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This page was generated on 2025-09-22 12:04 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1025/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
idr2d 1.23.0  (landing page)
Konstantin Krismer
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 2025)
git_url: https://git.bioconductor.org/packages/idr2d
git_branch: devel
git_last_commit: d7cafb1
git_last_commit_date: 2025-04-15 11:49:43 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for idr2d on lconway

To the developers/maintainers of the idr2d package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/idr2d.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: idr2d
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:idr2d.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings idr2d_1.23.0.tar.gz
StartedAt: 2025-09-21 21:45:26 -0400 (Sun, 21 Sep 2025)
EndedAt: 2025-09-21 21:49:17 -0400 (Sun, 21 Sep 2025)
EllapsedTime: 231.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: idr2d.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:idr2d.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings idr2d_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/idr2d.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 ‘idr2d/DESCRIPTION’ ... OK
* this is package ‘idr2d’ version ‘1.23.0’
* 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 ‘idr2d’ 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 whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
estimate_idr2d 5.844  0.541   6.450
estimate_idr   5.726  0.553   6.337
* 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:
  class(p) not equal to c("gg", "ggplot").
  Lengths differ: 5 is not 2
  ── Failure ('test-visualization.R:66:5'): draw_hic_contact_map ─────────────────
  class(p) not equal to c("gg", "ggplot").
  Lengths differ: 5 is not 2
  ── Failure ('test-visualization.R:81:5'): draw_hic_contact_map ─────────────────
  class(p) not equal to c("gg", "ggplot").
  Lengths differ: 5 is not 2
  ── Failure ('test-visualization.R:91:5'): draw_hic_contact_map ─────────────────
  class(p) not equal to c("gg", "ggplot").
  Lengths differ: 5 is not 2
  
  [ FAIL 9 | WARN 6 | SKIP 0 | PASS 123 ]
  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
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/idr2d.Rcheck/00check.log’
for details.


Installation output

idr2d.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL idr2d
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘idr2d’ ...
** this is package ‘idr2d’ version ‘1.23.0’
** using staged installation
** R
** data
** 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 (idr2d)

Tests output

idr2d.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.

> library(testthat)
> library(idr2d)
> 
> test_check("idr2d")
[ FAIL 9 | WARN 6 | SKIP 0 | PASS 123 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-visualization.R:33:5'): draw_idr_distribution_histogram ──────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2
── Failure ('test-visualization.R:41:5'): draw_rank_idr_scatterplot ────────────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2
── Failure ('test-visualization.R:44:5'): draw_rank_idr_scatterplot ────────────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2
── Failure ('test-visualization.R:52:5'): draw_value_idr_scatterplot ───────────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2
── Failure ('test-visualization.R:54:5'): draw_value_idr_scatterplot ───────────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2
── Failure ('test-visualization.R:57:5'): draw_value_idr_scatterplot ───────────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2
── Failure ('test-visualization.R:66:5'): draw_hic_contact_map ─────────────────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2
── Failure ('test-visualization.R:81:5'): draw_hic_contact_map ─────────────────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2
── Failure ('test-visualization.R:91:5'): draw_hic_contact_map ─────────────────
class(p) not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2

[ FAIL 9 | WARN 6 | SKIP 0 | PASS 123 ]
Error: Test failures
Execution halted

Example timings

idr2d.Rcheck/idr2d-Ex.timings

nameusersystemelapsed
calculate_midpoint_distance1d000
calculate_midpoint_distance2d0.0000.0010.002
calculate_relative_overlap1d0.0010.0000.001
calculate_relative_overlap2d0.0010.0000.002
determine_anchor_overlap0.5790.0050.586
draw_hic_contact_map3.3180.4473.790
draw_idr_distribution_histogram1.5240.1071.641
draw_rank_idr_scatterplot1.7260.0991.845
draw_value_idr_scatterplot1.5490.0861.649
establish_bijection0.2290.0050.236
establish_bijection1d0.2230.0060.231
establish_bijection2d1.8460.0311.890
establish_overlap1d0.1220.0020.124
establish_overlap2d0.3410.0100.354
estimate_idr5.7260.5536.337
estimate_idr1d1.1630.0771.247
estimate_idr2d5.8440.5416.450
estimate_idr2d_hic2.3870.2822.751
preprocess0.0020.0000.002
remove_nonstandard_chromosomes1d0.1300.0180.149
remove_nonstandard_chromosomes2d0.3110.0430.359