package testing

---

To get a feel for the various options for testing, I played around with all the options suggested.

First, I downloaded all the source code from github into pkg/ and unzipped, renaming the unzipped dir from codemetar-master/ to codemetar.

---

cmd line testing

Then in the terminal, I navigated to dir pkg/

build package:

Anna [master|✚ 2…190]

    17:27 $ R CMD build codemetar
    * checking for file ‘codemetar/DESCRIPTION’ ... OK
    * preparing ‘codemetar’:
    * checking DESCRIPTION meta-information ... OK
    * installing the package to build vignettes
    * creating vignettes ... OK
    * checking for LF line-endings in source and make files
    * checking for empty or unneeded directories
    * looking to see if a ‘data/datalist’ file should be added
    * building ‘codemetar_0.1.0.tar.gz’

All ok

check package

Anna [master|✚ 2…190]

    17:29 $ R CMD check codemetar_0.1.0.tar.gz
    * using log directory ‘/Users/Anna/Documents/workflows/rOpenSci/codemetar-review/pkg/codemetar.Rcheck’
    * using R version 3.4.1 (2017-06-30)
    * using platform: x86_64-apple-darwin15.6.0 (64-bit)
    * using session charset: UTF-8
    * checking for file ‘codemetar/DESCRIPTION’ ... OK
    * checking extension type ... Package
    * this is package ‘codemetar’ version ‘0.1.0’
    * 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 executable files ... OK
    * checking for hidden files and directories ... OK
    * checking for portable file names ... OK
    * checking for sufficient/correct file permissions ... OK
    * checking whether package ‘codemetar’ can be installed ... OK
    * checking installed package size ... OK
    * 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 loading without being on the library search path ... 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 R/sysdata.rda ... OK
    * checking installed files from ‘inst/doc’ ... OK
    * checking files in ‘vignettes’ ... OK
    * checking examples ... OK
    * 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 ...
       ‘codemeta-intro.Rmd’ using ‘UTF-8’ ... OK
       ‘codemeta-parsing.Rmd’ using ‘UTF-8’ ... OK
       ‘translating.Rmd’ using ‘UTF-8’ ... OK
       ‘validation-in-json-ld.Rmd’ using ‘UTF-8’ ... OK
     NONE
    * checking re-building of vignette outputs ... OK
    * checking PDF version of manual ... OK
    * DONE
    
    Status: OK

---

testing in Rstudio (from within notebook)

ran devtools test and check

library(devtools)
devtools::check("../pkg/codemetar")

Updating codemetar documentation

Loading codemetar

Setting env vars ---------------------------------------------------------

CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic

Building codemetar -------------------------------------------------------

'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file  \
  --no-environ --no-save --no-restore --quiet CMD build  \
  '/Users/Anna/Documents/workflows/rOpenSci/codemetar-review/pkg/codemetar'  \
  --no-resave-data --no-manual 

Setting env vars ---------------------------------------------------------

_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE

Checking codemetar -------------------------------------------------------

'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file  \
  --no-environ --no-save --no-restore --quiet CMD check  \
  '/var/folders/8p/87cqdx2s34vfvcgh04l6z72w0000gr/T//RtmplZ2dJ9/codemetar_0.1.0.tar.gz'  \
  --as-cran --timings --no-manual 

R CMD check results

0 errors | 0 warnings | 0 notes

devtools::test("../pkg/codemetar")

Loading codemetar

Loading required package: testthat

Testing codemetar

cloned repo: ..
codemeta_description.R: 
validate: ..
crosswalk.R: ....
test frame: ....
guess_metadata: ........
test-many-packages: S
parse citation: .
parse_depends.R: ....
parse_people.R: ....
spdx_license.R: ..
utils.R: ..
write_codemeta: ...W.W.

Skipped -------------------------------------------------------------------
1. Test the creation of codemeta for many packages (@test-many-packages.R#11) - not also testing against 100 random installed packages today...,
    consider testing that locally instead

Warnings ------------------------------------------------------------------
1. We can parse author lists
                    that use Authors@R, Authors, or both (@test-write_codemeta.R#64) - the condition has length > 1 and only the first element will be used

2. We can parse author lists
                    that use Authors@R, Authors, or both (@test-write_codemeta.R#77) - the condition has length > 1 and only the first element will be used

DONE ======================================================================

ran goodpractice checks

library(goodpractice)
gp("../pkg/codemetar")

Preparing: covr

Preparing: cyclocomp

Skipping 1 packages ahead of CRAN: Rcpp

Preparing: description

Preparing: lintr

Preparing: namespace

Preparing: rcmdcheck

── GP codemetar ───────────────────────────────────────────────────────────

It is good practice to

  ✖ write unit tests for all functions, and all package code in
    general. 98% of code lines are covered by test cases.

    R/codemeta_description.R:24:NA
    R/codemeta_validate.R:23:NA
    R/guess_metadata.R:127:NA
    R/guess_metadata.R:144:NA
    R/parse_citation.R:77:NA
    ... and 2 more lines

─────────────────────────────────────────────────────────────────────────── 

Also performed checks using testthat on the installed package from github

library(testthat)
library(codemetar)
test_package("codemetar")

cloned repo: ..
codemeta_description.R: 
validate: ..
crosswalk.R: ....
test frame: ....
guess_metadata: ........
test-many-packages: S
parse citation: .
parse_depends.R: ....
parse_people.R: ....
spdx_license.R: ..
utils.R: ..
write_codemeta: ...W.W.

Skipped -------------------------------------------------------------------
1. Test the creation of codemeta for many packages (@test-many-packages.R#7) - On CRAN

Warnings ------------------------------------------------------------------
1. We can parse author lists
                    that use Authors@R, Authors, or both (@test-write_codemeta.R#64) - the condition has length > 1 and only the first element will be used

2. We can parse author lists
                    that use Authors@R, Authors, or both (@test-write_codemeta.R#77) - the condition has length > 1 and only the first element will be used

DONE ======================================================================

This is essentially what is launched when running devtools::test()