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CHECK report for openPrimeR on tokay2

This page was generated on 2020-10-17 11:57:19 -0400 (Sat, 17 Oct 2020).

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 1237/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openPrimeR 1.10.4
Matthias Döring
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/openPrimeR
Branch: RELEASE_3_11
Last Commit: b79ca1e
Last Changed Date: 2020-08-14 03:49:12 -0400 (Fri, 14 Aug 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: openPrimeR
Version: 1.10.4
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings openPrimeR_1.10.4.tar.gz
StartedAt: 2020-10-17 06:38:15 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:47:50 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 575.1 seconds
RetCode: 0
Status:  OK  
CheckDir: openPrimeR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings openPrimeR_1.10.4.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/openPrimeR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.10.4'
* 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
Output       12.57   1.78   55.01
PrimerDesign 13.44   0.38   14.54
PrimerEval    6.97   0.20    7.18
Plots         6.63   0.47    7.10
Input         2.32   0.12    6.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
PrimerDesign 17.48   0.25   17.82
Output       15.10   1.42   44.89
Plots         7.72   0.44    8.16
PrimerEval    7.87   0.26    8.10
* 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-3.11-bioc/meat/openPrimeR.Rcheck/00check.log'
for details.



Installation output

openPrimeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/openPrimeR_1.10.4.tar.gz && rm -rf openPrimeR.buildbin-libdir && mkdir openPrimeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openPrimeR.buildbin-libdir openPrimeR_1.10.4.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL openPrimeR_1.10.4.zip && rm openPrimeR_1.10.4.tar.gz openPrimeR_1.10.4.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 1772k  100 1772k    0     0  24.3M      0 --:--:-- --:--:-- --:--:-- 26.6M

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
Melting not available
ViennaRNA not available
OligoArrayAux not available
** testing if installed package can be loaded from final location
Melting not available
ViennaRNA not available
OligoArrayAux not available
** 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
Melting not available
ViennaRNA not available
OligoArrayAux not available
* MD5 sums
packaged installation of 'openPrimeR' as openPrimeR_1.10.4.zip
* DONE (openPrimeR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'openPrimeR' successfully unpacked and MD5 sums checked

Tests output

openPrimeR.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
Melting not available
ViennaRNA not available
OligoArrayAux not available
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")
== testthat results  ===========================================================
[ OK: 1467 | SKIPPED: 8 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  50.01    2.60   74.90 

openPrimeR.Rcheck/tests_x64/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-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
Melting not available
ViennaRNA not available
OligoArrayAux not available
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")
== testthat results  ===========================================================
[ OK: 1467 | SKIPPED: 8 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  54.29    1.96   78.12 

Example timings

openPrimeR.Rcheck/examples_i386/openPrimeR-Ex.timings

nameusersystemelapsed
AnalysisStats1.410.011.42
Data0.510.020.54
Input2.320.126.70
Output12.57 1.7855.01
Plots6.630.477.10
PrimerDesign13.44 0.3814.54
PrimerEval6.970.207.18
Primers-method0.030.000.03
Scoring0.030.020.04
Settings0.400.401.13
Templates-method0.050.020.06
TemplatesFunctions0.450.030.49
runTutorial000

openPrimeR.Rcheck/examples_x64/openPrimeR-Ex.timings

nameusersystemelapsed
AnalysisStats1.910.021.92
Data0.600.010.63
Input1.580.041.61
Output15.10 1.4244.89
Plots7.720.448.16
PrimerDesign17.48 0.2517.82
PrimerEval7.870.268.10
Primers-method0.000.030.03
Scoring0.040.000.03
Settings0.310.140.78
Templates-method0.030.030.06
TemplatesFunctions0.450.020.47
runTutorial000