Multiple platform build/check report for BioC 3.12 - CHECK report for openPrimeR on tokay1

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

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###
### 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
###
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* 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.

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###
### 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
###
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  % 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


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


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

name	user	system	elapsed
AnalysisStats	1.71	0.02	1.72
Data	0.64	0.02	0.65
Input	2.09	0.04	3.38
Output	9.84	1.19	22.48
Plots	6.32	0.52	6.83
PrimerDesign	12.70	0.25	13.78
PrimerEval	4.88	0.20	5.08
Primers-method	0.03	0.00	0.03
Scoring	0.03	0.00	0.03
Settings	0.22	0.22	0.67
Templates-method	0.01	0.03	0.05
TemplatesFunctions	0.25	0.01	0.27
runTutorial	0	0	0

name	user	system	elapsed
AnalysisStats	3.06	0.05	3.11
Data	1.11	0.03	1.14
Input	2.61	0.05	2.66
Output	15.16	1.37	25.30
Plots	9.56	0.38	9.95
PrimerDesign	17.17	0.31	17.48
PrimerEval	7.16	0.41	7.57
Primers-method	0.05	0.00	0.04
Scoring	0.06	0.00	0.06
Settings	0.33	0.22	0.86
Templates-method	0.06	0.00	0.07
TemplatesFunctions	0.41	0.03	0.43
runTutorial	0	0	0

CHECK report for openPrimeR on tokay1

Summary

Command output

Installation output

Tests output

Example timings