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chopin
: Computation for Climate and Health research On Parallelized INfrastructure
#638
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Checks for chopin (v0.6.2.20240423)git hash: 26153abb
Important: All failing checks above must be addressed prior to proceeding Package License: MIT + file LICENSE 1. Package DependenciesDetails of Package Dependency Usage (click to open)
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.
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(<path/to/repo>)', and examining the 'external_calls' table. baselist (9), switch (9), lapply (7), c (6), unlist (6), split (5), which (5), names (4), grepl (3), if (3), mapply (3), nrow (3), abs (2), any (2), as.integer (2), ceiling (2), class (2), data.frame (2), expand.grid (2), log10 (2), mode (2), paste (2), round (2), rownames (2), seq (2), seq_len (2), sum (2), t (2), tryCatch (2), unique (2), args (1), as.data.frame (1), as.logical (1), as.numeric (1), as.vector (1), by (1), exp (1), for (1), formals (1), ifelse (1), intersect (1), lengths (1), pi (1), rbind (1), Reduce (1), search (1), seq_along (1), sort (1), sprintf (1), strsplit (1), suppressWarnings (1), table (1), try (1), vector (1) terrabuffer (9), crop (8), ext (4), rast (4), distance (3), crs (2), nearby (2), project (2), crds (1), intersect (1), is.lonlat (1), nlyr (1) chopindep_check (15), any_class_args (4), dep_switch (4), datamod (2), get_clip_ext (2), clip_ras_ext (1), clip_vec_ext (1), crs_check (1), ext2poly (1), extract_at_buffer_kernel (1), par_group_balanced (1) sfst_crs (3), st_relate (3), st_as_sf (2), st_area (1), st_as_sfc (1), st_bbox (1), st_centroid (1), st_coordinates (1), st_covered_by (1), st_geometry_type (1), st_intersection (1), st_intersects (1), st_make_grid (1), st_transform (1), st_within (1) graphicspoints (8) statsdist (3), quantile (3) dplyrn (2), left_join (1), mutate (1), summarize (1) methodsis (3), el (2) exactextractrexact_extract (3) future.applyfuture_lapply (3) rlanginject (3) igraphgraph_from_edgelist (2) utilscombn (2) anticlustbalanced_clustering (1) starsst_as_stars (1) 2. Statistical PropertiesThis package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing. Details of statistical properties (click to open)
The package has:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
|
id | name | conclusion | sha | run_number | date |
---|---|---|---|---|---|
8817187321 | pages build and deployment | success | a8aaed | 33 | 2024-04-24 |
8817133786 | pkgdown | success | 26153a | 69 | 2024-04-24 |
8817133742 | R-CMD-check | success | 26153a | 149 | 2024-04-24 |
8817133730 | test-coverage-local | success | 26153a | 17 | 2024-04-24 |
3b. goodpractice
results
R CMD check
with rcmdcheck
R CMD check generated the following notes:
- checking installed package size ... NOTE
installed size is 25.6Mb
sub-directories of 1Mb or more:
data 2.0Mb
extdata 23.1Mb - checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
...
--- re-building ‘v00_good_practice_parallelization.Rmd’ using rmarkdown
--- finished re-building ‘v00_good_practice_parallelization.Rmd’
--- re-building ‘v01_par_make_gridset.Rmd’ using rmarkdown
File figures/nc-load-1.png not found in resource path
Error: processing vignette 'v01_par_make_gridset.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v01_par_make_gridset.Rmd’
--- re-building ‘v02_climate_examples.Rmd’ using rmarkdown
File figures/climate-se-states.png not found in resource path
Error: processing vignette 'v02_climate_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v02_climate_examples.Rmd’
SUMMARY: processing the following files failed:
‘v01_par_make_gridset.Rmd’ ‘v02_climate_examples.Rmd’
Error: Vignette re-building failed.
Execution halted
R CMD check generated the following check_fail:
- rcmdcheck_reasonable_installed_size
Test coverage with covr
Package coverage: 99.65
Cyclocomplexity with cyclocomp
No functions have cyclocomplexity >= 15
Static code analyses with lintr
lintr found the following 1 potential issues:
message | number of times |
---|---|
Lines should not be more than 80 characters. | 1 |
Package Versions
package | version |
---|---|
pkgstats | 0.1.3.13 |
pkgcheck | 0.1.2.21 |
Editor-in-Chief Instructions:
Processing may not proceed until the items marked with ✖️ have been resolved.
@ropensci-review-bot check package |
Thanks, about to send the query. |
🚀 Editor check started 👋 |
Checks for chopin (v0.6.2.20240423)git hash: c0e53b6e
Package License: MIT + file LICENSE 1. Package DependenciesDetails of Package Dependency Usage (click to open)
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.
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(<path/to/repo>)', and examining the 'external_calls' table. baselist (9), switch (9), lapply (7), c (6), unlist (6), split (5), which (5), names (4), grepl (3), if (3), mapply (3), nrow (3), abs (2), any (2), as.integer (2), ceiling (2), class (2), data.frame (2), expand.grid (2), log10 (2), mode (2), paste (2), round (2), rownames (2), seq (2), seq_len (2), sum (2), t (2), tryCatch (2), unique (2), args (1), as.data.frame (1), as.logical (1), as.numeric (1), as.vector (1), by (1), exp (1), for (1), formals (1), ifelse (1), intersect (1), lengths (1), pi (1), rbind (1), Reduce (1), search (1), seq_along (1), sort (1), sprintf (1), strsplit (1), suppressWarnings (1), table (1), try (1), vector (1) terrabuffer (9), crop (8), ext (4), rast (4), distance (3), crs (2), nearby (2), project (2), crds (1), intersect (1), is.lonlat (1), nlyr (1) chopindep_check (15), any_class_args (4), dep_switch (4), datamod (2), get_clip_ext (2), clip_ras_ext (1), clip_vec_ext (1), crs_check (1), ext2poly (1), extract_at_buffer_kernel (1), par_group_balanced (1) sfst_crs (3), st_relate (3), st_as_sf (2), st_area (1), st_as_sfc (1), st_bbox (1), st_centroid (1), st_coordinates (1), st_covered_by (1), st_geometry_type (1), st_intersection (1), st_intersects (1), st_make_grid (1), st_transform (1), st_within (1) graphicspoints (8) statsdist (3), quantile (3) dplyrn (2), left_join (1), mutate (1), summarize (1) methodsis (3), el (2) exactextractrexact_extract (3) future.applyfuture_lapply (3) rlanginject (3) igraphgraph_from_edgelist (2) utilscombn (2) anticlustbalanced_clustering (1) starsst_as_stars (1) 2. Statistical PropertiesThis package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing. Details of statistical properties (click to open)
The package has:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
|
id | name | conclusion | sha | run_number | date |
---|---|---|---|---|---|
8818976584 | pages build and deployment | success | 1b88a2 | 36 | 2024-04-24 |
8818927586 | pkgdown | success | f8c659 | 71 | 2024-04-24 |
8818927598 | R-CMD-check | success | f8c659 | 151 | 2024-04-24 |
8818927585 | test-coverage-local | success | f8c659 | 19 | 2024-04-24 |
3b. goodpractice
results
R CMD check
with rcmdcheck
R CMD check generated the following notes:
- checking installed package size ... NOTE
installed size is 25.6Mb
sub-directories of 1Mb or more:
data 2.0Mb
extdata 23.1Mb - checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
...
--- re-building ‘v00_good_practice_parallelization.Rmd’ using rmarkdown
--- finished re-building ‘v00_good_practice_parallelization.Rmd’
--- re-building ‘v01_par_make_gridset.Rmd’ using rmarkdown
File figures/nc-load-1.png not found in resource path
Error: processing vignette 'v01_par_make_gridset.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v01_par_make_gridset.Rmd’
--- re-building ‘v02_climate_examples.Rmd’ using rmarkdown
File figures/climate-se-states.png not found in resource path
Error: processing vignette 'v02_climate_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v02_climate_examples.Rmd’
SUMMARY: processing the following files failed:
‘v01_par_make_gridset.Rmd’ ‘v02_climate_examples.Rmd’
Error: Vignette re-building failed.
Execution halted
R CMD check generated the following check_fail:
- rcmdcheck_reasonable_installed_size
Test coverage with covr
Package coverage: 99.65
Cyclocomplexity with cyclocomp
No functions have cyclocomplexity >= 15
Static code analyses with lintr
lintr found the following 1 potential issues:
message | number of times |
---|---|
Lines should not be more than 80 characters. | 1 |
Package Versions
package | version |
---|---|
pkgstats | 0.1.3.13 |
pkgcheck | 0.1.2.21 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
@ropensci-review-bot help |
Hello @sigmafelix, here are the things you can ask me to do:
|
@ropensci-review-bot submit response #638 (comment) |
Couldn't find entry for chopin in the packages log |
@ropensci-review-bot assign @beatrizmilz as editor |
Assigned! @beatrizmilz is now the editor |
Hello @sigmafelix ! Editor checks:
Editor comments
Can you please address these comments? |
@beatrizmilz I appreciate your time to review our package. I will address all your points in the revision on top of fixing some bugs we identified in the meantime and respond to you soon. Thank you. |
@beatrizmilz Thank you for your patience. I think I addressed all comments in the current version available in |
Submitting Author Name: Insang Song
Submitting Author Github Handle: @sigmafelix
Other Package Authors Github handles: (comma separated, delete if none) @kyle-messier
Repository: https://github.com/NIEHS/chopin
Version submitted: 0.6.2.20240423
Submission type: Standard
Editor: @beatrizmilz
Reviewers: TBD
Archive: TBD
Version accepted: TBD
Language: en
Scope
Please 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):
:
chopin
supports parallel processing for functions in popular spatial data manipulation packagessf
andterra
on a high-level parallelization frameworkfuture
. This feature fits to the geospatial data category.Who is the target audience and what are scientific applications of this package?
: Our first target audience group is spatial epidemiologists and health geographers who want to calculating spatial covariates from spatial and spatiotemporal datasets including climate, transportation, demographics, topography, hydrography, and others. We expect that users are cognizant of basic geographic information system/science. The wider audience could take advantage of the flexibility of this package for expediting spatial operations.
Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
: A selection of functions in
terra
(e.g.,*app
andpredict
) supports internal parallelization, where a single dataset is accepted. To the best of our knowledge, no packaged solution exists for parallelization of spatial operations where two datasets are involved. sprawl (GitHub-only; not maintained) partially overlaps this package's functionality in that it includes convenience functions connecting multiple basic spatial operations. Besides the R functions, a handful of teaching or demonstration materials briefly covered parallelization of spatial data applications ([1], [2], [3]).(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
: Not applicable
If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
: Presubmission inquiry of the previous version of this package -- Presubmission inquiry:
chopin
#630 commented by @ldecicco-USGSExplain reasons for any
pkgcheck
items which your package is unable to pass.: Coverage rate (99%) and installation size (25.7 MB; of which data (2.0 MB) and extdata (23.1 MB) exceeded recommended sizes) resulted in notes.
Technical checks
Confirm each of the following by checking the box.
This package:
Publication options
Do you intend for this package to go on CRAN?
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Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
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Thank you very much for your consideration!
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