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CHECK report for openPrimeR on malbec1

This page was generated on 2021-05-06 12:28:28 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the openPrimeR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1269/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openPrimeR 1.12.1  (landing page)
Matthias Döring
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/openPrimeR
Branch: RELEASE_3_12
Last Commit: cf7a7af
Last Changed Date: 2020-11-14 11:32:07 -0400 (Sat, 14 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: openPrimeR
Version: 1.12.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings openPrimeR_1.12.1.tar.gz
StartedAt: 2021-05-06 04:12:48 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:19:25 -0400 (Thu, 06 May 2021)
EllapsedTime: 396.9 seconds
RetCode: 0
Status:   OK  
CheckDir: openPrimeR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings openPrimeR_1.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/openPrimeR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘openPrimeR/DESCRIPTION’ ... OK
* this is package ‘openPrimeR’ version ‘1.12.1’
* 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 ‘openPrimeR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata  10.3Mb
* 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 ... NOTE
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
PrimerDesign 20.972 16.768  32.713
Output       22.476  5.436  31.370
Plots        10.736  3.932  13.861
PrimerEval    9.192  4.252   9.484
Settings      0.472  9.004  10.701
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/openPrimeR.Rcheck/00check.log’
for details.



Installation output

openPrimeR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL openPrimeR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘openPrimeR’ ...
** using staged installation
** R
** data
** 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
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
The number of cores for was set to '2' by 'parallel_setup()'.
** testing if installed package can be loaded from final location
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
The number of cores for was set to '2' by 'parallel_setup()'.
** testing if installed package keeps a record of temporary installation path
* DONE (openPrimeR)

Tests output

openPrimeR.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> require(testthat)
Loading required package: testthat
> require(openPrimeR)
Loading required package: openPrimeR
There are missing/non-functioning external tools.
To use the full potential of openPrimeR, please make sure
that the required versions of the speciied tools are
 
                installed and that they are functional:
o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/)
o ViennaRNA (http://www.tbi.univie.ac.at/RNA/)
o OligoArrayAux (http://unafold.rna.albany.edu/OligoArrayAux.php)
o MAFFT (http://mafft.cbrc.jp/alignment/software/)
The number of cores for was set to '2' by 'parallel_setup()'.
Warning messages:
1: In check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
2: In check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
> #test_package("openPrimeR") 
> test_check("openPrimeR")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• MAFFT not available. (1)
• OligoArrayAux not available. (5)
• On Bioconductor (1)
• Secondary structure tests require ViennaRNA. (1)

[ FAIL 0 | WARN 55 | SKIP 8 | PASS 1467 ]
> 
> proc.time()
   user  system elapsed 
 63.232  42.704 109.402 

Example timings

openPrimeR.Rcheck/openPrimeR-Ex.timings

nameusersystemelapsed
AnalysisStats2.0680.0482.118
Data0.9920.0401.032
Input1.6120.3722.174
Output22.476 5.43631.370
Plots10.736 3.93213.861
PrimerDesign20.97216.76832.713
PrimerEval9.1924.2529.484
Primers-method0.0320.0080.039
Scoring0.0680.0080.074
Settings 0.472 9.00410.701
Templates-method0.0440.0080.052
TemplatesFunctions1.1600.3881.610
runTutorial000