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This page was generated on 2025-09-11 12:04 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4539
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4474
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 160/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bedbaser 1.1.2  (landing page)
Andres Wokaty
Snapshot Date: 2025-09-10 13:45 -0400 (Wed, 10 Sep 2025)
git_url: https://git.bioconductor.org/packages/bedbaser
git_branch: devel
git_last_commit: 7a7e805
git_last_commit_date: 2025-07-16 11:48:23 -0400 (Wed, 16 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for bedbaser on lconway

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: 1.1.2
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_1.1.2.tar.gz
StartedAt: 2025-09-10 20:32:22 -0400 (Wed, 10 Sep 2025)
EndedAt: 2025-09-10 20:35:43 -0400 (Wed, 10 Sep 2025)
EllapsedTime: 201.5 seconds
RetCode: 0
Status:   OK  
CheckDir: bedbaser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.1.2.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 ‘1.1.2’
* 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 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     21.310  1.752  23.957
bb_to_grangeslist 15.377  1.564  29.925
bb_list_bedsets    0.367  0.017   5.384
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck/00check.log’
for details.


Installation output

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 ‘1.1.2’
** 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)

Tests output

bedbaser.Rcheck/tests/testthat.Rout


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/d/2/d2b4e20da5070915045f1dc276ff59d3.bed.gz'
Content type 'binary/octet-stream' length 688729 bytes (672 KB)
==================================================
downloaded 672 KB


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/a/b/abe12f6f5d6ee293567c4fb000c09048.bed.gz'
Content type 'binary/octet-stream' length 1041725 bytes (1017 KB)
==================================================
downloaded 1017 KB


Attaching package: 'BSgenome.Hsapiens.UCSC.hg19'

The following object is masked from 'package:BSgenome.Hsapiens.UCSC.hg38':

    Hsapiens

trying URL 'https://api.bedbase.org/v1/files/files/9/2/92d3a1798afcd559cab03be17359b078.bed.gz'
Content type 'binary/octet-stream' length 1627925 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://api.bedbase.org/v1/files/files/9/2/925e0b89c4c4165e34f051c4cf7afefa.bed.gz'
Content type 'binary/octet-stream' length 9693 bytes
==================================================
downloaded 9693 bytes

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/c/9/c9012f0089876e55c0da0e0a0d36ad21.bed.gz'
Content type 'binary/octet-stream' length 27571 bytes (26 KB)
==================================================
downloaded 26 KB

trying URL 'https://api.bedbase.org/v1/files/files/0/1/01aa44dada209ded5012a697823255e8.bed.gz'
Content type 'binary/octet-stream' length 340567 bytes (332 KB)
==================================================
downloaded 332 KB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 51 ]
> 
> proc.time()
   user  system elapsed 
 38.050   3.281  71.543 

Example timings

bedbaser.Rcheck/bedbaser-Ex.timings

nameusersystemelapsed
BEDbase1.0760.0601.926
bb_bed_text_search0.1830.0231.042
bb_beds_in_bedset0.1450.0060.447
bb_example0.1720.0110.482
bb_list_beds0.3050.0171.134
bb_list_bedsets0.3670.0175.384
bb_metadata0.1820.0090.578
bb_save0.2120.0492.334
bb_stats0.1090.0060.443
bb_to_granges21.310 1.75223.957
bb_to_grangeslist15.377 1.56429.925
getCache-BEDbase-method0.1630.0190.469
operations-BEDbase-method0.1110.0100.299
schemas-BEDbase-method0.0990.0100.284
setCache-BEDbase-method0.1530.0120.344
tags-BEDbase-method0.1470.0060.338