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This page was generated on 2023-03-20 11:05:48 -0400 (Mon, 20 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4297
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4286
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4150
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 palomino3


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 960/2189HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
idr2d 1.13.0  (landing page)
Konstantin Krismer
Snapshot Date: 2023-03-19 14:00:12 -0400 (Sun, 19 Mar 2023)
git_url: https://git.bioconductor.org/packages/idr2d
git_branch: master
git_last_commit: 8c8b82b
git_last_commit_date: 2022-11-01 11:20:29 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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: 1.13.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:idr2d.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings idr2d_1.13.0.tar.gz
StartedAt: 2023-03-20 02:44:11 -0400 (Mon, 20 Mar 2023)
EndedAt: 2023-03-20 02:47:45 -0400 (Mon, 20 Mar 2023)
EllapsedTime: 214.0 seconds
RetCode: 0
Status:   OK  
CheckDir: idr2d.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:idr2d.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings idr2d_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/idr2d.Rcheck'
* using R Under development (unstable) (2023-03-15 r83984 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'idr2d/DESCRIPTION' ... OK
* this is package 'idr2d' version '1.13.0'
* 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 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 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_idr   6.86   1.96    8.82
estimate_idr2d 6.71   1.29    8.00
* 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:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL idr2d
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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)

Tests output

idr2d.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  55.03    3.89   61.56 

Example timings

idr2d.Rcheck/idr2d-Ex.timings

nameusersystemelapsed
calculate_midpoint_distance1d000
calculate_midpoint_distance2d000
calculate_relative_overlap1d000
calculate_relative_overlap2d000
determine_anchor_overlap0.330.000.32
draw_hic_contact_map3.620.013.64
draw_idr_distribution_histogram1.490.101.66
draw_rank_idr_scatterplot1.370.121.50
draw_value_idr_scatterplot1.380.051.42
establish_bijection0.200.010.22
establish_bijection1d0.200.020.22
establish_bijection2d1.600.011.61
establish_overlap1d0.110.020.12
establish_overlap2d0.320.010.34
estimate_idr6.861.968.82
estimate_idr1d1.070.041.11
estimate_idr2d6.711.298.00
estimate_idr2d_hic3.040.003.03
preprocess0.000.010.01
remove_nonstandard_chromosomes1d0.170.000.17
remove_nonstandard_chromosomes2d0.360.060.43