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This page was generated on 2023-01-02 09:00:42 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for openPrimeR on palomino5


To the developers/maintainers of the openPrimeR package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1388/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openPrimeR 1.21.0  (landing page)
Matthias Döring
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/openPrimeR
git_branch: master
git_last_commit: 18b4ee4
git_last_commit_date: 2022-11-01 11:16:20 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: openPrimeR
Version: 1.21.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:openPrimeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings openPrimeR_1.21.0.tar.gz
StartedAt: 2022-12-29 02:02:14 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 02:05:53 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 218.7 seconds
RetCode: 0
Status:   OK  
CheckDir: openPrimeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:openPrimeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings openPrimeR_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/openPrimeR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'openPrimeR/DESCRIPTION' ... OK
* this is package 'openPrimeR' version '1.21.0'
* 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 whether package 'openPrimeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.9Mb
  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
* 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 9.41   0.49    9.95
Output       8.41   0.75   27.40
Plots        5.04   0.23    5.29
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/openPrimeR.Rcheck/00check.log'
for details.



Installation output

openPrimeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL openPrimeR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openPrimeR)

Tests output

openPrimeR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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")
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
[ FAIL 0 | WARN 6 | SKIP 9 | PASS 1467 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• MAFFT not available. (1)
• OligoArrayAux not available. (5)
• On Bioconductor (1)
• Secondary structure tests require ViennaRNA. (1)
• empty test (1)

[ FAIL 0 | WARN 6 | SKIP 9 | PASS 1467 ]
> 
> proc.time()
   user  system elapsed 
  28.62    2.14   38.75 

Example timings

openPrimeR.Rcheck/openPrimeR-Ex.timings

nameusersystemelapsed
AnalysisStats1.240.011.25
Data0.750.030.78
Input1.730.021.77
Output 8.41 0.7527.40
Plots5.040.235.29
PrimerDesign9.410.499.95
PrimerEval3.920.124.05
Primers-method0.020.000.01
Scoring0.030.000.03
Settings0.180.300.72
Templates-method0.010.020.03
TemplatesFunctions0.200.010.22
runTutorial000