Package: idr2d

Version: 1.0.4

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:idr2d.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings idr2d_1.0.4.tar.gz

StartedAt: 2020-04-15 06:52:28 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:55:06 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 157.9 seconds

RetCode: 0

Status:  OK

CheckDir: idr2d.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:idr2d.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings idr2d_1.0.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/idr2d.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘idr2d/DESCRIPTION’ ... OK
* this is package ‘idr2d’ 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 ‘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 or elapsed time > 5s
                user system elapsed
estimate_idr2d 6.020  0.040   6.075
estimate_idr   5.852  0.072   5.932
* 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

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL idr2d
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  5.588   0.164   5.784 

name	user	system	elapsed
calculate_midpoint_distance1d	0	0	0
calculate_midpoint_distance2d	0.000	0.000	0.001
calculate_relative_overlap1d	0.000	0.000	0.002
calculate_relative_overlap2d	0.004	0.000	0.001
determine_anchor_overlap	0.368	0.000	0.367
draw_hic_contact_map	4.024	0.036	4.081
draw_idr_distribution_histogram	1.580	0.032	1.618
draw_rank_idr_scatterplot	1.324	0.008	1.336
draw_value_idr_scatterplot	1.056	0.016	1.070
establish_bijection	0.144	0.004	0.150
establish_bijection1d	0.148	0.000	0.150
establish_bijection2d	0.836	0.000	0.842
establish_overlap1d	0.164	0.000	0.164
establish_overlap2d	0.812	0.000	0.814
estimate_idr	5.852	0.072	5.932
estimate_idr1d	1.056	0.004	1.063
estimate_idr2d	6.020	0.040	6.075
estimate_idr2d_hic	3.048	0.000	3.054
preprocess	0.004	0.000	0.005
remove_nonstandard_chromosomes1d	0.232	0.000	0.236
remove_nonstandard_chromosomes2d	0.456	0.004	0.460