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CHECK report for miRNAmeConverter on celaya2

This page was generated on 2020-01-16 13:44:38 -0500 (Thu, 16 Jan 2020).

Package 1054/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRNAmeConverter 1.15.0
Stefan J. Haunsberger
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/miRNAmeConverter
Branch: master
Last Commit: d1a8f8e
Last Changed Date: 2019-10-29 13:40:36 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: miRNAmeConverter
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:miRNAmeConverter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings miRNAmeConverter_1.15.0.tar.gz
StartedAt: 2020-01-16 06:35:05 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 06:37:40 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 155.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: miRNAmeConverter.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:miRNAmeConverter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings miRNAmeConverter_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/miRNAmeConverter.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miRNAmeConverter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRNAmeConverter’ version ‘1.15.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘miRNAmeConverter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’.
 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 ... NOTE
MiRNANameConverter,ANY: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getMirnasForMirbaseVersion’
Undocumented S4 methods:
  generic 'getMirnasForMirbaseVersion' and siglist 'MiRNANameConverter'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/miRNAmeConverter.Rcheck/00check.log’
for details.



Installation output

miRNAmeConverter.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL miRNAmeConverter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘miRNAmeConverter’ ...
** using staged installation
It is recommended to use ‘given’ instead of ‘middle’.
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘MiRNANameConverter’ in package ‘miRNAmeConverter’
** help
*** installing help indices
** building package indices
** 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 (miRNAmeConverter)

Tests output

miRNAmeConverter.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(miRNAmeConverter)
Loading required package: miRBaseVersions.db
> 
> test_check("miRNAmeConverter")
	miRNA 'hsa-let-7a-3p' is the same as 'hsa-let-7a*'.
	->hsa-let-7a-3p is the most recent one and will be used. The other ones will be neglected.
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 13.403   0.876  14.296 

Example timings

miRNAmeConverter.Rcheck/miRNAmeConverter-Ex.timings

nameusersystemelapsed
MiRNANameConverter-ANY-method0.3150.6782.574
assessVersion0.4820.0120.494
checkMiRNAName0.2730.0030.275
currentVersion0.1400.0020.142
miRNAmeConverter1.1050.0231.130
nOrganisms0.1590.0020.160
nTotalEntries0.1540.0020.155
saveResults1.4650.0261.536
translateMiRNAName1.4540.0171.525
validOrganisms0.1420.0010.143
validVersions0.1460.0120.158