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chopin
: Computation for Climate and Health research On Parallelized INfrastructure
#638
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Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type |
🚀 Editor check started 👋 |
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 |
Thank you @sigmafelix ! |
@ropensci-review-bot seeking reviewers |
Please add this badge to the README of your package repository: [![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/638_status.svg)](https://github.com/ropensci/software-review/issues/638) Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news |
@ropensci-review-bot check package |
Thanks, about to send the query. |
🚀 Editor check started 👋 |
Checks for chopin (v0.6.3.20240515)git hash: 094a6460
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), c (7), lapply (7), by (6), data.frame (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), 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), 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) dplyrleft_join (6), n (2), mutate (1), summarize (1) graphicspoints (8) statsdist (3), quantile (3) 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 |
---|---|---|---|---|---|
9116757038 | pages build and deployment | success | 9e3af8 | 43 | 2024-05-16 |
9116716549 | pkgdown | success | 094a64 | 77 | 2024-05-16 |
9116716555 | R-CMD-check | success | 094a64 | 157 | 2024-05-16 |
9116716552 | test-coverage-local | success | 094a64 | 25 | 2024-05-16 |
3b. goodpractice
results
R CMD check
with rcmdcheck
R CMD check generated the following error:
- checking re-building of vignette outputs ... ERROR
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-gen-points-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 note:
- checking installed package size ... NOTE
installed size is 25.8Mb
sub-directories of 1Mb or more:
data 2.0Mb
extdata 23.1Mb
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 2 potential issues:
message | number of times |
---|---|
Avoid using sapply, consider vapply instead, that's type safe | 1 |
Lines should not be more than 80 characters. This line is 81 characters. | 1 |
Package Versions
package | version |
---|---|
pkgstats | 0.1.5.2 |
pkgcheck | 0.1.2.34 |
Editor-in-Chief Instructions:
Processing may not proceed until the items marked with ✖️ have been resolved.
Hi @sigmafelix ! Thank you! |
@beatrizmilz Thank you for the update. In the most recent version of |
@ropensci-review-bot check package |
Thanks, about to send the query. |
🚀 Editor check started 👋 |
Checks for chopin (v0.7.0.20240525)git hash: 052c8627
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 (10), switch (9), c (7), lapply (7), by (6), unlist (6), nrow (5), which (5), data.frame (4), if (4), names (4), split (4), mapply (3), try (3), abs (2), any (2), as.integer (2), ceiling (2), class (2), expand.grid (2), grep (2), grepl (2), length (2), log10 (2), mode (2), paste (2), round (2), seq (2), seq_len (2), sum (2), t (2), tryCatch (2), unique (2), unname (2), args (1), as.data.frame (1), as.list (1), as.logical (1), as.numeric (1), as.vector (1), exp (1), for (1), formals (1), ifelse (1), intersect (1), lengths (1), matrix (1), ncol (1), paste0 (1), pi (1), rbind (1), Reduce (1), search (1), seq_along (1), sort (1), sprintf (1), startsWith (1), strsplit (1), suppressWarnings (1), table (1), vector (1) terrabuffer (9), crop (8), crs (6), distance (4), ext (4), vect (4), nearby (2), project (2), rast (2), intersect (1), is.lonlat (1), nlyr (1) chopindep_check (14), any_class_args (4), dep_switch (4), datamod (2), get_clip_ext (2), check_subject (1), clip_ras_ext (1), clip_vec_ext (1), crs_check (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) dplyrleft_join (6), n (2), mutate (1), summarize (1) graphicspoints (8) methodsis (4), el (2) statsquantile (3), dist (2) collapserowbind (3) exactextractrexact_extract (3) future.applyfuture_lapply (3) rlanginject (3) anticlustbalanced_clustering (2) igraphgraph_from_edgelist (2) utilscombn (2) 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 |
---|---|---|---|---|---|
9308315230 | pages build and deployment | success | 764f4b | 53 | 2024-05-30 |
9308277371 | pkgdown | success | 052c86 | 88 | 2024-05-30 |
9308277362 | R-CMD-check | success | 052c86 | 168 | 2024-05-30 |
9308277364 | test-coverage-local | success | 052c86 | 36 | 2024-05-30 |
3b. goodpractice
results
R CMD check
with rcmdcheck
R CMD check generated the following note:
- checking installed package size ... NOTE
installed size is 25.7Mb
sub-directories of 1Mb or more:
data 2.0Mb
extdata 23.1Mb
R CMD check generated the following check_fail:
- rcmdcheck_reasonable_installed_size
Test coverage with covr
Package coverage: 98.11
Cyclocomplexity with cyclocomp
The following function have cyclocomplexity >= 15:
function | cyclocomplexity |
---|---|
par_grid | 15 |
Static code analyses with lintr
lintr found the following 7 potential issues:
message | number of times |
---|---|
Avoid library() and require() calls in packages | 7 |
Package Versions
package | version |
---|---|
pkgstats | 0.1.5.2 |
pkgcheck | 0.1.2.41 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
Great! |
@ropensci-review-bot assign @robitalec as reviewer |
@robitalec added to the reviewers list. Review due date is 2024-06-20. Thanks @robitalec for accepting to review! Please refer to our reviewer guide. rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more. |
@robitalec: If you haven't done so, please fill this form for us to update our reviewers records. |
Submitting Author Name: Insang Song
Due date for @robitalec: 2024-06-20Submitting 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: @robitalec
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?
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:
MEE Options
Code of conduct
Thank you very much for your consideration!
The text was updated successfully, but these errors were encountered: