sebastien-plutniak / archeofrag Goto Github PK
View Code? Open in Web Editor NEWR package for Refitting and Spatial Analysis in Archaeology
License: GNU General Public License v3.0
R package for Refitting and Spatial Analysis in Archaeology
License: GNU General Public License v3.0
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:
?archeofrag
). I use usethis::use_package_doc()
to generate this automatically, but I don't think it works without roxygen.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.
Checking package installation as part of the JOSS review openjournals/joss-reviews#4335...
The package is on CRAN (https://cran.r-project.org/web/packages/archeofrag/index.html) but the README only gives instructions for installing the dev version from GitHub. I think install.packages("archeofrag")
is much simpler for less experienced R users (read: most archaeologists!) and could be added.
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.
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.
For openjournals/joss-reviews#4335, typo error:
df.sr
and df.cr
are mispelled in the man/
folder: Line 17 in 6d8a155
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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