adokter
commented
6 years ago You might want to check whether it is not a problem that our package uses an external Docker image that contains an important part of the code and functionality
Open peterdesmet opened 6 years ago
adokter
commented
6 years ago You might want to check whether it is not a problem that our package uses an external Docker image that contains an important part of the code and functionality
peterdesmet
commented
1 year ago Below is the full template for submitting an rOpenSci package for review. @adokter I suggest we edit this comment in preparation for submission. We should tackle all TODOs
Submitting Author Name: Adriaan Dokter Submitting Author Github Handle: !--author1-->@adokter<!--end-author1-- Other Package Authors Github handles: (comma separated, delete if none) @peterdesmet, @github_handle2, TODO Repository: https://github.com/adokter/bioRad/ Version submitted: TODO Submission type: Standard Editor: TBD Reviewers: TBD
Archive: TBD Version accepted: TBD Language: en
TODOPlease indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
TODO
TODO
TODO
Not applicable
Not applicable
pkgcheck items which your package is unable to pass.TODO
Confirm each of the following by checking the box.
TODO
This package:
TODO
[x] Do you intend for this package to go on CRAN?
[ ] Do you intend for this package to go on Bioconductor?
[ ] Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
PietrH
commented
1 year ago We could consider using the rOpenSci github action for pkgcheck to check on our current status: https://docs.ropensci.org/pkgcheck/
I've generated a report locally and I'll include it below:
git hash: 52616411
Important: All failing checks above must be addressed prior to proceeding
(Checks marked with :eyes: may be optionally addressed.)
Package License: MIT + file LICENSE
The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.
|type |package | ncalls|
|:----------|:-----------|------:|
|internal |base | 1036|
|internal |bioRad | 240|
|internal |grDevices | 11|
|imports |stats | 78|
|imports |methods | 29|
|imports |raster | 28|
|imports |dplyr | 25|
|imports |glue | 7|
|imports |graphics | 6|
|imports |lubridate | 5|
|imports |utils | 4|
|imports |rlang | 3|
|imports |lutz | 2|
|imports |maptools | 2|
|imports |viridis | 2|
|imports |curl | 1|
|imports |readr | 1|
|imports |tidyr | 1|
|imports |viridisLite | 1|
|imports |assertthat | NA|
|imports |fields | NA|
|imports |ggplot2 | NA|
|imports |rgdal | NA|
|imports |rhdf5 | NA|
|imports |sp | NA|
|suggests |vol2birdR | 7|
|suggests |aws.s3 | 4|
|suggests |ggmap | 2|
|suggests |tidyselect | 2|
|suggests |knitr | NA|
|suggests |rmarkdown | NA|
|suggests |testthat | NA|
|suggests |vdiffr | NA|
|linking_to |NA | NA|
Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(
c (89), data.frame (77), sapply (58), list (49), file (42), length (42), lapply (33), max (33), attributes (31), min (29), paste (23), unique (22), dim (18), do.call (18), range (18), for (17), seq (17), names (15), seq_along (14), by (12), ifelse (12), pi (12), scan (12), is.null (11), as.numeric (10), as.POSIXct (10), colSums (10), row (10), which (10), format (9), nrow (9), F (8), t (8), col (7), if (7), rep (7), as.Date (6), date (6), dir (6), getOption (6), pmin (6), T (6), as.data.frame (5), attr (5), basename (5), cbind (5), gsub (5), ncol (5), source (5), suppressWarnings (5), tryCatch (5), units (5), apply (4), cos (4), cumsum (4), eval (4), matrix (4), sin (4), sum (4), tempfile (4), abs (3), all (3), atan2 (3), difftime (3), expand.grid (3), labels (3), mapply (3), paste0 (3), rbind (3), rowSums (3), substring (3), unlist (3), url (3), withCallingHandlers (3), as.integer (2), as.list (2), findInterval (2), floor (2), is.na (2), levels (2), mean (2), pmax (2), row.names (2), setdiff (2), sort (2), sprintf (2), stopifnot (2), strsplit (2), substitute (2), substr (2), vapply (2), which.min (2), all.equal (1), args (1), as.character (1), as.difftime (1), as.double (1), as.vector (1), ceiling (1), character (1), colnames (1), diff (1), dirname (1), drop (1), file.path (1), integer (1), is.finite (1), is.nan (1), load (1), match (1), months (1), nchar (1), normalizePath (1), order (1), q (1), seq_len (1), sqrt (1), startsWith (1), suppressMessages (1), Sys.info (1), table (1), UseMethod (1), warning (1)
get_quantity (26), add_expected_eta_to_scan (7), rcs (7), scan_to_raster (6), sunrise (6), sunset (6), map (5), sd_vvp_threshold (5), check_night (4), error (4), errorf (4), polar_to_index (4), beam_profile_overlap_help (3), cartesian_to_polar (3), color_scale_fill (3), combined_heights (3), earth_radius (3), get_odim_object_type (3), add_color_transparency (2), beam_distance (2), beam_height (2), beam_profile (2), beam_profile_overlap (2), beam_range (2), calculate_vp (2), extract_string (2), get_elevation_angles (2), integrate_profile.vp (2), is.vp (2), is.vpts (2), match_filenames (2), proj_to_wgs (2), sample_polar (2), scan_to_spatial (2), add_heights_vp (1), add_heights_vpts (1), apply_mistnet (1), apply_mistnet_body (1), as.data.frame.vp (1), as.data.frame.vpts (1), beam_height_internal (1), beam_width (1), beam_width_internal (1), bind_into_vpts (1), bind_into_vpts.list (1), bind_into_vpts.vp (1), bind_into_vpts.vpts (1), c.vp (1), calculate_param (1), calculate_param.ppi (1), calculate_param.pvol (1), calculate_param.scan (1), check_date_format (1), check_docker (1), check_night.default (1), check_night.list (1), check_night.pvol (1), check_night.vp (1), check_night.vpi (1), check_night.vpts (1), check_radar_codes (1), col_func (1), color_palette (1), color_palette_to_scale_colour (1), color_scale (1), convert_legacy (1), convert_legacy.vp (1), convert_legacy.vpts (1), dbz_to_eta (1), dim.ppi (1), dim.pvol (1), dim.scan (1), dim.vp (1), dim.vpts (1), download_basemap (1), download_pvolfiles (1), download_vpfiles (1), doy (1), doy.default (1), doy.pvol (1), doy.vp (1), doy.vpi (1), doy.vpts (1), eta_expected (1), eta_to_dbz (1), filter_vpts (1), format_reason_vol2bird (1), gaussian_beam_profile (1), gaussian_beam_profile_internal (1), get_elevation_angles.param (1), get_elevation_angles.pvol (1), get_elevation_angles.scan (1), get_iris_raw_task (1), get_param (1), get_quantity.list (1), get_quantity.vp (1), get_quantity.vpts (1), get_scan (1), get_zlim (1), integrate_profile (1), integrate_profile.list (1), integrate_profile.vpts (1), integrate_to_ppi (1), is.na2 (1), is.nan.data.frame (1), is.odimfile (1), is.param (1), is.ppi (1), is.pvol (1), is.pvolfile (1), is.scan (1), is.vpfile (1), is.vpi (1), list_vpts_aloft (1), map.ppi (1), nexrad_to_odim (1), noy (1), noy.default (1), noy.pvol (1), noy.vp (1), noy.vpi (1), noy.vpts (1), nyquist_velocity (1), plot_wind_barbs (1), plot.ppi (1), plot.scan (1), plot.vp (1), plot.vpi (1), plot.vpts (1), print.param (1), print.ppi (1), print.pvol (1), print.scan (1), print.vp (1), print.vpts (1), project_as_ppi (1), read_pvolfile (1), read_vp (1), read_vpfiles (1), wgs_to_proj (1)
rt (26), offset (18), ts (12), dt (6), profile (4), weighted.mean (4), df (3), median (2), approx (1), cov (1), step (1)
is (18), as (11)
raster (9), brick (5), extent (4), as.data.frame (3), flip (2), crs (1), projection (1), rasterToPoints (1), setValues (1), weighted.mean (1)
join (9), left_join (9), bind_rows (4), distinct (1), if_else (1), pull (1)
colors (4), palette (3), colours (2), col2rgb (1), rgb (1)
glue (3), glue_collapse (3), backtick (1)
vol2bird_config (4), rsl2odim (3)
grid (5), par (1)
ym (2), ceiling_date (1), floor_date (1), make_difftime (1)
get_bucket_df (3), bucket_exists (1)
read.table (2), read.csv (1), txtProgressBar (1)
check_installed (2), expr (1)
calc_zoom (1), get_map (1)
tz_lookup_coords (2)
crepuscule (2)
eval_select (2)
scale_colour_viridis (1), scale_fill_viridis (1)
curl_fetch_disk (1)
read_lines (1)
fill (1)
viridis (1)
base
bioRad
stats
methods
raster
dplyr
grDevices
glue
vol2birdR
graphics
lubridate
aws.s3
utils
rlang
ggmap
lutz
maptools
tidyselect
viridis
curl
readr
tidyr
**NOTE:** Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.
viridisLite
This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.
The package has: - code in R (100% in 61 files) and - 3 authors - 3 vignettes - 3 internal data files - 22 imported packages - 151 exported functions (median 7 lines of code) - 254 non-exported functions in R (median 9 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|-------:|----------:|:----------| |files_R | 61| 97.3| | |files_vignettes | 3| 92.4| | |files_tests | 58| 99.4| | |loc_R | 4970| 95.3|TRUE | |loc_vignettes | 438| 74.8| | |loc_tests | 1937| 93.9| | |num_vignettes | 3| 94.2| | |data_size_total | 1451194| 96.5|TRUE | |data_size_median | 544736| 97.2|TRUE | |n_fns_r | 405| 96.2|TRUE | |n_fns_r_exported | 151| 97.6|TRUE | |n_fns_r_not_exported | 254| 95.2|TRUE | |n_fns_per_file_r | 4| 58.9| | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 8| 20.0| | |loc_per_fn_r_exp | 7| 13.5| | |loc_per_fn_r_not_exp | 9| 27.1| | |rel_whitespace_R | 10| 88.5| | |rel_whitespace_vignettes | 48| 85.6| | |rel_whitespace_tests | 15| 89.8| | |doclines_per_fn_exp | 52| 65.3| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 228| 89.9| | ---
Github doesn't allow uploading html files!
goodpractice and other checks--- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following error: 1. checking PDF version of manual without index ... ERROR Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Converting parsed Rd's to LaTeX ........ Creating pdf output from LaTeX ... Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -Rf /tmp/RtmpD2FFw2/Rd2pdf829f681852ef' R CMD check generated the following warning: 1. checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. R CMD check generated the following check_fails: 1. cyclocomp 2. no_import_package_as_a_whole 3. rcmdcheck_can_convert_rd_to_pdf_2 #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 68.28 The following files are not completely covered by tests: file | coverage --- | --- R/apply_mistnet.R | 0% R/bioRad-deprecated.R | 0% R/color_scale.R | 29.31% R/composite_ppi.R | 0% R/download_basemap.R | 0% R/download_vpfiles.R | 43.1% R/filter_vpts.R | 66.67% R/iris.R | 0% R/map.R | 0% R/nexrad_odim.R | 0% R/nyquist_velocity.R | 0% R/plot.vpi.R | 61.33% R/plot.vpts.R | 69.01% R/read_cajun.R | 0% R/read_vpts.R | 0% R/select_vpfiles.R | 0% #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- composite_ppi | 54 read_pvolfile_body | 46 integrate_to_ppi | 45 plot.vpts | 45 scan_to_raster | 44 plot_wind_barbs | 43 read_vpts | 41 plot.vpi | 37 get_zlim | 31 calculate_vp | 24 filter_vpts | 22 map.ppi | 21 scan_to_spdf | 20 add_expected_eta_to_scan | 19 download_basemap | 17 beam_profile_overlap | 16 regularize_vpts | 16 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 714 potential issues: message | number of times --- | --- Avoid 1:length(...) expressions, use seq_len. | 9 Avoid 1:nrow(...) expressions, use seq_len. | 1 Avoid changing the working directory, or restore it in on.exit | 1 Avoid library() and require() calls in packages | 4 Avoid trailing semicolons, they are not needed. | 1 Avoid using sapply, consider vapply instead, that's type safe | 50 Lines should not be more than 80 characters. | 612 Use <-, not ->, for assignment. | 2 Use <-, not =, for assignment. | 34
:heavy_multiplication_x: Package contains the following (potentially) obsolete packages: - sp - maptools - rgdal See our [Recommended Scaffolding](https://devguide.ropensci.org/building.html?q=scaffol#recommended-scaffolding) for alternatives. :heavy_multiplication_x: The following 5 function names are duplicated in other packages: - - `doy` from solaR - - `get_param` from EpiModel, gplite, ldamatch, mapbayr, phenofit - - `map` from aphid, arakno, BGData, BGGM, bgmm, bReeze, gapmap, html5, jqr, kohonen, listenv, mapfit, maps, mclust, missSOM, mlr3misc, modchart, narray, neuroim, onemap, OpenRepGrid, pomp, purrr, Qtools, SpatialExtremes, spidR, tipsae, Z10 - - `rcs` from dplR, rms - - `sunrise` from reactablefmtr
|package |version | |:--------|:--------| |pkgstats |0.1.1 | |pkgcheck |0.1.1.20 |
Guide: https://ropensci.github.io/dev_guide/index.html. Things I noticed that might not be covered yet:
codemeta.jsonusingcodemetar::write_codemeta(): 5683c0dmessage()andwarning()to communicate with the userstyler::style_pkg(filetype = c("R", "Rmd")): dc9dff6goodpractice::gp(): getting