Multiple platform build/check report for BioC 3.14 - CHECK results for ribor 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: ribor

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ribor.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ribor_1.6.0.tar.gz

StartedAt: 2022-04-13 01:43:50 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 01:46:51 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 181.2 seconds

RetCode: 0

Status: OK

CheckDir: ribor.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:ribor.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ribor_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ribor.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 'ribor/DESCRIPTION' ... OK
* this is package 'ribor' version '1.6.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ribor' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
get_internal_region_coordinates 2.28    0.1    5.07
** running examples for arch 'x64' ... OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ribor.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/ribor_1.6.0.tar.gz && rm -rf ribor.buildbin-libdir && mkdir ribor.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ribor.buildbin-libdir ribor_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ribor_1.6.0.zip && rm ribor_1.6.0.tar.gz ribor_1.6.0.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
 10 3396k   10  353k    0     0  1040k      0  0:00:03 --:--:--  0:00:03 1041k
 73 3396k   73 2511k    0     0  1833k      0  0:00:01  0:00:01 --:--:-- 1834k
100 3396k  100 3396k    0     0  2036k      0  0:00:01  0:00:01 --:--:-- 2036k

install for i386

* installing *source* package 'ribor' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ribor'
    finding HTML links ... done
    get_coverage                            html  
    get_experiments                         html  
    get_info                                html  
    get_internal_region_coordinates         html  
    get_internal_region_lengths             html  
    get_length_distribution                 html  
    get_metadata                            html  
    get_metagene                            html  
    get_original_region_coordinates         html  
    get_original_region_lengths             html  
    get_reference_names                     html  
    get_region_coordinates                  html  
    get_region_counts                       html  
    get_region_lengths                      html  
    get_rnaseq                              html  
    get_tidy_metagene                       html  
    plot_length_distribution                html  
    plot_metagene                           html  
    plot_region_counts                      html  
    rename_default                          html  
    rename_transcripts                      html  
    ribo-class                              html  
    ribor                                   html  
    set_aliases                             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 'ribor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ribor' as ribor_1.6.0.zip
* DONE (ribor)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ribor' 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(ribor)
> 
> test_check("ribor")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 96 ]
> 
> proc.time()
   user  system elapsed 
  20.84    1.34   22.18


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(ribor)
> 
> test_check("ribor")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 96 ]
> 
> proc.time()
   user  system elapsed 
  23.14    1.31   24.43

name	user	system	elapsed
get_coverage	0.47	0.11	1.39
get_experiments	0.14	0.02	0.16
get_info	0.24	0.01	0.25
get_internal_region_coordinates	2.28	0.10	5.07
get_internal_region_lengths	2.02	0.11	2.13
get_length_distribution	0.27	0.00	0.26
get_metadata	0.04	0.03	0.08
get_metagene	0.42	0.05	0.47
get_original_region_coordinates	2.00	0.01	2.02
get_original_region_lengths	2.63	0.05	2.67
get_reference_names	0.94	0.06	1.00
get_region_counts	0.26	0.00	0.26
get_rnaseq	0.24	0.03	0.27
get_tidy_metagene	0.67	0.00	0.67
plot_length_distribution	0.90	0.03	0.94
plot_metagene	1.35	0.02	1.36
plot_region_counts	1.00	0.01	1.01
rename_default	0	0	0
rename_transcripts	1.56	0.02	1.58
ribo-class	1.49	0.03	1.52
set_aliases	1.78	0.02	1.81

name	user	system	elapsed
get_coverage	0.54	0.11	0.70
get_experiments	0.22	0.02	0.24
get_info	0.19	0.03	0.22
get_internal_region_coordinates	1.89	0.03	1.92
get_internal_region_lengths	1.78	0.10	1.88
get_length_distribution	0.25	0.03	0.28
get_metadata	0.08	0.01	0.09
get_metagene	0.43	0.08	0.52
get_original_region_coordinates	2.43	0.09	2.52
get_original_region_lengths	2.32	0.05	2.37
get_reference_names	0.58	0.06	0.64
get_region_counts	0.28	0.05	0.33
get_rnaseq	0.32	0.03	0.35
get_tidy_metagene	0.71	0.00	0.72
plot_length_distribution	0.96	0.03	0.98
plot_metagene	0.97	0.12	1.10
plot_region_counts	0.98	0.00	0.98
rename_default	0	0	0
rename_transcripts	1.67	0.08	1.75
ribo-class	1.83	0.03	1.86
set_aliases	1.34	0.02	1.36

CHECK results for ribor on tokay2

Summary

Command output

Installation output

Tests output

Example timings