pkgcheck results - main

[github-actions]

Checks for gtexr (v0.2.0.9001)

git hash: b9421b16

• ✔️ Package is already on CRAN.
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 100%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Function names are duplicated in other packages

(Checks marked with 👀 may be optionally addressed.)

Package License: MIT + file LICENSE

---

1. Package Dependencies

Details 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.

type	package	ncalls
internal	base	60
internal	gtexr	37
internal	utils	10
internal	stats	1
imports	rlang	19
imports	tibble	12
imports	cli	8
imports	purrr	7
imports	dplyr	4
imports	httr2	2
imports	tidyr	2
suggests	curl	NA
suggests	httptest2	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	spelling	NA
suggests	stringr	NA
suggests	testthat	NA
suggests	withr	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(<path/to/repo>)', and examining the 'external_calls' table.

base

c (14), list (10), as.integer (4), as.numeric (4), names (4), url (4), call (3), class (3), message (3), tryCatch (3), with (2), gsub (1), ifelse (1), length (1), options (1), unlist (1), which (1)

gtexr

calculate_expression_quantitative_trait_loci (1), calculate_splicing_quantitative_trait_loci (1), convert_null_to_na (1), download (1), get_annotation (1), get_clustered_median_exon_expression (1), get_clustered_median_gene_expression (1), get_clustered_median_junction_expression (1), get_clustered_median_transcript_expression (1), get_collapsed_gene_model_exon (1), get_dataset_info (1), get_downloads_page_data (1), get_eqtl_genes (1), get_exons (1), get_expression_pca (1), get_file_list (1), get_fine_mapping (1), get_full_get_collapsed_gene_model_exon (1), get_functional_annotation (1), get_gene_expression (1), get_gene_search (1), get_genes (1), get_genomic_features (1), get_gwas_catalog_by_location (1), get_image (1), get_independent_eqtl (1), get_linkage_disequilibrium_by_variant_data (1), get_linkage_disequilibrium_data (1), get_maintenance_message (1), get_median_exon_expression (1), get_median_gene_expression (1), get_median_junction_expression (1), get_median_transcript_expression (1), get_multi_tissue_eqtls (1), gtexr_arguments (1), name_unnamed_items (1), perform_gtex_request_json (1)

rlang

caller_env (10), env_get (7), caller_fn (1), fn_fmls_names (1)

tibble

tibble (12)

utils

data (5), packageDescription (4), page (1)

cli

format_inline (7), cli_warn (1)

purrr

map (3), map_depth (2), map_at (1), set_names (1)

dplyr

mutate (3), bind_rows (1)

httr2

req_error (1), request (1)

tidyr

unnest (2)

stats

start (1)

---

2. Statistical Properties

This 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:

• code in R (100% in 61 files) and
• 5 authors
• 2 vignettes
• no internal data file
• 7 imported packages
• 55 exported functions (median 5 lines of code)
• 144 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

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	96.9
files_inst	2	96.8
files_vignettes	2	82.0
files_tests	62	99.4
loc_R	1204	70.7
loc_inst	365	62.0
loc_vignettes	154	38.6
loc_tests	1987	92.2
num_vignettes	2	85.5
n_fns_r	199	88.5
n_fns_r_exported	55	88.7
n_fns_r_not_exported	144	88.3
n_fns_per_file_r	2	31.1
num_params_per_fn	7	84.0
loc_per_fn_r	8	20.2
loc_per_fn_r_exp	5	8.4
loc_per_fn_r_not_exp	9	27.3
rel_whitespace_R	9	52.1
rel_whitespace_inst	19	62.9
rel_whitespace_vignettes	26	28.9
rel_whitespace_tests	11	84.4
doclines_per_fn_exp	53	65.9
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	70	72.0

---

2a. Network visualisation

An interactive visualisation of calls between objects in the package has been uploaded as a workflow artefact. To view it, click on results from the latest 'pkgcheck' action, scroll to the bottom, and click on the 'visual-network' artefact.

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
15310213204	Deploy to shinyapps.io	success	b9421b	91	2025-05-28
15310213201	Draft PDF	success	b9421b	34	2025-05-28
15310213207	pkgcheck	NA	b9421b	26	2025-05-28
15310213213	R-CMD-check	NA	b9421b	68	2025-05-28
15310213196	test-coverage	NA	b9421b	89	2025-05-28

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following note:

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

R CMD check generated the following check_fail:

1. rcmdcheck_citation_file_at_standard_place

Test coverage with covr

Package coverage: 100

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 330 potential issues:

message	number of times
Avoid library() and require() calls in packages	8
Lines should not be more than 80 characters. This line is 100 characters.	4
Lines should not be more than 80 characters. This line is 101 characters.	3
Lines should not be more than 80 characters. This line is 102 characters.	5
Lines should not be more than 80 characters. This line is 1025 characters.	1
Lines should not be more than 80 characters. This line is 103 characters.	8
Lines should not be more than 80 characters. This line is 104 characters.	2
Lines should not be more than 80 characters. This line is 107 characters.	5
Lines should not be more than 80 characters. This line is 108 characters.	2
Lines should not be more than 80 characters. This line is 109 characters.	2
Lines should not be more than 80 characters. This line is 110 characters.	3
Lines should not be more than 80 characters. This line is 111 characters.	1
Lines should not be more than 80 characters. This line is 112 characters.	1
Lines should not be more than 80 characters. This line is 113 characters.	2
Lines should not be more than 80 characters. This line is 115 characters.	3
Lines should not be more than 80 characters. This line is 116 characters.	3
Lines should not be more than 80 characters. This line is 117 characters.	1
Lines should not be more than 80 characters. This line is 118 characters.	6
Lines should not be more than 80 characters. This line is 119 characters.	3
Lines should not be more than 80 characters. This line is 120 characters.	2
Lines should not be more than 80 characters. This line is 121 characters.	1
Lines should not be more than 80 characters. This line is 1215 characters.	1
Lines should not be more than 80 characters. This line is 1219 characters.	1
Lines should not be more than 80 characters. This line is 122 characters.	1
Lines should not be more than 80 characters. This line is 123 characters.	1
Lines should not be more than 80 characters. This line is 124 characters.	1
Lines should not be more than 80 characters. This line is 125 characters.	3
Lines should not be more than 80 characters. This line is 126 characters.	1
Lines should not be more than 80 characters. This line is 127 characters.	1
Lines should not be more than 80 characters. This line is 128 characters.	4
Lines should not be more than 80 characters. This line is 131 characters.	3
Lines should not be more than 80 characters. This line is 133 characters.	1
Lines should not be more than 80 characters. This line is 134 characters.	5
Lines should not be more than 80 characters. This line is 136 characters.	2
Lines should not be more than 80 characters. This line is 137 characters.	1
Lines should not be more than 80 characters. This line is 138 characters.	1
Lines should not be more than 80 characters. This line is 140 characters.	1
Lines should not be more than 80 characters. This line is 141 characters.	1
Lines should not be more than 80 characters. This line is 142 characters.	1
Lines should not be more than 80 characters. This line is 143 characters.	3
Lines should not be more than 80 characters. This line is 144 characters.	1
Lines should not be more than 80 characters. This line is 146 characters.	1
Lines should not be more than 80 characters. This line is 147 characters.	2
Lines should not be more than 80 characters. This line is 148 characters.	2
Lines should not be more than 80 characters. This line is 149 characters.	1
Lines should not be more than 80 characters. This line is 150 characters.	3
Lines should not be more than 80 characters. This line is 152 characters.	1
Lines should not be more than 80 characters. This line is 153 characters.	2
Lines should not be more than 80 characters. This line is 154 characters.	1
Lines should not be more than 80 characters. This line is 157 characters.	1
Lines should not be more than 80 characters. This line is 159 characters.	4
Lines should not be more than 80 characters. This line is 160 characters.	1
Lines should not be more than 80 characters. This line is 161 characters.	1
Lines should not be more than 80 characters. This line is 162 characters.	2
Lines should not be more than 80 characters. This line is 163 characters.	1
Lines should not be more than 80 characters. This line is 164 characters.	3
Lines should not be more than 80 characters. This line is 165 characters.	2
Lines should not be more than 80 characters. This line is 167 characters.	2
Lines should not be more than 80 characters. This line is 169 characters.	2
Lines should not be more than 80 characters. This line is 170 characters.	1
Lines should not be more than 80 characters. This line is 171 characters.	1
Lines should not be more than 80 characters. This line is 172 characters.	3
Lines should not be more than 80 characters. This line is 173 characters.	1
Lines should not be more than 80 characters. This line is 174 characters.	2
Lines should not be more than 80 characters. This line is 175 characters.	2
Lines should not be more than 80 characters. This line is 176 characters.	2
Lines should not be more than 80 characters. This line is 178 characters.	1
Lines should not be more than 80 characters. This line is 181 characters.	1
Lines should not be more than 80 characters. This line is 182 characters.	1
Lines should not be more than 80 characters. This line is 183 characters.	2
Lines should not be more than 80 characters. This line is 189 characters.	1
Lines should not be more than 80 characters. This line is 190 characters.	1
Lines should not be more than 80 characters. This line is 191 characters.	3
Lines should not be more than 80 characters. This line is 192 characters.	1
Lines should not be more than 80 characters. This line is 193 characters.	1
Lines should not be more than 80 characters. This line is 195 characters.	1
Lines should not be more than 80 characters. This line is 201 characters.	1
Lines should not be more than 80 characters. This line is 202 characters.	1
Lines should not be more than 80 characters. This line is 203 characters.	1
Lines should not be more than 80 characters. This line is 210 characters.	1
Lines should not be more than 80 characters. This line is 211 characters.	1
Lines should not be more than 80 characters. This line is 223 characters.	1
Lines should not be more than 80 characters. This line is 249 characters.	1
Lines should not be more than 80 characters. This line is 252 characters.	1
Lines should not be more than 80 characters. This line is 81 characters.	9
Lines should not be more than 80 characters. This line is 82 characters.	15
Lines should not be more than 80 characters. This line is 83 characters.	15
Lines should not be more than 80 characters. This line is 84 characters.	5
Lines should not be more than 80 characters. This line is 85 characters.	17
Lines should not be more than 80 characters. This line is 86 characters.	7
Lines should not be more than 80 characters. This line is 87 characters.	13
Lines should not be more than 80 characters. This line is 88 characters.	8
Lines should not be more than 80 characters. This line is 89 characters.	12
Lines should not be more than 80 characters. This line is 90 characters.	9
Lines should not be more than 80 characters. This line is 91 characters.	4
Lines should not be more than 80 characters. This line is 911 characters.	1
Lines should not be more than 80 characters. This line is 92 characters.	11
Lines should not be more than 80 characters. This line is 93 characters.	9
Lines should not be more than 80 characters. This line is 94 characters.	7
Lines should not be more than 80 characters. This line is 95 characters.	9
Lines should not be more than 80 characters. This line is 96 characters.	8
Lines should not be more than 80 characters. This line is 98 characters.	5
Lines should not be more than 80 characters. This line is 99 characters.	1

---

4. Other Checks

Details of other checks (click to open)

✖️ The following 7 function names are duplicated in other packages:

• • download from basedosdados, BrownDog, downloader, geoknife, icesTAF, TAF, textreadr
• • get_annotation from geniusr
• • get_dataset_info from previsionio
• • get_genes from dnapath, immunarch, taxize
• • get_image from imguR
• • get_transcripts from childesr
• • get_variant from Rga4gh, zonator

---

Package Versions

package	version
pkgstats	0.2.0.54
pkgcheck	0.1.2.132

[github-actions]

Checks for gtexr (v0.2.0.9001)

git hash: 5ece9684

• ✔️ Package is already on CRAN.
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✖️ Package fails continuous integration checks.
• ✔️ Package coverage is 100%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.
• 👀 Function names are duplicated in other packages

Important: All failing checks above must be addressed prior to proceeding

(Checks marked with 👀 may be optionally addressed.)

Package License: MIT + file LICENSE

---

1. Package Dependencies

Details 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.

type	package	ncalls
internal	base	60
internal	gtexr	37
internal	utils	10
internal	stats	1
imports	rlang	19
imports	tibble	12
imports	cli	8
imports	purrr	7
imports	dplyr	4
imports	httr2	2
imports	tidyr	2
suggests	curl	NA
suggests	httptest2	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	spelling	NA
suggests	stringr	NA
suggests	testthat	NA
suggests	withr	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(<path/to/repo>)', and examining the 'external_calls' table.

base

c (14), list (10), as.integer (4), as.numeric (4), names (4), url (4), call (3), class (3), message (3), tryCatch (3), with (2), gsub (1), ifelse (1), length (1), options (1), unlist (1), which (1)

gtexr

calculate_expression_quantitative_trait_loci (1), calculate_splicing_quantitative_trait_loci (1), convert_null_to_na (1), download (1), get_annotation (1), get_clustered_median_exon_expression (1), get_clustered_median_gene_expression (1), get_clustered_median_junction_expression (1), get_clustered_median_transcript_expression (1), get_collapsed_gene_model_exon (1), get_dataset_info (1), get_downloads_page_data (1), get_eqtl_genes (1), get_exons (1), get_expression_pca (1), get_file_list (1), get_fine_mapping (1), get_full_get_collapsed_gene_model_exon (1), get_functional_annotation (1), get_gene_expression (1), get_gene_search (1), get_genes (1), get_genomic_features (1), get_gwas_catalog_by_location (1), get_image (1), get_independent_eqtl (1), get_linkage_disequilibrium_by_variant_data (1), get_linkage_disequilibrium_data (1), get_maintenance_message (1), get_median_exon_expression (1), get_median_gene_expression (1), get_median_junction_expression (1), get_median_transcript_expression (1), get_multi_tissue_eqtls (1), gtexr_arguments (1), name_unnamed_items (1), perform_gtex_request_json (1)

rlang

caller_env (10), env_get (7), caller_fn (1), fn_fmls_names (1)

tibble

tibble (12)

utils

data (5), packageDescription (4), page (1)

cli

format_inline (7), cli_warn (1)

purrr

map (3), map_depth (2), map_at (1), set_names (1)

dplyr

mutate (3), bind_rows (1)

httr2

req_error (1), request (1)

tidyr

unnest (2)

stats

start (1)

---

2. Statistical Properties

This 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:

• code in R (100% in 61 files) and
• 5 authors
• 2 vignettes
• no internal data file
• 7 imported packages
• 55 exported functions (median 5 lines of code)
• 144 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

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	96.8
files_inst	2	96.1
files_vignettes	2	81.8
files_tests	62	99.4
loc_R	1204	70.4
loc_inst	365	62.1
loc_vignettes	154	38.4
loc_tests	1987	92.0
num_vignettes	2	85.3
n_fns_r	199	88.3
n_fns_r_exported	55	88.6
n_fns_r_not_exported	144	88.1
n_fns_per_file_r	2	30.9
num_params_per_fn	7	84.0
loc_per_fn_r	8	20.2
loc_per_fn_r_exp	5	8.4
loc_per_fn_r_not_exp	9	27.2
rel_whitespace_R	9	51.8
rel_whitespace_inst	19	63.0
rel_whitespace_vignettes	26	28.8
rel_whitespace_tests	11	84.2
doclines_per_fn_exp	53	66.0
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	70	71.6

---

2a. Network visualisation

An interactive visualisation of calls between objects in the package has been uploaded as a workflow artefact. To view it, click on results from the latest 'pkgcheck' action, scroll to the bottom, and click on the 'visual-network' artefact.

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following note:

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

R CMD check generated the following check_fail:

1. rcmdcheck_citation_file_at_standard_place

Test coverage with covr

Package coverage: 100

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found no issues with this package!

---

4. Other Checks

Details of other checks (click to open)

✖️ The following 7 function names are duplicated in other packages:

• • download from basedosdados, BrownDog, downloader, geoknife, icesTAF, TAF, textreadr
• • get_annotation from geniusr
• • get_dataset_info from previsionio
• • get_genes from dnapath, immunarch, taxize
• • get_image from imguR
• • get_transcripts from childesr
• • get_variant from Rga4gh, zonator

---

Package Versions

package	version
pkgstats	0.2.0.61
pkgcheck	0.1.2.214

[github-actions]

Checks for gtexr (v0.2.1)

git hash: e70327d9

• ✔️ Package is already on CRAN.
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✖️ Package fails continuous integration checks.
• ✔️ Package coverage is 100%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.
• 👀 Function names are duplicated in other packages

Important: All failing checks above must be addressed prior to proceeding

(Checks marked with 👀 may be optionally addressed.)

Package License: MIT + file LICENSE

---

1. Package Dependencies

Details 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.

type	package	ncalls
internal	base	60
internal	gtexr	37
internal	utils	10
internal	stats	1
imports	rlang	19
imports	tibble	12
imports	cli	8
imports	purrr	7
imports	dplyr	4
imports	httr2	2
imports	tidyr	2
suggests	curl	NA
suggests	httptest2	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	spelling	NA
suggests	stringr	NA
suggests	testthat	NA
suggests	withr	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(<path/to/repo>)', and examining the 'external_calls' table.

base

c (14), list (10), as.integer (4), as.numeric (4), names (4), url (4), call (3), class (3), message (3), tryCatch (3), with (2), gsub (1), ifelse (1), length (1), options (1), unlist (1), which (1)

gtexr

calculate_expression_quantitative_trait_loci (1), calculate_splicing_quantitative_trait_loci (1), convert_null_to_na (1), download (1), get_annotation (1), get_clustered_median_exon_expression (1), get_clustered_median_gene_expression (1), get_clustered_median_junction_expression (1), get_clustered_median_transcript_expression (1), get_collapsed_gene_model_exon (1), get_dataset_info (1), get_downloads_page_data (1), get_eqtl_genes (1), get_exons (1), get_expression_pca (1), get_file_list (1), get_fine_mapping (1), get_full_get_collapsed_gene_model_exon (1), get_functional_annotation (1), get_gene_expression (1), get_gene_search (1), get_genes (1), get_genomic_features (1), get_gwas_catalog_by_location (1), get_image (1), get_independent_eqtl (1), get_linkage_disequilibrium_by_variant_data (1), get_linkage_disequilibrium_data (1), get_maintenance_message (1), get_median_exon_expression (1), get_median_gene_expression (1), get_median_junction_expression (1), get_median_transcript_expression (1), get_multi_tissue_eqtls (1), gtexr_arguments (1), name_unnamed_items (1), perform_gtex_request_json (1)

rlang

caller_env (10), env_get (7), caller_fn (1), fn_fmls_names (1)

tibble

tibble (12)

utils

data (5), packageDescription (4), page (1)

cli

format_inline (7), cli_warn (1)

purrr

map (3), map_depth (2), map_at (1), set_names (1)

dplyr

mutate (3), bind_rows (1)

httr2

req_error (1), request (1)

tidyr

unnest (2)

stats

start (1)

---

2. Statistical Properties

This 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:

• code in R (100% in 61 files) and
• 5 authors
• 2 vignettes
• no internal data file
• 7 imported packages
• 55 exported functions (median 5 lines of code)
• 144 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

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	96.8
files_inst	2	96.1
files_vignettes	2	81.8
files_tests	62	99.4
loc_R	1204	70.4
loc_inst	365	62.1
loc_vignettes	154	38.4
loc_tests	1987	92.0
num_vignettes	2	85.3
n_fns_r	199	88.3
n_fns_r_exported	55	88.6
n_fns_r_not_exported	144	88.1
n_fns_per_file_r	2	30.9
num_params_per_fn	7	84.0
loc_per_fn_r	8	20.2
loc_per_fn_r_exp	5	8.4
loc_per_fn_r_not_exp	9	27.2
rel_whitespace_R	9	51.8
rel_whitespace_inst	19	63.0
rel_whitespace_vignettes	26	28.8
rel_whitespace_tests	11	84.2
doclines_per_fn_exp	53	66.0
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	70	71.6

---

2a. Network visualisation

An interactive visualisation of calls between objects in the package has been uploaded as a workflow artefact. To view it, click on results from the latest 'pkgcheck' action, scroll to the bottom, and click on the 'visual-network' artefact.

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following note:

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

R CMD check generated the following check_fail:

1. rcmdcheck_citation_file_at_standard_place

Test coverage with covr

Package coverage: 100

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found no issues with this package!

---

4. Other Checks

Details of other checks (click to open)

✖️ The following 7 function names are duplicated in other packages:

• • download from basedosdados, BrownDog, downloader, geoknife, icesTAF, TAF, textreadr
• • get_annotation from geniusr
• • get_dataset_info from previsionio
• • get_genes from dnapath, immunarch, taxize
• • get_image from imguR
• • get_transcripts from childesr
• • get_variant from Rga4gh, zonator

---

Package Versions

package	version
pkgstats	0.2.0.61
pkgcheck	0.1.2.214

[github-actions]

Checks for gtexr (v0.2.1.9000)

git hash: 4000cd0e

• ✔️ Package is already on CRAN.
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✖️ Package fails continuous integration checks.
• ✔️ Package coverage is 100%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.
• 👀 Function names are duplicated in other packages

Important: All failing checks above must be addressed prior to proceeding

(Checks marked with 👀 may be optionally addressed.)

Package License: MIT + file LICENSE

---

1. Package Dependencies

Details 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.

type	package	ncalls
internal	base	60
internal	gtexr	37
internal	utils	10
internal	stats	1
imports	rlang	19
imports	tibble	12
imports	cli	8
imports	purrr	7
imports	dplyr	4
imports	httr2	2
imports	tidyr	2
suggests	curl	NA
suggests	httptest2	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	spelling	NA
suggests	stringr	NA
suggests	testthat	NA
suggests	withr	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(<path/to/repo>)', and examining the 'external_calls' table.

base

c (14), list (10), as.integer (4), as.numeric (4), names (4), url (4), call (3), class (3), message (3), tryCatch (3), with (2), gsub (1), ifelse (1), length (1), options (1), unlist (1), which (1)

gtexr

calculate_expression_quantitative_trait_loci (1), calculate_splicing_quantitative_trait_loci (1), convert_null_to_na (1), download (1), get_annotation (1), get_clustered_median_exon_expression (1), get_clustered_median_gene_expression (1), get_clustered_median_junction_expression (1), get_clustered_median_transcript_expression (1), get_collapsed_gene_model_exon (1), get_dataset_info (1), get_downloads_page_data (1), get_eqtl_genes (1), get_exons (1), get_expression_pca (1), get_file_list (1), get_fine_mapping (1), get_full_get_collapsed_gene_model_exon (1), get_functional_annotation (1), get_gene_expression (1), get_gene_search (1), get_genes (1), get_genomic_features (1), get_gwas_catalog_by_location (1), get_image (1), get_independent_eqtl (1), get_linkage_disequilibrium_by_variant_data (1), get_linkage_disequilibrium_data (1), get_maintenance_message (1), get_median_exon_expression (1), get_median_gene_expression (1), get_median_junction_expression (1), get_median_transcript_expression (1), get_multi_tissue_eqtls (1), gtexr_arguments (1), name_unnamed_items (1), perform_gtex_request_json (1)

rlang

caller_env (10), env_get (7), caller_fn (1), fn_fmls_names (1)

tibble

tibble (12)

utils

data (5), packageDescription (4), page (1)

cli

format_inline (7), cli_warn (1)

purrr

map (3), map_depth (2), map_at (1), set_names (1)

dplyr

mutate (3), bind_rows (1)

httr2

req_error (1), request (1)

tidyr

unnest (2)

stats

start (1)

---

2. Statistical Properties

This 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:

• code in R (100% in 61 files) and
• 5 authors
• 2 vignettes
• no internal data file
• 7 imported packages
• 55 exported functions (median 5 lines of code)
• 144 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

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	96.8
files_inst	2	96.0
files_vignettes	2	81.8
files_tests	62	99.4
loc_R	1204	70.4
loc_inst	365	62.1
loc_vignettes	154	38.4
loc_tests	1987	92.0
num_vignettes	2	85.3
n_fns_r	199	88.3
n_fns_r_exported	55	88.6
n_fns_r_not_exported	144	88.0
n_fns_per_file_r	2	30.9
num_params_per_fn	7	84.0
loc_per_fn_r	8	20.2
loc_per_fn_r_exp	5	8.4
loc_per_fn_r_not_exp	9	27.2
rel_whitespace_R	9	51.8
rel_whitespace_inst	19	62.9
rel_whitespace_vignettes	26	28.8
rel_whitespace_tests	11	84.2
doclines_per_fn_exp	53	66.0
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	70	71.5

---

2a. Network visualisation

An interactive visualisation of calls between objects in the package has been uploaded as a workflow artefact. To view it, click on results from the latest 'pkgcheck' action, scroll to the bottom, and click on the 'visual-network' artefact.

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

---

3b. goodpractice results

Test coverage with covr

Package coverage: 100

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found no issues with this package!

---

4. Other Checks

Details of other checks (click to open)

✖️ The following 7 function names are duplicated in other packages:

• • download from basedosdados, BrownDog, downloader, geoknife, icesTAF, TAF, textreadr
• • get_annotation from geniusr
• • get_dataset_info from previsionio
• • get_genes from dnapath, immunarch, taxize
• • get_image from imguR
• • get_transcripts from childesr
• • get_variant from Rga4gh, zonator

---

Package Versions

package	version
pkgstats	0.2.0.61
pkgcheck	0.1.2.214