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CHECK report for openPrimeR on tokay1

This page was generated on 2021-05-06 12:32:38 -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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings openPrimeR_1.12.1.tar.gz
StartedAt: 2021-05-06 05:15:23 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:23:19 -0400 (Thu, 06 May 2021)
EllapsedTime: 475.7 seconds
RetCode: 0
Status:   OK   
CheckDir: openPrimeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings openPrimeR_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/openPrimeR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'openPrimeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata  10.0Mb
* 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
PrimerDesign 12.70   0.25   13.78
Output        9.84   1.19   22.48
Plots         6.32   0.52    6.83
PrimerEval    4.88   0.20    5.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
PrimerDesign 17.17   0.31   17.48
Output       15.16   1.37   25.30
Plots         9.56   0.38    9.95
PrimerEval    7.16   0.41    7.57
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/openPrimeR.Rcheck/00check.log'
for details.



Installation output

openPrimeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/openPrimeR_1.12.1.tar.gz && rm -rf openPrimeR.buildbin-libdir && mkdir openPrimeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openPrimeR.buildbin-libdir openPrimeR_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL openPrimeR_1.12.1.zip && rm openPrimeR_1.12.1.tar.gz openPrimeR_1.12.1.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 1771k  100 1771k    0     0  39.7M      0 --:--:-- --:--:-- --:--:-- 41.1M

install for i386

* installing *source* package 'openPrimeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'openPrimeR'
    finding HTML links ... done
    AnalysisStats                           html  
    Data                                    html  
    Input                                   html  
    Output                                  html  
    Plots                                   html  
    PrimerDesign                            html  
    PrimerEval                              html  
    Primers-method                          html  
    Scoring                                 html  
    Settings                                html  
    Templates-method                        html  
    TemplatesFunctions                      html  
    check_cvg_constraints                   html  
    create_report-Primers-Templates-method
                                            html  
    create_report-list-list-method          html  
    filterLimits-methods                    html  
    filters-methods                         html  
    get_cvg_stats-Primers-method            html  
    get_cvg_stats-list-method               html  
    openPrimeR-package                      html  
    plot_constraint-Primers-method          html  
    plot_constraint-list-method             html  
    plot_constraint_deviation-Primers-method
                                            html  
    plot_constraint_deviation-list-method   html  
    plot_constraint_fulfillment-Primers-method
                                            html  
    plot_constraint_fulfillment-list-method
                                            html  
    plot_cvg_constraints-Primers-method     html  
    plot_cvg_constraints-list-method        html  
    plot_primer_binding_regions-Primers-Templates-method
                                            html  
    plot_primer_binding_regions-list-list-method
                                            html  
    plot_primer_cvg-Primers-Templates-method
                                            html  
    plot_primer_cvg-list-list-method        html  
    plot_template_cvg-Primers-Templates-method
                                            html  
    plot_template_cvg-list-list-method      html  
    runTutorial                             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 'openPrimeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'openPrimeR' as openPrimeR_1.12.1.zip
* DONE (openPrimeR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'openPrimeR' successfully unpacked and MD5 sums checked

Tests output

openPrimeR.Rcheck/tests_i386/testthat.Rout


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

> 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/)
> #test_package("openPrimeR") 
> test_check("openPrimeR")
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
== Skipped tests ===============================================================
* MAFFT not available. (1)
* OligoArrayAux not available. (5)
* On Bioconductor (1)
* Secondary structure tests require ViennaRNA. (1)

[ FAIL 0 | WARN 2 | SKIP 8 | PASS 1467 ]
> 
> proc.time()
   user  system elapsed 
  52.04    2.53   58.26 

openPrimeR.Rcheck/tests_x64/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-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.

> 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/)
> #test_package("openPrimeR") 
> test_check("openPrimeR")
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
== Skipped tests ===============================================================
* MAFFT not available. (1)
* OligoArrayAux not available. (5)
* On Bioconductor (1)
* Secondary structure tests require ViennaRNA. (1)

[ FAIL 0 | WARN 2 | SKIP 8 | PASS 1467 ]
> 
> proc.time()
   user  system elapsed 
  61.18    1.84   75.04 

Example timings

openPrimeR.Rcheck/examples_i386/openPrimeR-Ex.timings

nameusersystemelapsed
AnalysisStats1.710.021.72
Data0.640.020.65
Input2.090.043.38
Output 9.84 1.1922.48
Plots6.320.526.83
PrimerDesign12.70 0.2513.78
PrimerEval4.880.205.08
Primers-method0.030.000.03
Scoring0.030.000.03
Settings0.220.220.67
Templates-method0.010.030.05
TemplatesFunctions0.250.010.27
runTutorial000

openPrimeR.Rcheck/examples_x64/openPrimeR-Ex.timings

nameusersystemelapsed
AnalysisStats3.060.053.11
Data1.110.031.14
Input2.610.052.66
Output15.16 1.3725.30
Plots9.560.389.95
PrimerDesign17.17 0.3117.48
PrimerEval7.160.417.57
Primers-method0.050.000.04
Scoring0.060.000.06
Settings0.330.220.86
Templates-method0.060.000.07
TemplatesFunctions0.410.030.43
runTutorial000