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archeofrag's Issues

Improve description of the package in README and documentation

Checking "statement of need" as part of the JOSS review openjournals/joss-reviews#4335...

I think the purpose of the package is most clearly explained in the DESCRIPTION file. So users can find it more easily, perhaps you could copy this to:

  • The top of README.md
  • A package-level documentation file (i.e. ?archeofrag). I use usethis::use_package_doc() to generate this automatically, but I don't think it works without roxygen.

Is the RBGL dependency absolutely necessary?

Checking package installation as part of the JOSS review openjournals/joss-reviews#4335...

RBGL is not available on CRAN, only BioConductor. This is flagged in the README and the vignette, but I still think it's not ideal. It makes installation more difficult for new users and, I don't know about you, but in ten years of using R for archaeology I've never had to install a package from BioConductor!

I'm not sure how many times functions from RBGL are used (#2 would help with that), but is it at all possible to e.g. substitute them for functions in a package available on CRAN, or copy the functions you need into archaeofrag? RBGL is licensed under https://opensource.org/licenses/Artistic-2.0 which I'm not familiar with though.

Package should import not depend on igraph and RBGL

Checking package installation as part of the JOSS review openjournals/joss-reviews#4335.

igraph and RBGL are specified as Depends in DESCRIPTION, but this is generally recommended against (as explained here: https://r-pkgs.org/namespace.html#search-path).

Converting these to Imports and updating the code to use explicit namespaces (e.g. igraph::graph_from_adjacency_matrix()) would make the code more transparent and avoid unnecessarily loading all of igraph and RBGL (both big packages!) into the global namespace.

No unit tests

Checking tests as part of the JOSS review openjournals/joss-reviews#4335...

The package currently has basic automated tests from the examples in the .Rd files, run on GitHub actions.

You might consider more specific unit tests, especially if you intend to keep developing the package in a way that might break backwards compatibility. I've found testthat + covr to be an effective framework for unit testing. See https://r-pkgs.org/tests.html for a guide.

CRAN check notes

Checking package installation as part of the JOSS review openjournals/joss-reviews/issues/4335.

devtools::check() on the latest version reports two NOTEs for the package:

  • LICENSE is not mentioned in DESCRIPTION (it should be GPL-3 + file LICENSE I believe)
  • CITATION is at the top level of the package instead of in inst/
> devtools::check()
── Building ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── archeofrag ──
Setting env vars:
• CFLAGS    : -Wall -pedantic -fdiagnostics-color=always
• CXXFLAGS  : -Wall -pedantic -fdiagnostics-color=always
• CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/home/joeroe/g/work/dev/archeofrag/DESCRIPTION’ ...
─  preparing ‘archeofrag’:
✔  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes
✔  creating vignettes (18.7s)
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘archeofrag_0.8.tar.gz’
   
── Checking ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── archeofrag ──
Setting env vars:
• _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
• _R_CHECK_CRAN_INCOMING_REMOTE_    : FALSE
• _R_CHECK_CRAN_INCOMING_           : FALSE
• _R_CHECK_FORCE_SUGGESTS_          : FALSE
• NOT_CRAN                          : true
── R CMD check ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/tmp/RtmpLs1SEN/archeofrag.Rcheck’
─  using R version 4.2.0 (2022-04-22)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  using session charset: UTF-8
─  using options ‘--no-manual --as-cran’
✔  checking for file ‘archeofrag/DESCRIPTION’
─  checking extension type ... Package
─  this is package ‘archeofrag’ version ‘0.8’
─  package encoding: UTF-8
✔  checking package namespace information ...
✔  checking package dependencies (584ms)
✔  checking if this is a source package ...
✔  checking if there is a namespace
✔  checking for executable files ...
✔  checking for hidden files and directories
✔  checking for portable file names
✔  checking for sufficient/correct file permissions ...
✔  checking serialization versions
✔  checking whether package ‘archeofrag’ can be installed (2s)
✔  checking installed package size ...
✔  checking package directory ...
✔  checking for future file timestamps ...
✔  checking ‘build’ directory
✔  checking DESCRIPTION meta-information ...
N  checking top-level files ...
   File
     LICENSE
   is not mentioned in the DESCRIPTION file.
   Non-standard file/directory found at top level:
     ‘CITATION’
✔  checking for left-over files
✔  checking index information ...
N  checking package subdirectories ...
   Found the following CITATION file in a non-standard place:
     CITATION
   Most likely ‘inst/CITATION’ should be used instead.
✔  checking R files for non-ASCII characters ...
✔  checking R files for syntax errors ...
✔  checking whether the package can be loaded ...
✔  checking whether the package can be loaded with stated dependencies ...
✔  checking whether the package can be unloaded cleanly ...
✔  checking whether the namespace can be loaded with stated dependencies ...
✔  checking whether the namespace can be unloaded cleanly ...
✔  checking loading without being on the library search path ...
✔  checking dependencies in R code (353ms)
✔  checking S3 generic/method consistency (822ms)
✔  checking replacement functions ...
✔  checking foreign function calls ...
✔  checking R code for possible problems (2.8s)
✔  checking Rd files ...
✔  checking Rd metadata ...
✔  checking Rd line widths ...
✔  checking Rd cross-references ...
✔  checking for missing documentation entries ...
✔  checking for code/documentation mismatches (853ms)
✔  checking Rd \usage sections (924ms)
✔  checking Rd contents ...
✔  checking for unstated dependencies in examples ...
✔  checking contents of ‘data’ directory ...
✔  checking data for non-ASCII characters ...
✔  checking data for ASCII and uncompressed saves ...
✔  checking installed files from ‘inst/doc’ ...
✔  checking files in ‘vignettes’ ...
✔  checking examples (2.1s)
✔  checking for unstated dependencies in vignettes ...
✔  checking package vignettes in ‘inst/doc’ ...
✔  checking re-building of vignette outputs (16.8s)
✔  checking for non-standard things in the check directory
✔  checking for detritus in the temp directory
   
   See
     ‘/tmp/RtmpLs1SEN/archeofrag.Rcheck/00check.log’
   for details.
   
   
── R CMD check results ─────────────────────────────────────────────────────────────────────────────────────────────────────── archeofrag 0.8 ────
Duration: 31.7s

❯ checking top-level files ... NOTE
  File
    LICENSE
  is not mentioned in the DESCRIPTION file.
  Non-standard file/directory found at top level:
    ‘CITATION’

❯ checking package subdirectories ... NOTE
  Found the following CITATION file in a non-standard place:
    CITATION
  Most likely ‘inst/CITATION’ should be used instead.

0 errors ✔ | 0 warnings ✔ | 2 notes ✖

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