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This page was generated on 2021-07-23 12:05:03 -0400 (Fri, 23 Jul 2021).

CHECK results for ribor on riesling1

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? here for more information.
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raw results

Package 1554/2008HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ribor 1.5.0  (landing page)
Michael Geng
Snapshot Date: 2021-07-22 14:50:06 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/ribor
Branch: master
Last Commit: c603704
Last Changed Date: 2021-05-19 12:50:02 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / 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: ribor
Version: 1.5.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ribor.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ribor_1.5.0.tar.gz
StartedAt: 2021-07-23 01:59:49 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 02:02:33 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 164.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ribor.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ribor.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ribor_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/ribor.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.5.0'
* 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
** 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
  'D:/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_1.5.0.tar.gz && rm -rf ribor.buildbin-libdir && mkdir ribor.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ribor.buildbin-libdir ribor_1.5.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ribor_1.5.0.zip && rm ribor_1.5.0.tar.gz ribor_1.5.0.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
100 3396k  100 3396k    0     0  8708k      0 --:--:-- --:--:-- --:--:-- 8708k

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_1.5.0.zip
* DONE (ribor)
* installing to library 'D:/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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 
  14.73    1.10   15.81 

ribor.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 
  15.67    1.14   16.85 

Example timings

ribor.Rcheck/examples_i386/ribor-Ex.timings

nameusersystemelapsed
get_coverage0.190.050.23
get_experiments0.080.000.08
get_info0.070.030.10
get_internal_region_coordinates1.280.011.30
get_internal_region_lengths1.280.071.34
get_length_distribution0.170.010.19
get_metadata0.060.000.06
get_metagene0.240.050.28
get_original_region_coordinates1.480.051.53
get_original_region_lengths1.380.071.45
get_reference_names0.620.020.65
get_region_counts0.100.030.12
get_rnaseq0.120.030.16
get_tidy_metagene0.360.030.39
plot_length_distribution0.550.050.59
plot_metagene0.620.030.66
plot_region_counts0.530.030.56
rename_default000
rename_transcripts0.990.031.02
ribo-class0.970.051.01
set_aliases1.090.001.09

ribor.Rcheck/examples_x64/ribor-Ex.timings

nameusersystemelapsed
get_coverage0.210.070.26
get_experiments0.070.000.08
get_info0.090.000.09
get_internal_region_coordinates1.350.031.37
get_internal_region_lengths1.370.061.44
get_length_distribution0.140.050.19
get_metadata0.070.010.08
get_metagene0.260.020.28
get_original_region_coordinates1.610.061.67
get_original_region_lengths1.580.061.64
get_reference_names0.70.00.7
get_region_counts0.130.020.14
get_rnaseq0.140.010.16
get_tidy_metagene0.400.070.47
plot_length_distribution0.620.010.64
plot_metagene0.690.020.70
plot_region_counts0.600.030.62
rename_default000
rename_transcripts1.120.011.14
ribo-class1.090.041.13
set_aliases1.190.011.20