Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 159/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bedbaser 1.1.2 (landing page) Andres Wokaty
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: bedbaser |
Version: 1.1.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings bedbaser_1.1.2.tar.gz |
StartedAt: 2025-08-01 04:25:56 -0000 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 04:31:47 -0000 (Fri, 01 Aug 2025) |
EllapsedTime: 350.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: bedbaser.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings bedbaser_1.1.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bedbaser/DESCRIPTION’ ... OK * this is package ‘bedbaser’ version ‘1.1.2’ * 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 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 ... 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 17.441 0.584 28.880 bb_to_grangeslist 14.617 0.510 34.940 bb_list_bedsets 0.453 0.008 8.091 bb_save 0.269 0.067 11.422 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck/00check.log’ for details.
bedbaser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL bedbaser ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘bedbaser’ ... ** this is package ‘bedbaser’ version ‘1.1.2’ ** 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
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" 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(bedbaser) > > test_check("bedbaser") trying URL 'https://api.bedbase.org/v1/files/files/5/6/56c13eab3e01dad1c54919e01423f5ae.bed.gz' Content type 'binary/octet-stream' length 471166 bytes (460 KB) ================================================== downloaded 460 KB trying URL 'https://api.bedbase.org/v1/files/files/3/4/34cdaf2d7d42b98cb0a1cfd613bcb21f.bed.gz' Content type 'binary/octet-stream' length 573397 bytes (559 KB) ================================================== downloaded 559 KB trying URL 'https://api.bedbase.org/v1/files/files/3/8/38be011ab09d152c868078850d45b4ad.bed.gz' Content type 'binary/octet-stream' length 51085 bytes (49 KB) ================================================== downloaded 49 KB trying URL 'https://api.bedbase.org/v1/files/files/3/8/38ebc406980999cd0db62de8b23cf7db.bed.gz' Content type 'binary/octet-stream' length 417561 bytes (407 KB) ================================================== downloaded 407 KB 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/0/2/02930e51dac1820ef8879909ce6edf70.bed.gz' Content type 'binary/octet-stream' length 14826 bytes (14 KB) ================================================== downloaded 14 KB trying URL 'https://api.bedbase.org/v1/files/files/3/b/3b56d2689a821ef80da854e789e7c4bc.bed.gz' Content type 'binary/octet-stream' length 7729736 bytes (7.4 MB) ================================================== downloaded 7.4 MB [ FAIL 0 | WARN 0 | SKIP 0 | PASS 51 ] > > proc.time() user system elapsed 43.508 3.265 194.062
bedbaser.Rcheck/bedbaser-Ex.timings
name | user | system | elapsed | |
BEDbase | 1.110 | 0.045 | 3.910 | |
bb_bed_text_search | 0.203 | 0.040 | 2.122 | |
bb_beds_in_bedset | 0.196 | 0.039 | 1.708 | |
bb_example | 0.219 | 0.063 | 1.537 | |
bb_list_beds | 0.350 | 0.037 | 2.561 | |
bb_list_bedsets | 0.453 | 0.008 | 8.091 | |
bb_metadata | 0.209 | 0.039 | 2.314 | |
bb_save | 0.269 | 0.067 | 11.422 | |
bb_stats | 0.132 | 0.002 | 1.732 | |
bb_to_granges | 17.441 | 0.584 | 28.880 | |
bb_to_grangeslist | 14.617 | 0.510 | 34.940 | |
getCache-BEDbase-method | 0.182 | 0.023 | 1.464 | |
operations-BEDbase-method | 0.126 | 0.008 | 1.054 | |
schemas-BEDbase-method | 0.114 | 0.008 | 0.784 | |
setCache-BEDbase-method | 0.176 | 0.012 | 0.845 | |
tags-BEDbase-method | 0.162 | 0.012 | 0.830 | |