Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-22 12:04 -0400 (Wed, 22 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4890 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4680 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4625 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
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 162/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bedbaser 1.1.3 (landing page) Andres Wokaty
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the bedbaser package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bedbaser.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: bedbaser |
Version: 1.1.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bedbaser_1.1.3.tar.gz |
StartedAt: 2025-10-21 20:25:13 -0400 (Tue, 21 Oct 2025) |
EndedAt: 2025-10-21 20:28:13 -0400 (Tue, 21 Oct 2025) |
EllapsedTime: 180.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: bedbaser.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bedbaser_1.1.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bedbaser/DESCRIPTION’ ... OK * this is package ‘bedbaser’ version ‘1.1.3’ * 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 ‘bedbaser’ 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 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 ... NOTE .get_url: no visible binding for global variable ‘access_methods’ .get_url: no visible binding for global variable ‘access_url’ .get_url: no visible binding for global variable ‘name’ .get_url: no visible binding for global variable ‘access_id’ bb_list_bedsets: no visible binding for global variable ‘bed_ids’ bb_list_bedsets: no visible binding for global variable ‘id’ bb_list_bedsets: no visible binding for global variable ‘name’ bb_list_bedsets: no visible binding for global variable ‘md5sum’ bb_list_bedsets: no visible binding for global variable ‘submission_date’ bb_list_bedsets: no visible binding for global variable ‘last_update_date’ bb_list_bedsets: no visible binding for global variable ‘description’ bb_list_bedsets: no visible binding for global variable ‘author’ Undefined global functions or variables: access_id access_methods access_url author bed_ids description id last_update_date md5sum name submission_date * 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 bb_to_granges 15.689 1.565 17.949 bb_to_grangeslist 12.786 0.648 14.365 bb_list_bedsets 0.384 0.020 5.566 bb_save 0.211 0.034 6.484 * 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: downloaded 467 KB [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-utils.R:28:5'): .get_extra_cols returns a named vector ───────── Error in `.get_extra_cols(file_path, 4, 1)`: x + y == dim(t)[2] is not TRUE Backtrace: ▆ 1. └─bedbaser:::.get_extra_cols(file_path, 4, 1) at test-utils.R:28:5 2. └─base::stopifnot(x + y == dim(t)[2]) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ] 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, 1 NOTE See ‘/Users/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck/00check.log’ for details.
bedbaser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bedbaser ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘bedbaser’ ... ** this is package ‘bedbaser’ version ‘1.1.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘tags’ from package ‘AnVIL’ in package ‘bedbaser’ ** 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 (bedbaser)
bedbaser.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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(bedbaser) > > test_check("bedbaser") trying URL 'https://api.bedbase.org/v1/files/files/7/b/7b50b054de8eeff19a3c8f6535444d24.bed.gz' Content type 'binary/octet-stream' length 24377 bytes (23 KB) ================================================== downloaded 23 KB trying URL 'https://api.bedbase.org/v1/files/files/3/0/30a8fd55a051a5c1248d1d8564513130.bed.gz' Content type 'binary/octet-stream' length 5216611 bytes (5.0 MB) ================================================== downloaded 5.0 MB Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit trying URL 'https://api.bedbase.org/v1/files/files/f/9/f9cd6fcfc408da29926679d1b6146788.bed.gz' Content type 'binary/octet-stream' length 162724 bytes (158 KB) ================================================== downloaded 158 KB trying URL 'https://api.bedbase.org/v1/files/files/0/2/0287e389049c021174dfdaf0f54d0621.bed.gz' Content type 'binary/octet-stream' length 640532 bytes (625 KB) ================================================== downloaded 625 KB Attaching package: 'BSgenome.Hsapiens.UCSC.hg38' The following object is masked from 'package:BSgenome.Hsapiens.UCSC.hg19': Hsapiens trying URL 'https://api.bedbase.org/v1/files/files/b/b/bbad85f21962bb8d972444f7f9a3a932.bed.gz' Content type 'binary/octet-stream' length 641053 bytes (626 KB) ================================================== downloaded 626 KB trying URL 'https://api.bedbase.org/v1/files/files/8/7/87a679e22c6f2b3cca3df5a71b69ef57.bed.gz' Content type 'binary/octet-stream' length 346099 bytes (337 KB) ================================================== downloaded 337 KB trying URL 'https://api.bedbase.org/v1/files/files/0/6/0692dfe199d26353af23dcbf354a6548.bed.gz' Content type 'binary/octet-stream' length 478938 bytes (467 KB) ================================================== downloaded 467 KB [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-utils.R:28:5'): .get_extra_cols returns a named vector ───────── Error in `.get_extra_cols(file_path, 4, 1)`: x + y == dim(t)[2] is not TRUE Backtrace: ▆ 1. └─bedbaser:::.get_extra_cols(file_path, 4, 1) at test-utils.R:28:5 2. └─base::stopifnot(x + y == dim(t)[2]) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ] Error: Test failures Execution halted
bedbaser.Rcheck/bedbaser-Ex.timings
name | user | system | elapsed | |
BEDbase | 1.127 | 0.059 | 1.603 | |
bb_bed_text_search | 0.195 | 0.024 | 0.754 | |
bb_beds_in_bedset | 0.174 | 0.006 | 0.418 | |
bb_example | 0.178 | 0.009 | 0.460 | |
bb_list_beds | 0.330 | 0.019 | 0.726 | |
bb_list_bedsets | 0.384 | 0.020 | 5.566 | |
bb_metadata | 0.154 | 0.008 | 0.525 | |
bb_save | 0.211 | 0.034 | 6.484 | |
bb_stats | 0.100 | 0.005 | 0.406 | |
bb_to_granges | 15.689 | 1.565 | 17.949 | |
bb_to_grangeslist | 12.786 | 0.648 | 14.365 | |
getCache-BEDbase-method | 0.158 | 0.014 | 0.330 | |
operations-BEDbase-method | 0.114 | 0.010 | 0.284 | |
schemas-BEDbase-method | 0.105 | 0.007 | 0.271 | |
setCache-BEDbase-method | 0.144 | 0.010 | 0.311 | |
tags-BEDbase-method | 0.144 | 0.007 | 0.312 | |