Multiple platform build/check report for BioC 3.14 - CHECK results for segmenter on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

Package: segmenter

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmenter.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings segmenter_1.0.0.tar.gz

StartedAt: 2022-04-13 02:40:12 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 02:53:20 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 787.9 seconds

RetCode: 0

Status: OK

CheckDir: segmenter.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmenter.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings segmenter_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/segmenter.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'segmenter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmenter' version '1.0.0'
* 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 'segmenter' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   3.8Mb
* 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 LazyData ... 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
annotate_segments 26.10   1.33   44.31
learn_model        0.27   0.08   15.46
binarize_bam       0.00   0.02    9.93
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
annotate_segments 21.69   0.42   22.11
learn_model        0.27   0.04   16.89
binarize_bam       0.02   0.00    9.17
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/segmenter.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/segmenter_1.0.0.tar.gz && rm -rf segmenter.buildbin-libdir && mkdir segmenter.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=segmenter.buildbin-libdir segmenter_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL segmenter_1.0.0.zip && rm segmenter_1.0.0.tar.gz segmenter_1.0.0.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
  2 3923k    2 99687    0     0   510k      0  0:00:07 --:--:--  0:00:07  509k
 48 3923k   48 1911k    0     0  1622k      0  0:00:02  0:00:01  0:00:01 1622k
100 3923k  100 3923k    0     0  2018k      0  0:00:01  0:00:01 --:--:-- 2018k

install for i386

* installing *source* package 'segmenter' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'segmenter'
    finding HTML links ... done
    accessors                               html  
    annotate_segments                       html  
    binarize_bam                            html  
    binarize_bed                            html  
    compare_models                          html  
    count_reads_ranges                      html  
    dot-Binarize                            html  
    dot-LearnModel                          html  
    emissions_file                          html  
    enrichment_files                        html  
    get_frequency                           html  
    get_width                               html  
    learn_model                             html  
    merge_segments_bins                     html  
    methods                                 html  
    model_file                              html  
    overlap_files                           html  
    plot_heatmap                            html  
    range_bins                              html  
    range_counts                            html  
    read_bam_file                           html  
    read_bins_file                          html  
    read_cellmark_file                      html  
    read_chromsize_file                     html  
    read_emissions_file                     html  
    read_enrichment_file                    html  
    read_model_file                         html  
    read_overlap_file                       html  
    read_segements_file                     html  
    read_transitions_file                   html  
    segmentation                            html  
    segments_files                          html  
    test_obj                                html  
    test_objs                               html  
    tidy_ranges                             html  
    transitions_file                        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 'segmenter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmenter' as segmenter_1.0.0.zip
* DONE (segmenter)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'segmenter' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(segmenter)

> 
> test_check("segmenter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 123 ]
> 
> proc.time()
   user  system elapsed 
  60.46    5.15  146.46


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(segmenter)

> 
> test_check("segmenter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 123 ]
> 
> proc.time()
   user  system elapsed 
  58.78    3.93  149.57

name	user	system	elapsed
accessors	0.08	0.00	0.08
annotate_segments	26.10	1.33	44.31
binarize_bam	0.00	0.02	9.93
compare_models	0.02	0.00	0.01
emissions_file	0	0	0
enrichment_files	0	0	0
get_frequency	0.03	0.01	0.05
get_width	0.45	0.24	0.69
learn_model	0.27	0.08	15.46
methods	0	0	0
model_file	0	0	0
overlap_files	0	0	0
plot_heatmap	0.64	0.03	0.68
read_bam_file	0.06	0.01	0.07
read_bins_file	2.00	0.17	2.18
read_cellmark_file	0	0	0
read_chromsize_file	0	0	0
read_emissions_file	0	0	0
read_enrichment_file	0.02	0.00	0.01
read_model_file	0	0	0
read_overlap_file	0	0	0
read_segements_file	0.03	0.00	0.03
read_transitions_file	0	0	0
segments_files	0	0	0
tidy_ranges	0.03	0.00	0.03
transitions_file	0	0	0

name	user	system	elapsed
accessors	0.10	0.00	0.09
annotate_segments	21.69	0.42	22.11
binarize_bam	0.02	0.00	9.17
compare_models	0	0	0
emissions_file	0	0	0
enrichment_files	0	0	0
get_frequency	0.03	0.00	0.03
get_width	0.50	0.18	0.68
learn_model	0.27	0.04	16.89
methods	0	0	0
model_file	0	0	0
overlap_files	0	0	0
plot_heatmap	0.79	0.01	0.81
read_bam_file	0.02	0.02	0.03
read_bins_file	2.73	0.25	2.99
read_cellmark_file	0	0	0
read_chromsize_file	0	0	0
read_emissions_file	0	0	0
read_enrichment_file	0.02	0.00	0.01
read_model_file	0	0	0
read_overlap_file	0	0	0
read_segements_file	0.04	0.00	0.05
read_transitions_file	0	0	0
segments_files	0	0	0
tidy_ranges	0.07	0.00	0.06
transitions_file	0	0	0

CHECK results for segmenter on tokay2

Summary

Command output

Installation output

Tests output

Example timings