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This page was generated on 2024-06-07 20:27 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1477/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openPrimeR 1.26.0  (landing page)
Matthias Döring
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/openPrimeR
git_branch: RELEASE_3_19
git_last_commit: 655b4ae
git_last_commit_date: 2024-04-30 11:00:37 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for openPrimeR on lconway

To the developers/maintainers of the openPrimeR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: openPrimeR
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings openPrimeR_1.26.0.tar.gz
StartedAt: 2024-06-05 22:04:24 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 22:13:20 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 535.3 seconds
RetCode: 0
Status:   OK  
CheckDir: openPrimeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings openPrimeR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/openPrimeR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘openPrimeR/DESCRIPTION’ ... OK
* this is package ‘openPrimeR’ version ‘1.26.0’
* 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 12.1Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata  10.2Mb
* 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 code 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 whether startup messages can be suppressed ... NOTE
The number of cores for was set to '2' by 'parallel_setup()'.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'get_cvg_stats-Primers-method.Rd':
  ‘primer.df’ ‘template.df’

Documented arguments not in \usage in Rd file 'plot_constraint-list-method.Rd':
  ‘constraint.settings’

Documented arguments not in \usage in Rd file 'plot_constraint_deviation-list-method.Rd':
  ‘constraint.df’

Documented arguments not in \usage in Rd file 'plot_primer_cvg-Primers-Templates-method.Rd':
  ‘p.df’ ‘template.df’ ‘excluded.seqs’

Documented arguments not in \usage in Rd file 'plot_template_cvg-list-list-method.Rd':
  ‘colors’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Output       38.134 27.734  47.702
Plots        11.678 35.955  35.283
PrimerDesign 17.501 18.385  51.649
PrimerEval    9.745 17.024  28.730
Settings      1.164  1.881  13.530
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/openPrimeR.Rcheck/00check.log’
for details.


Installation output

openPrimeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL openPrimeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
[ FAIL 0 | WARN 2 | SKIP 8 | PASS 1474 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• MAFFT not available. (1): 'test_primer_design.R:125:9'
• OligoArrayAux not available. (5): 'test_con_dimerization.R:7:9',
  'test_con_dimerization.R:42:9', 'test_con_primer_coverage.R:50:9',
  'test_con_primer_coverage.R:77:9', 'test_con_primer_specificity.R:40:9'
• On Bioconductor (1): 'test_primer_design.R:137:5'
• empty test (1): 'test_primers.R:29:1'

[ FAIL 0 | WARN 2 | SKIP 8 | PASS 1474 ]
> 
> proc.time()
   user  system elapsed 
 67.406  31.140 179.062 

Example timings

openPrimeR.Rcheck/openPrimeR-Ex.timings

nameusersystemelapsed
AnalysisStats1.4130.0211.436
Data0.8970.0420.941
Input1.6160.1291.903
Output38.13427.73447.702
Plots11.67835.95535.283
PrimerDesign17.50118.38551.649
PrimerEval 9.74517.02428.730
Primers-method0.0270.0240.051
Scoring0.0450.0150.060
Settings 1.164 1.88113.530
Templates-method0.0370.0070.045
TemplatesFunctions0.2740.0920.890
runTutorial000