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This page was generated on 2021-10-15 15:05:47 -0400 (Fri, 15 Oct 2021).

CHECK results for openPrimeR on nebbiolo1

To the developers/maintainers of the openPrimeR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/openPrimeR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1313/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openPrimeR 1.14.0  (landing page)
Matthias Döring
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/openPrimeR
git_branch: RELEASE_3_13
git_last_commit: cc9c24b
git_last_commit_date: 2021-05-19 12:30:17 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: openPrimeR
Version: 1.14.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings openPrimeR_1.14.0.tar.gz
StartedAt: 2021-10-14 10:52:46 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:56:19 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 213.3 seconds
RetCode: 0
Status:   OK  
CheckDir: openPrimeR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings openPrimeR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/openPrimeR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.14.0’
* 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 ‘openPrimeR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    extdata   3.3Mb
* 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 ... 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 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 13.517  4.826  12.316
Output       16.006  1.419  16.860
PrimerEval    5.458  1.919   4.551
Plots         5.359  1.011   5.590
* 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-3.13-bioc/meat/openPrimeR.Rcheck/00check.log’
for details.



Installation output

openPrimeR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL openPrimeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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
The number of cores for was set to '2' by 'parallel_setup()'.
** testing if installed package can be loaded from final location
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 4.1.1 (2021-08-10) -- "Kick Things"
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 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()'.
> #test_package("openPrimeR") 
> test_check("openPrimeR")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• MAFFT not available. (1)
• OligoArrayAux not available. (5)
• On Bioconductor (1)
• empty test (1)

[ FAIL 0 | WARN 6 | SKIP 8 | PASS 1474 ]
> 
> proc.time()
   user  system elapsed 
 43.641  11.534  44.809 

Example timings

openPrimeR.Rcheck/openPrimeR-Ex.timings

nameusersystemelapsed
AnalysisStats1.9070.0801.988
Data0.5370.0450.582
Input0.9430.0500.997
Output16.006 1.41916.860
Plots5.3591.0115.590
PrimerDesign13.517 4.82612.316
PrimerEval5.4581.9194.551
Primers-method0.0830.0850.022
Scoring0.0270.0070.035
Settings0.7540.2100.963
Templates-method0.0470.0000.048
TemplatesFunctions0.2700.0660.336
runTutorial0.0000.0000.001