Multiple platform build/check report for BioC 3.11 - CHECK report for idr2d on tokay2

Package: idr2d

Version: 1.2.2

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:idr2d.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings idr2d_1.2.2.tar.gz

StartedAt: 2020-10-17 05:09:35 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 05:16:54 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 438.9 seconds

RetCode: 0

Status: OK

CheckDir: idr2d.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:idr2d.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings idr2d_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/idr2d.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'idr2d/DESCRIPTION' ... OK
* this is package 'idr2d' version '1.2.2'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
estimate_idr2d       8.03   0.17    8.20
estimate_idr         7.74   0.08    7.81
draw_hic_contact_map 5.62   0.14    5.77
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
estimate_idr2d                  6.91   0.08    6.99
estimate_idr                    5.11   0.04    5.16
draw_idr_distribution_histogram 1.71   0.11    6.87
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/idr2d_1.2.2.tar.gz && rm -rf idr2d.buildbin-libdir && mkdir idr2d.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=idr2d.buildbin-libdir idr2d_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL idr2d_1.2.2.zip && rm idr2d_1.2.2.tar.gz idr2d_1.2.2.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  796k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  796k  100  796k    0     0  1862k      0 --:--:-- --:--:-- --:--:-- 1891k

install for i386

* installing *source* package 'idr2d' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'idr2d'
    finding HTML links ... done
    calculate_midpoint_distance1d           html  
    calculate_midpoint_distance2d           html  
    calculate_relative_overlap1d            html  
    calculate_relative_overlap2d            html  
    chiapet                                 html  
    chipseq                                 html  
    determine_anchor_overlap                html  
    draw_hic_contact_map                    html  
    draw_idr_distribution_histogram         html  
    draw_rank_idr_scatterplot               html  
    draw_value_idr_scatterplot              html  
    establish_bijection                     html  
    establish_bijection1d                   html  
    establish_bijection2d                   html  
    establish_overlap1d                     html  
    establish_overlap2d                     html  
    estimate_idr                            html  
    estimate_idr1d                          html  
    estimate_idr2d                          html  
    estimate_idr2d_hic                      html  
    hic                                     html  
    parse_hic_pro_matrix                    html  
    parse_juicer_matrix                     html  
    preprocess                              html  
    remove_nonstandard_chromosomes1d        html  
    remove_nonstandard_chromosomes2d        html  
** 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

install for x64

* installing *source* package 'idr2d' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'idr2d' as idr2d_1.2.2.zip
* DONE (idr2d)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'idr2d' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 131 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  61.93    1.21   63.12


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 132 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  56.95    1.28  130.54

name	user	system	elapsed
calculate_midpoint_distance1d	0	0	0
calculate_midpoint_distance2d	0	0	0
calculate_relative_overlap1d	0	0	0
calculate_relative_overlap2d	0	0	0
determine_anchor_overlap	0.32	0.00	0.31
draw_hic_contact_map	5.62	0.14	5.77
draw_idr_distribution_histogram	2.00	0.12	2.12
draw_rank_idr_scatterplot	1.41	0.00	1.41
draw_value_idr_scatterplot	1.45	0.03	1.48
establish_bijection	0.2	0.0	0.2
establish_bijection1d	0.18	0.00	0.18
establish_bijection2d	0.68	0.11	0.79
establish_overlap1d	0.17	0.00	0.18
establish_overlap2d	0.80	0.00	0.79
estimate_idr	7.74	0.08	7.81
estimate_idr1d	1.17	0.02	1.19
estimate_idr2d	8.03	0.17	8.20
estimate_idr2d_hic	4.71	0.00	4.70
preprocess	0	0	0
remove_nonstandard_chromosomes1d	0.14	0.01	0.16
remove_nonstandard_chromosomes2d	0.40	0.03	0.44

name	user	system	elapsed
calculate_midpoint_distance1d	0	0	0
calculate_midpoint_distance2d	0	0	0
calculate_relative_overlap1d	0.02	0.00	0.02
calculate_relative_overlap2d	0	0	0
determine_anchor_overlap	0.19	0.00	0.18
draw_hic_contact_map	4.18	0.05	4.24
draw_idr_distribution_histogram	1.71	0.11	6.87
draw_rank_idr_scatterplot	1.26	0.01	1.28
draw_value_idr_scatterplot	1.21	0.02	1.22
establish_bijection	0.15	0.00	0.16
establish_bijection1d	0.16	0.00	0.15
establish_bijection2d	1.01	0.00	1.02
establish_overlap1d	0.14	0.00	0.14
establish_overlap2d	0.30	0.01	0.31
estimate_idr	5.11	0.04	5.16
estimate_idr1d	1.75	0.06	1.81
estimate_idr2d	6.91	0.08	6.99
estimate_idr2d_hic	3.53	0.00	3.53
preprocess	0	0	0
remove_nonstandard_chromosomes1d	0.14	0.01	0.16
remove_nonstandard_chromosomes2d	0.31	0.02	0.32

CHECK report for idr2d on tokay2

Summary

Command output

Installation output

Tests output

Example timings