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CHECK report for ribor on malbec2

This page was generated on 2020-10-17 11:55:35 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ribor PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1488/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ribor 1.0.0
Michael Geng
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ribor
Branch: RELEASE_3_11
Last Commit: ddfe3dd
Last Changed Date: 2020-04-27 15:34:28 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ribor
Version: 1.0.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ribor.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ribor_1.0.0.tar.gz
StartedAt: 2020-10-17 04:47:58 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:49:28 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 90.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ribor.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ribor.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ribor_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ribor.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ribor/DESCRIPTION’ ... OK
* this is package ‘ribor’ 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 ... 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ribor’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/ribor.Rcheck/00check.log’
for details.



Installation output

ribor.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ribor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘ribor’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (ribor)

Tests output

ribor.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 88 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 23.405   0.371  24.156 

Example timings

ribor.Rcheck/ribor-Ex.timings

nameusersystemelapsed
get_coverage0.4550.0320.638
get_experiments0.1020.0040.105
get_info0.1870.0000.187
get_length_distribution0.3600.0040.363
get_metadata0.0850.0040.090
get_metagene0.3120.0040.316
get_reference_names0.6840.0040.722
get_region_coordinates2.0730.0202.102
get_region_counts0.2060.0000.206
get_region_lengths2.0100.0122.021
get_rnaseq0.2370.0040.241
get_tidy_metagene0.7400.0160.756
plot_length_distribution1.1050.0161.131
plot_metagene1.2760.0081.284
plot_region_counts1.0910.0081.099
rename_default000
rename_transcripts2.1960.0122.207
ribo-class2.0840.0042.089
set_aliases1.2910.0081.299