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CHECK report for idr2d on merida1

This page was generated on 2021-05-06 12:35:21 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the idr2d package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 875/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
idr2d 1.4.0  (landing page)
Konstantin Krismer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/idr2d
Branch: RELEASE_3_12
Last Commit: 53471a2
Last Changed Date: 2020-10-29 13:13:10 -0400 (Thu, 29 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: idr2d
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:idr2d.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings idr2d_1.4.0.tar.gz
StartedAt: 2021-05-06 02:47:26 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:51:19 -0400 (Thu, 06 May 2021)
EllapsedTime: 233.5 seconds
RetCode: 0
Status:   OK  
CheckDir: idr2d.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:idr2d.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings idr2d_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/idr2d.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.4.0’
* 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   5.577  0.664   6.255
estimate_idr2d 5.575  0.566   6.149
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 0 | SKIP 0 | PASS 132 ]
> 
> proc.time()
   user  system elapsed 
 54.261   4.922  59.230 

Example timings

idr2d.Rcheck/idr2d-Ex.timings

nameusersystemelapsed
calculate_midpoint_distance1d0.0010.0020.002
calculate_midpoint_distance2d0.0020.0020.003
calculate_relative_overlap1d0.0010.0010.002
calculate_relative_overlap2d0.0020.0000.002
determine_anchor_overlap0.2780.0070.287
draw_hic_contact_map4.1940.4894.698
draw_idr_distribution_histogram1.6420.1181.767
draw_rank_idr_scatterplot1.4480.1011.555
draw_value_idr_scatterplot1.4980.0941.595
establish_bijection0.2300.0040.235
establish_bijection1d0.2100.0060.216
establish_bijection2d1.2860.0261.324
establish_overlap1d0.1640.0020.167
establish_overlap2d0.3620.0030.366
estimate_idr5.5770.6646.255
estimate_idr1d1.2810.1041.386
estimate_idr2d5.5750.5666.149
estimate_idr2d_hic3.4440.3283.791
preprocess0.0030.0000.003
remove_nonstandard_chromosomes1d0.2310.0210.253
remove_nonstandard_chromosomes2d0.3950.0210.418