Last updated on 2026-07-26 18:49:28 CEST.
| Package | OK | NOTE | ERROR |
|---|---|---|---|
| climateStability | 11 | 2 | |
| occCite | 7 | 6 | |
| spocc | 13 | ||
| voluModel | 9 | 4 |
Current CRAN status: OK: 11, NOTE: 2
Version: 0.1.4
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Hannah Owens <hannah.owens@gmail.com>’
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 7, ERROR: 6
Version: 0.6.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/293s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(occCite)
>
> test_check("occCite")
Saving _problems/test-occCitation-80.R
Saving _problems/test-occCitation-82.R
Saving _problems/test-occCitation-86.R
Saving _problems/test-occCitation-89.R
Saving _problems/test-occCitation-93.R
Saving _problems/test-occCitation-95.R
Saving _problems/test-occCitation-99.R
Saving _problems/test-occCitation-101.R
Saving _problems/test-occCitation-105.R
Saving _problems/test-occCitation-107.R
Saving _problems/test-occCitation-110.R
Saving _problems/test-occCitation-111.R
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif, bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2334 17
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2189 13
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 145 4
[1] "Checking ggplot version...4.0.3"
Failed with error: 'there is no package called 'waffle''
Failed with error: 'there is no package called 'waffle''
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
══ Skipped tests (20) ══════════════════════════════════════════════════════════
• !requireNamespace(paste0("waf", "fle"), quietly = TRUE) is TRUE (2):
'test-sumFig.R:47:3', 'test-sumFig.R:56:3'
• GBIF login available (1): 'test-GBIFLoginManager.R:16:3'
• On CRAN (14): 'test-GBIFLoginManager.R:24:3', 'test-GBIFtableCleanup.R:6:3',
'test-gbifRetriever.R:6:3', 'test-gbifRetriever.R:29:3',
'test-getBIENpoints.R:6:3', 'test-getBIENpoints.R:28:3',
'test-getGBIFpoints.R:6:3', 'test-getGBIFpoints.R:24:3',
'test-occCitation.R:26:3', 'test-prevGBIFdownload.R:6:3',
'test-prevGBIFdownload.R:34:3', 'test-tabGBIF.R:9:3', 'test-tabGBIF.R:24:3',
'test-tabGBIF.R:48:3'
• empty test (2): 'test-sumFig.R:13:1', 'test-sumFig.R:25:1'
• internet connection established (1): 'test-occCitation.R:115:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-occCitation.R:80:3'): outputs for BIEN results are as expected ──
Expected `class(testResults) == "occCiteCitation"` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:82:3'): outputs for BIEN results are as expected ──
Expected `"occCitationResults" %in% names(testResults)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:83:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]])` to equal "data.frame".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── Failure ('test-occCitation.R:88:3'): outputs for BIEN results are as expected ──
Expected `"occSearch" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:90:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$occSearch)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:94:3'): outputs for BIEN results are as expected ──
Expected `"Dataset Key" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:96:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$`Dataset Key`)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:100:3'): outputs for BIEN results are as expected ──
Expected `"Citation" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:102:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$Citation)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:106:3'): outputs for BIEN results are as expected ──
Expected `"Accession Date" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:109:3'): outputs for BIEN results are as expected ──
Expected `"Number of Occurrences" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:111:3'): outputs for BIEN results are as expected ──
Expected `is.numeric(testResults$occCitationResults[[1]]$`Number of Occurrences`)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.6.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/289s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(occCite)
>
> test_check("occCite")
Saving _problems/test-occCitation-80.R
Saving _problems/test-occCitation-82.R
Saving _problems/test-occCitation-86.R
Saving _problems/test-occCitation-89.R
Saving _problems/test-occCitation-93.R
Saving _problems/test-occCitation-95.R
Saving _problems/test-occCitation-99.R
Saving _problems/test-occCitation-101.R
Saving _problems/test-occCitation-105.R
Saving _problems/test-occCitation-107.R
Saving _problems/test-occCitation-110.R
Saving _problems/test-occCitation-111.R
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif, bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2334 17
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2189 13
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 145 4
[1] "Checking ggplot version...4.0.3"
Failed with error: 'there is no package called 'waffle''
Failed with error: 'there is no package called 'waffle''
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
══ Skipped tests (20) ══════════════════════════════════════════════════════════
• !requireNamespace(paste0("waf", "fle"), quietly = TRUE) is TRUE (2):
'test-sumFig.R:47:3', 'test-sumFig.R:56:3'
• GBIF login available (1): 'test-GBIFLoginManager.R:16:3'
• On CRAN (14): 'test-GBIFLoginManager.R:24:3', 'test-GBIFtableCleanup.R:6:3',
'test-gbifRetriever.R:6:3', 'test-gbifRetriever.R:29:3',
'test-getBIENpoints.R:6:3', 'test-getBIENpoints.R:28:3',
'test-getGBIFpoints.R:6:3', 'test-getGBIFpoints.R:24:3',
'test-occCitation.R:26:3', 'test-prevGBIFdownload.R:6:3',
'test-prevGBIFdownload.R:34:3', 'test-tabGBIF.R:9:3', 'test-tabGBIF.R:24:3',
'test-tabGBIF.R:48:3'
• empty test (2): 'test-sumFig.R:13:1', 'test-sumFig.R:25:1'
• internet connection established (1): 'test-occCitation.R:115:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-occCitation.R:80:3'): outputs for BIEN results are as expected ──
Expected `class(testResults) == "occCiteCitation"` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:82:3'): outputs for BIEN results are as expected ──
Expected `"occCitationResults" %in% names(testResults)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:83:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]])` to equal "data.frame".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── Failure ('test-occCitation.R:88:3'): outputs for BIEN results are as expected ──
Expected `"occSearch" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:90:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$occSearch)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:94:3'): outputs for BIEN results are as expected ──
Expected `"Dataset Key" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:96:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$`Dataset Key`)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:100:3'): outputs for BIEN results are as expected ──
Expected `"Citation" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:102:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$Citation)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:106:3'): outputs for BIEN results are as expected ──
Expected `"Accession Date" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:109:3'): outputs for BIEN results are as expected ──
Expected `"Number of Occurrences" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:111:3'): outputs for BIEN results are as expected ──
Expected `is.numeric(testResults$occCitationResults[[1]]$`Number of Occurrences`)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/286s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(occCite)
>
> test_check("occCite")
Saving _problems/test-occCitation-80.R
Saving _problems/test-occCitation-82.R
Saving _problems/test-occCitation-86.R
Saving _problems/test-occCitation-89.R
Saving _problems/test-occCitation-93.R
Saving _problems/test-occCitation-95.R
Saving _problems/test-occCitation-99.R
Saving _problems/test-occCitation-101.R
Saving _problems/test-occCitation-105.R
Saving _problems/test-occCitation-107.R
Saving _problems/test-occCitation-110.R
Saving _problems/test-occCitation-111.R
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif, bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2334 17
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2189 13
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 145 4
[1] "Checking ggplot version...4.0.3"
Failed with error: 'there is no package called 'waffle''
Failed with error: 'there is no package called 'waffle''
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
══ Skipped tests (20) ══════════════════════════════════════════════════════════
• !requireNamespace(paste0("waf", "fle"), quietly = TRUE) is TRUE (2):
'test-sumFig.R:47:3', 'test-sumFig.R:56:3'
• GBIF login available (1): 'test-GBIFLoginManager.R:16:3'
• On CRAN (14): 'test-GBIFLoginManager.R:24:3', 'test-GBIFtableCleanup.R:6:3',
'test-gbifRetriever.R:6:3', 'test-gbifRetriever.R:29:3',
'test-getBIENpoints.R:6:3', 'test-getBIENpoints.R:28:3',
'test-getGBIFpoints.R:6:3', 'test-getGBIFpoints.R:24:3',
'test-occCitation.R:26:3', 'test-prevGBIFdownload.R:6:3',
'test-prevGBIFdownload.R:34:3', 'test-tabGBIF.R:9:3', 'test-tabGBIF.R:24:3',
'test-tabGBIF.R:48:3'
• empty test (2): 'test-sumFig.R:13:1', 'test-sumFig.R:25:1'
• internet connection established (1): 'test-occCitation.R:115:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-occCitation.R:80:3'): outputs for BIEN results are as expected ──
Expected `class(testResults) == "occCiteCitation"` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:82:3'): outputs for BIEN results are as expected ──
Expected `"occCitationResults" %in% names(testResults)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:83:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]])` to equal "data.frame".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── Failure ('test-occCitation.R:88:3'): outputs for BIEN results are as expected ──
Expected `"occSearch" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:90:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$occSearch)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:94:3'): outputs for BIEN results are as expected ──
Expected `"Dataset Key" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:96:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$`Dataset Key`)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:100:3'): outputs for BIEN results are as expected ──
Expected `"Citation" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:102:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$Citation)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:106:3'): outputs for BIEN results are as expected ──
Expected `"Accession Date" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:109:3'): outputs for BIEN results are as expected ──
Expected `"Number of Occurrences" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:111:3'): outputs for BIEN results are as expected ──
Expected `is.numeric(testResults$occCitationResults[[1]]$`Number of Occurrences`)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.6.2
Check: tests
Result: ERROR
Running 'testthat.R' [58s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(occCite)
>
> test_check("occCite")
Saving _problems/test-occCitation-80.R
Saving _problems/test-occCitation-82.R
Saving _problems/test-occCitation-86.R
Saving _problems/test-occCitation-89.R
Saving _problems/test-occCitation-93.R
Saving _problems/test-occCitation-95.R
Saving _problems/test-occCitation-99.R
Saving _problems/test-occCitation-101.R
Saving _problems/test-occCitation-105.R
Saving _problems/test-occCitation-107.R
Saving _problems/test-occCitation-110.R
Saving _problems/test-occCitation-111.R
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif, bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2334 17
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2189 13
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 145 4
[1] "Checking ggplot version...4.0.3"
Failed with error: 'there is no package called 'waffle''
Failed with error: 'there is no package called 'waffle''
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
══ Skipped tests (20) ══════════════════════════════════════════════════════════
• !requireNamespace(paste0("waf", "fle"), quietly = TRUE) is TRUE (2):
'test-sumFig.R:47:3', 'test-sumFig.R:56:3'
• GBIF login available (1): 'test-GBIFLoginManager.R:16:3'
• On CRAN (14): 'test-GBIFLoginManager.R:24:3', 'test-GBIFtableCleanup.R:6:3',
'test-gbifRetriever.R:6:3', 'test-gbifRetriever.R:29:3',
'test-getBIENpoints.R:6:3', 'test-getBIENpoints.R:28:3',
'test-getGBIFpoints.R:6:3', 'test-getGBIFpoints.R:24:3',
'test-occCitation.R:26:3', 'test-prevGBIFdownload.R:6:3',
'test-prevGBIFdownload.R:34:3', 'test-tabGBIF.R:9:3', 'test-tabGBIF.R:24:3',
'test-tabGBIF.R:48:3'
• empty test (2): 'test-sumFig.R:13:1', 'test-sumFig.R:25:1'
• internet connection established (1): 'test-occCitation.R:115:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-occCitation.R:80:3'): outputs for BIEN results are as expected ──
Expected `class(testResults) == "occCiteCitation"` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:82:3'): outputs for BIEN results are as expected ──
Expected `"occCitationResults" %in% names(testResults)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:83:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]])` to equal "data.frame".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── Failure ('test-occCitation.R:88:3'): outputs for BIEN results are as expected ──
Expected `"occSearch" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:90:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$occSearch)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:94:3'): outputs for BIEN results are as expected ──
Expected `"Dataset Key" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:96:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$`Dataset Key`)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:100:3'): outputs for BIEN results are as expected ──
Expected `"Citation" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:102:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$Citation)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:106:3'): outputs for BIEN results are as expected ──
Expected `"Accession Date" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:109:3'): outputs for BIEN results are as expected ──
Expected `"Number of Occurrences" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:111:3'): outputs for BIEN results are as expected ──
Expected `is.numeric(testResults$occCitationResults[[1]]$`Number of Occurrences`)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.6.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/294s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(occCite)
>
> test_check("occCite")
Saving _problems/test-occCitation-80.R
Saving _problems/test-occCitation-82.R
Saving _problems/test-occCitation-86.R
Saving _problems/test-occCitation-89.R
Saving _problems/test-occCitation-93.R
Saving _problems/test-occCitation-95.R
Saving _problems/test-occCitation-99.R
Saving _problems/test-occCitation-101.R
Saving _problems/test-occCitation-105.R
Saving _problems/test-occCitation-107.R
Saving _problems/test-occCitation-110.R
Saving _problems/test-occCitation-111.R
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif, bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2334 17
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2189 13
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 145 4
[1] "Checking ggplot version...4.0.3"
Failed with error: 'there is no package called 'waffle''
Failed with error: 'there is no package called 'waffle''
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
══ Skipped tests (20) ══════════════════════════════════════════════════════════
• !requireNamespace(paste0("waf", "fle"), quietly = TRUE) is TRUE (2):
'test-sumFig.R:47:3', 'test-sumFig.R:56:3'
• GBIF login available (1): 'test-GBIFLoginManager.R:16:3'
• On CRAN (14): 'test-GBIFLoginManager.R:24:3', 'test-GBIFtableCleanup.R:6:3',
'test-gbifRetriever.R:6:3', 'test-gbifRetriever.R:29:3',
'test-getBIENpoints.R:6:3', 'test-getBIENpoints.R:28:3',
'test-getGBIFpoints.R:6:3', 'test-getGBIFpoints.R:24:3',
'test-occCitation.R:26:3', 'test-prevGBIFdownload.R:6:3',
'test-prevGBIFdownload.R:34:3', 'test-tabGBIF.R:9:3', 'test-tabGBIF.R:24:3',
'test-tabGBIF.R:48:3'
• empty test (2): 'test-sumFig.R:13:1', 'test-sumFig.R:25:1'
• internet connection established (1): 'test-occCitation.R:115:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-occCitation.R:80:3'): outputs for BIEN results are as expected ──
Expected `class(testResults) == "occCiteCitation"` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:82:3'): outputs for BIEN results are as expected ──
Expected `"occCitationResults" %in% names(testResults)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:83:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]])` to equal "data.frame".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── Failure ('test-occCitation.R:88:3'): outputs for BIEN results are as expected ──
Expected `"occSearch" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:90:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$occSearch)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:94:3'): outputs for BIEN results are as expected ──
Expected `"Dataset Key" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:96:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$`Dataset Key`)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:100:3'): outputs for BIEN results are as expected ──
Expected `"Citation" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:102:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$Citation)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:106:3'): outputs for BIEN results are as expected ──
Expected `"Accession Date" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:109:3'): outputs for BIEN results are as expected ──
Expected `"Number of Occurrences" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:111:3'): outputs for BIEN results are as expected ──
Expected `is.numeric(testResults$occCitationResults[[1]]$`Number of Occurrences`)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.6.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/295s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(occCite)
>
> test_check("occCite")
Saving _problems/test-occCitation-80.R
Saving _problems/test-occCitation-82.R
Saving _problems/test-occCitation-86.R
Saving _problems/test-occCitation-89.R
Saving _problems/test-occCitation-93.R
Saving _problems/test-occCitation-95.R
Saving _problems/test-occCitation-99.R
Saving _problems/test-occCitation-101.R
Saving _problems/test-occCitation-105.R
Saving _problems/test-occCitation-107.R
Saving _problems/test-occCitation-110.R
Saving _problems/test-occCitation-111.R
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif, bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2334 17
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: gbif
Species Occurrences Sources
1 Protea cynaroides (L.) L. 2189 13
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c
OccCite query occurred on: 20 June, 2024
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: GBIF Backbone Taxonomy
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy
Sources for occurrence data: bien
Species Occurrences Sources
1 Protea cynaroides (L.) L. 145 4
[1] "Checking ggplot version...4.0.3"
Failed with error: 'there is no package called 'waffle''
Failed with error: 'there is no package called 'waffle''
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
══ Skipped tests (20) ══════════════════════════════════════════════════════════
• !requireNamespace(paste0("waf", "fle"), quietly = TRUE) is TRUE (2):
'test-sumFig.R:47:3', 'test-sumFig.R:56:3'
• GBIF login available (1): 'test-GBIFLoginManager.R:16:3'
• On CRAN (14): 'test-GBIFLoginManager.R:24:3', 'test-GBIFtableCleanup.R:6:3',
'test-gbifRetriever.R:6:3', 'test-gbifRetriever.R:29:3',
'test-getBIENpoints.R:6:3', 'test-getBIENpoints.R:28:3',
'test-getGBIFpoints.R:6:3', 'test-getGBIFpoints.R:24:3',
'test-occCitation.R:26:3', 'test-prevGBIFdownload.R:6:3',
'test-prevGBIFdownload.R:34:3', 'test-tabGBIF.R:9:3', 'test-tabGBIF.R:24:3',
'test-tabGBIF.R:48:3'
• empty test (2): 'test-sumFig.R:13:1', 'test-sumFig.R:25:1'
• internet connection established (1): 'test-occCitation.R:115:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-occCitation.R:80:3'): outputs for BIEN results are as expected ──
Expected `class(testResults) == "occCiteCitation"` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:82:3'): outputs for BIEN results are as expected ──
Expected `"occCitationResults" %in% names(testResults)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:83:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]])` to equal "data.frame".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── Failure ('test-occCitation.R:88:3'): outputs for BIEN results are as expected ──
Expected `"occSearch" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:90:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$occSearch)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:94:3'): outputs for BIEN results are as expected ──
Expected `"Dataset Key" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:96:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$`Dataset Key`)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:100:3'): outputs for BIEN results are as expected ──
Expected `"Citation" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:102:3'): outputs for BIEN results are as expected ──
Expected `class(testResults$occCitationResults[[1]]$Citation)` to equal "character".
Differences:
1/1 mismatches
x[1]: "NULL"
y[1]: "character"
── Failure ('test-occCitation.R:106:3'): outputs for BIEN results are as expected ──
Expected `"Accession Date" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:109:3'): outputs for BIEN results are as expected ──
Expected `"Number of Occurrences" %in% names(testResults$occCitationResults[[1]])` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-occCitation.R:111:3'): outputs for BIEN results are as expected ──
Expected `is.numeric(testResults$occCitationResults[[1]]$`Number of Occurrences`)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 12 | WARN 0 | SKIP 20 | PASS 154 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 9, ERROR: 4
Version: 0.2.4
Check: examples
Result: ERROR
Running examples in ‘voluModel-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pointCompMap
> ### Title: Comparative point mapping
> ### Aliases: pointCompMap
> ### Keywords: plotting
>
> ### ** Examples
>
> set.seed(5)
> occs <- data.frame(cbind(decimalLatitude = sample(seq(7,35), 24),
+ decimalLongitude = sample(seq(-97, -70), 24)))
>
> set.seed(0)
> occs1 <- occs[sample(1:nrow(occs),
+ size = 12, replace = FALSE),]
> set.seed(10)
> occs2 <- occs[sample(1:nrow(occs),
+ size = 12, replace = FALSE),]
>
> pointCompMap(occs1 = occs1, occs2 = occs2,
+ occs1Col = "red", occs2Col = "orange",
+ agreeCol = "purple",
+ occs1Name = "2D",
+ occs2Name = "3D",
+ waterCol = "steelblue",
+ spName = "Steindachneria argentea",
+ ptSize = 2,
+ verbose = FALSE)
Warning: Use of `occ_dat[[occ_datIndices$xIndex]]` is discouraged.
ℹ Use `.data[[occ_datIndices$xIndex]]` instead.
Warning: Use of `occ_dat[[occ_datIndices$yIndex]]` is discouraged.
ℹ Use `.data[[occ_datIndices$yIndex]]` instead.
Error: gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a_Introduction.Rmd’ using rmarkdown
--- finished re-building ‘a_Introduction.Rmd’
--- re-building ‘b_RasterProcessing.Rmd’ using rmarkdown
--- finished re-building ‘b_RasterProcessing.Rmd’
--- re-building ‘c_DataSampling.Rmd’ using rmarkdown
Quitting from c_DataSampling.Rmd:123-130 [plot downsample]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
---
Backtrace:
▆
1. ├─base::withVisible(knit_print(x, ...))
2. ├─knitr::knit_print(x, ...)
3. └─knitr:::knit_print.default(x, ...)
4. └─knitr::normal_print(x)
5. ├─base::print(x)
6. └─ggplot2 (local) `print.ggplot2::ggplot`(x)
7. ├─ggplot2::ggplot_gtable(data)
8. └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. └─ggplot2::element_render(...)
10. ├─ggplot2::element_grob(el, ...)
11. └─ggtext:::element_grob.element_markdown(el, ...)
12. └─gridtext::richtext_grob(...)
13. └─base::mapply(...)
14. └─gridtext (local) `<fn>`(...)
15. └─gridtext:::process_tags(xml2::as_list(doctree)$html$body, drawing_context)
16. └─gridtext:::dispatch_tag(node[[i]], tags[i], drawing_context)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'c_DataSampling.Rmd' failed with diagnostics:
gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
--- failed re-building ‘c_DataSampling.Rmd’
--- re-building ‘d_Visualization.Rmd’ using rmarkdown
Quitting from d_Visualization.Rmd:133-138 [pointCompMap]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
---
Backtrace:
▆
1. ├─base::withVisible(knit_print(x, ...))
2. ├─knitr::knit_print(x, ...)
3. └─knitr:::knit_print.default(x, ...)
4. └─knitr::normal_print(x)
5. ├─base::print(x)
6. └─ggplot2 (local) `print.ggplot2::ggplot`(x)
7. ├─ggplot2::ggplot_gtable(data)
8. └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. └─ggplot2::element_render(...)
10. ├─ggplot2::element_grob(el, ...)
11. └─ggtext:::element_grob.element_markdown(el, ...)
12. └─gridtext::richtext_grob(...)
13. └─base::mapply(...)
14. └─gridtext (local) `<fn>`(...)
15. └─gridtext:::process_tags(xml2::as_list(doctree)$html$body, drawing_context)
16. └─gridtext:::dispatch_tag(node[[i]], tags[i], drawing_context)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'd_Visualization.Rmd' failed with diagnostics:
gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
--- failed re-building ‘d_Visualization.Rmd’
--- re-building ‘e_GLMWorkflow.Rmd’ using rmarkdown
Quitting from e_GLMWorkflow.Rmd:106-130 [downsample to voxel]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
---
Backtrace:
▆
1. ├─base::withVisible(knit_print(x, ...))
2. ├─knitr::knit_print(x, ...)
3. └─knitr:::knit_print.default(x, ...)
4. └─knitr::normal_print(x)
5. ├─base::print(x)
6. └─ggplot2 (local) `print.ggplot2::ggplot`(x)
7. ├─ggplot2::ggplot_gtable(data)
8. └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. └─ggplot2::element_render(...)
10. ├─ggplot2::element_grob(el, ...)
11. └─ggtext:::element_grob.element_markdown(el, ...)
12. └─gridtext::richtext_grob(...)
13. └─base::mapply(...)
14. └─gridtext (local) `<fn>`(...)
15. └─gridtext:::process_tags(xml2::as_list(doctree)$html$body, drawing_context)
16. └─gridtext:::dispatch_tag(node[[i]], tags[i], drawing_context)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'e_GLMWorkflow.Rmd' failed with diagnostics:
gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
--- failed re-building ‘e_GLMWorkflow.Rmd’
SUMMARY: processing the following files failed:
‘c_DataSampling.Rmd’ ‘d_Visualization.Rmd’ ‘e_GLMWorkflow.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 0.2.4
Check: examples
Result: ERROR
Running examples in 'voluModel-Ex.R' failed
The error most likely occurred in:
> ### Name: pointCompMap
> ### Title: Comparative point mapping
> ### Aliases: pointCompMap
> ### Keywords: plotting
>
> ### ** Examples
>
> set.seed(5)
> occs <- data.frame(cbind(decimalLatitude = sample(seq(7,35), 24),
+ decimalLongitude = sample(seq(-97, -70), 24)))
>
> set.seed(0)
> occs1 <- occs[sample(1:nrow(occs),
+ size = 12, replace = FALSE),]
> set.seed(10)
> occs2 <- occs[sample(1:nrow(occs),
+ size = 12, replace = FALSE),]
>
> pointCompMap(occs1 = occs1, occs2 = occs2,
+ occs1Col = "red", occs2Col = "orange",
+ agreeCol = "purple",
+ occs1Name = "2D",
+ occs2Name = "3D",
+ waterCol = "steelblue",
+ spName = "Steindachneria argentea",
+ ptSize = 2,
+ verbose = FALSE)
Warning: Use of `occ_dat[[occ_datIndices$xIndex]]` is discouraged.
ℹ Use `.data[[occ_datIndices$xIndex]]` instead.
Warning: Use of `occ_dat[[occ_datIndices$yIndex]]` is discouraged.
ℹ Use `.data[[occ_datIndices$yIndex]]` instead.
Error: gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
Execution halted
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'a_Introduction.Rmd' using rmarkdown
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
--- finished re-building 'a_Introduction.Rmd'
--- re-building 'b_RasterProcessing.Rmd' using rmarkdown
--- finished re-building 'b_RasterProcessing.Rmd'
--- re-building 'c_DataSampling.Rmd' using rmarkdown
Quitting from c_DataSampling.Rmd:123-130 [plot downsample]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
---
Backtrace:
▆
1. ├─base::withVisible(knit_print(x, ...))
2. ├─knitr::knit_print(x, ...)
3. └─knitr:::knit_print.default(x, ...)
4. └─knitr::normal_print(x)
5. ├─base::print(x)
6. └─ggplot2 (local) `print.ggplot2::ggplot`(x)
7. ├─ggplot2::ggplot_gtable(data)
8. └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. └─ggplot2::element_render(...)
10. ├─ggplot2::element_grob(el, ...)
11. └─ggtext:::element_grob.element_markdown(el, ...)
12. └─gridtext::richtext_grob(...)
13. └─base::mapply(...)
14. └─gridtext (local) `<fn>`(...)
15. └─gridtext:::process_tags(xml2::as_list(doctree)$html$body, drawing_context)
16. └─gridtext:::dispatch_tag(node[[i]], tags[i], drawing_context)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'c_DataSampling.Rmd' failed with diagnostics:
gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
--- failed re-building 'c_DataSampling.Rmd'
--- re-building 'd_Visualization.Rmd' using rmarkdown
Quitting from d_Visualization.Rmd:133-138 [pointCompMap]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
---
Backtrace:
▆
1. ├─base::withVisible(knit_print(x, ...))
2. ├─knitr::knit_print(x, ...)
3. └─knitr:::knit_print.default(x, ...)
4. └─knitr::normal_print(x)
5. ├─base::print(x)
6. └─ggplot2 (local) `print.ggplot2::ggplot`(x)
7. ├─ggplot2::ggplot_gtable(data)
8. └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. └─ggplot2::element_render(...)
10. ├─ggplot2::element_grob(el, ...)
11. └─ggtext:::element_grob.element_markdown(el, ...)
12. └─gridtext::richtext_grob(...)
13. └─base::mapply(...)
14. └─gridtext (local) `<fn>`(...)
15. └─gridtext:::process_tags(xml2::as_list(doctree)$html$body, drawing_context)
16. └─gridtext:::dispatch_tag(node[[i]], tags[i], drawing_context)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'd_Visualization.Rmd' failed with diagnostics:
gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
--- failed re-building 'd_Visualization.Rmd'
--- re-building 'e_GLMWorkflow.Rmd' using rmarkdown
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Quitting from e_GLMWorkflow.Rmd:106-130 [downsample to voxel]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
---
Backtrace:
▆
1. ├─base::withVisible(knit_print(x, ...))
2. ├─knitr::knit_print(x, ...)
3. └─knitr:::knit_print.default(x, ...)
4. └─knitr::normal_print(x)
5. ├─base::print(x)
6. └─ggplot2 (local) `print.ggplot2::ggplot`(x)
7. ├─ggplot2::ggplot_gtable(data)
8. └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. └─ggplot2::element_render(...)
10. ├─ggplot2::element_grob(el, ...)
11. └─ggtext:::element_grob.element_markdown(el, ...)
12. └─gridtext::richtext_grob(...)
13. └─base::mapply(...)
14. └─gridtext (local) `<fn>`(...)
15. └─gridtext:::process_tags(xml2::as_list(doctree)$html$body, drawing_context)
16. └─gridtext:::dispatch_tag(node[[i]], tags[i], drawing_context)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'e_GLMWorkflow.Rmd' failed with diagnostics:
gridtext has encountered a tag that isn't supported yet: <pre>
Only a very limited number of tags are currently supported.
--- failed re-building 'e_GLMWorkflow.Rmd'
SUMMARY: processing the following files failed:
'c_DataSampling.Rmd' 'd_Visualization.Rmd' 'e_GLMWorkflow.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64