Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-16 11:37 -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 160/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bedbaser 1.0.4  (landing page)
Andres Wokaty
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/bedbaser
git_branch: RELEASE_3_21
git_last_commit: 1eb42ba
git_last_commit_date: 2025-10-12 15:54:07 -0400 (Sun, 12 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for bedbaser on nebbiolo1

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.

raw results


Summary

Package: bedbaser
Version: 1.0.4
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings bedbaser_1.0.4.tar.gz
StartedAt: 2025-10-15 21:05:14 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 21:09:25 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 251.2 seconds
RetCode: 0
Status:   OK  
CheckDir: bedbaser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings bedbaser_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/bedbaser.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* this is package ‘bedbaser’ version ‘1.0.4’
* 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_grangeslist 15.656  2.531  24.181
bb_to_granges     13.181  1.086  16.069
bb_list_bedsets    0.341  0.148   6.690
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/bedbaser.Rcheck/00check.log’
for details.


Installation output

bedbaser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL bedbaser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘bedbaser’ ...
** this is package ‘bedbaser’ version ‘1.0.4’
** 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)

Tests output

bedbaser.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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/c/9/c937049d6147b43aca93e6d93a7dc35c.bed.gz'
Content type 'binary/octet-stream' length 553032 bytes (540 KB)
==================================================
downloaded 540 KB

trying URL 'https://api.bedbase.org/v1/files/files/8/4/84b20b868b341ac35af8eaa5da0b4aff.bed.gz'
Content type 'binary/octet-stream' length 1120767 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://api.bedbase.org/v1/files/files/9/d/9d3f9567a1771ccbad1d2e1dc67112fe.bed.gz'
Content type 'binary/octet-stream' length 1030411 bytes (1006 KB)
==================================================
downloaded 1006 KB

trying URL 'https://api.bedbase.org/v1/files/files/9/d/9dbcf939666f1606ae25258271e22db5.bed.gz'
Content type 'binary/octet-stream' length 686183 bytes (670 KB)
==================================================
downloaded 670 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/4/5/45407c12e57a8a5db4e0ce6376815c93.bed.gz'
Content type 'binary/octet-stream' length 358912 bytes (350 KB)
==================================================
downloaded 350 KB

trying URL 'https://api.bedbase.org/v1/files/files/3/0/3053b7b8be8ca1502b46946dde0e4ced.bed.gz'
Content type 'binary/octet-stream' length 3871087 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 51 ]
> 
> proc.time()
   user  system elapsed 
 40.254   1.949  78.714 

Example timings

bedbaser.Rcheck/bedbaser-Ex.timings

nameusersystemelapsed
BEDbase0.8560.0151.565
bb_bed_text_search0.1600.0350.740
bb_beds_in_bedset0.1450.0050.392
bb_example0.1790.0050.471
bb_list_beds0.3460.0151.322
bb_list_bedsets0.3410.1486.690
bb_metadata0.1660.0380.571
bb_save0.3100.0142.099
bb_stats0.1110.0050.436
bb_to_granges13.181 1.08616.069
bb_to_grangeslist15.656 2.53124.181
getCache-BEDbase-method0.1420.0190.579
operations-BEDbase-method0.0960.0130.281
schemas-BEDbase-method0.0940.0040.274
setCache-BEDbase-method0.1240.0180.312
tags-BEDbase-method0.1260.0050.302