAERS-methods | 0.206 | 0.016 | 0.224 | |
faers | 0.06 | 0.00 | 0.06 | |
faers_available | 1.899 | 0.056 | 6.691 | |
faers_before_period | 0.001 | 0.000 | 0.000 | |
faers_clearcache | 0.014 | 0.000 | 0.015 | |
faers_combine | 0.105 | 0.005 | 0.111 | |
faers_counts | 0.518 | 0.015 | 0.538 | |
faers_dedup | 0.180 | 0.020 | 0.205 | |
faers_download | 0.029 | 0.000 | 0.029 | |
faers_load | 0.006 | 0.000 | 0.006 | |
faers_merge | 0.126 | 0.000 | 0.126 | |
faers_meta | 1.700 | 0.016 | 2.979 | |
faers_parse | 0.031 | 0.004 | 0.034 | |
faers_phv_signal | 0.163 | 0.000 | 0.163 | |
faers_standardize | 0.151 | 0.004 | 0.156 | |
fda_drugs | 1.106 | 0.125 | 4.280 | |
phv_signal | 3.298 | 0.152 | 3.458 | |