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This page was generated on 2022-04-13 12:07:13 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for ribor on tokay2


To the developers/maintainers of the ribor package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ribor.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 1607/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ribor 1.6.0  (landing page)
Michael Geng
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/ribor
git_branch: RELEASE_3_14
git_last_commit: fa3edd7
git_last_commit_date: 2021-10-26 12:57:45 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.



Installation output

ribor.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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

Tests output

ribor.Rcheck/tests_i386/testthat.Rout


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 

ribor.Rcheck/tests_x64/testthat.Rout


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 

Example timings

ribor.Rcheck/examples_i386/ribor-Ex.timings

nameusersystemelapsed
get_coverage0.470.111.39
get_experiments0.140.020.16
get_info0.240.010.25
get_internal_region_coordinates2.280.105.07
get_internal_region_lengths2.020.112.13
get_length_distribution0.270.000.26
get_metadata0.040.030.08
get_metagene0.420.050.47
get_original_region_coordinates2.000.012.02
get_original_region_lengths2.630.052.67
get_reference_names0.940.061.00
get_region_counts0.260.000.26
get_rnaseq0.240.030.27
get_tidy_metagene0.670.000.67
plot_length_distribution0.900.030.94
plot_metagene1.350.021.36
plot_region_counts1.000.011.01
rename_default000
rename_transcripts1.560.021.58
ribo-class1.490.031.52
set_aliases1.780.021.81

ribor.Rcheck/examples_x64/ribor-Ex.timings

nameusersystemelapsed
get_coverage0.540.110.70
get_experiments0.220.020.24
get_info0.190.030.22
get_internal_region_coordinates1.890.031.92
get_internal_region_lengths1.780.101.88
get_length_distribution0.250.030.28
get_metadata0.080.010.09
get_metagene0.430.080.52
get_original_region_coordinates2.430.092.52
get_original_region_lengths2.320.052.37
get_reference_names0.580.060.64
get_region_counts0.280.050.33
get_rnaseq0.320.030.35
get_tidy_metagene0.710.000.72
plot_length_distribution0.960.030.98
plot_metagene0.970.121.10
plot_region_counts0.980.000.98
rename_default000
rename_transcripts1.670.081.75
ribo-class1.830.031.86
set_aliases1.340.021.36