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This page was generated on 2022-10-19 13:23:07 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for idr2d on merida1


To the developers/maintainers of the idr2d package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 939/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
idr2d 1.10.0  (landing page)
Konstantin Krismer
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/idr2d
git_branch: RELEASE_3_15
git_last_commit: f92649a
git_last_commit_date: 2022-04-26 11:59:00 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: idr2d
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2022-10-19 03:35:51 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 03:41:30 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 338.5 seconds
RetCode: 0
Status:   OK  
CheckDir: idr2d.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/idr2d.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘idr2d/DESCRIPTION’ ... OK
* this is package ‘idr2d’ version ‘1.10.0’
* 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 R 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 ... 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_idr         9.282  0.661   9.954
estimate_idr2d       9.136  0.558   9.711
draw_hic_contact_map 5.662  0.543   6.215
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


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/4.2/Resources/library’
* installing *source* package ‘idr2d’ ...
** 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


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 0 | WARN 1 | SKIP 0 | PASS 132 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 132 ]
> 
> proc.time()
   user  system elapsed 
 90.391   5.348  95.860 

Example timings

idr2d.Rcheck/idr2d-Ex.timings

nameusersystemelapsed
calculate_midpoint_distance1d0.0010.0000.001
calculate_midpoint_distance2d0.0010.0010.001
calculate_relative_overlap1d0.0020.0010.002
calculate_relative_overlap2d0.0020.0010.002
determine_anchor_overlap0.3750.0050.381
draw_hic_contact_map5.6620.5436.215
draw_idr_distribution_histogram2.5500.1102.665
draw_rank_idr_scatterplot2.4740.0872.564
draw_value_idr_scatterplot2.5850.0792.669
establish_bijection0.4440.0080.454
establish_bijection1d0.4700.0070.477
establish_bijection2d3.4700.0193.492
establish_overlap1d0.2080.0070.216
establish_overlap2d0.5120.0040.517
estimate_idr9.2820.6619.954
estimate_idr1d2.0600.0692.131
estimate_idr2d9.1360.5589.711
estimate_idr2d_hic4.5420.3264.874
preprocess0.0040.0000.004
remove_nonstandard_chromosomes1d0.2990.0140.313
remove_nonstandard_chromosomes2d0.5860.0340.621