New Upstream Snapshot - r-cran-taxize
Ready changes
Summary
Merged new upstream version: 0.9.100+git20230103.0.d04e35d+ds (was: 0.9.100+git20221026.1.9ec1839+ds).
Resulting package
Built on 2023-01-19T14:09 (took 13m56s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots r-cran-taxize
Lintian Result
Diff
diff --git a/DESCRIPTION b/DESCRIPTION
index f30f2f90..b92f123d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -77,13 +77,14 @@ Imports: graphics, methods, stats, utils, crul (>= 0.7.0), xml2 (>=
0.7.6), worrms (>= 0.4.0), natserv (>= 1.0.0), wikitaxa (>=
0.3.0), R6, crayon, cli, phangorn, conditionz
Suggests: testthat, vegan, vcr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
+Roxygen: list(markdown = TRUE)
X-schema.org-applicationCategory: Taxonomy
X-schema.org-keywords: taxonomy, biology, nomenclature, JSON, API, web,
api-client, identifiers, species, names
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
-Packaged: 2022-04-21 16:12:25 UTC; fosterz
+Packaged: 2023-01-19 14:01:51 UTC; root
Author: Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Eduard Szoecs [aut],
Zachary Foster [aut, cre],
@@ -102,5 +103,3 @@ Author: Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Matthias Grenié [ctb],
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
-Repository: CRAN
-Date/Publication: 2022-04-22 08:30:02 UTC
diff --git a/MD5 b/MD5
deleted file mode 100644
index c62dfd6e..00000000
--- a/MD5
+++ /dev/null
@@ -1,613 +0,0 @@
-802f064be4931afeea4cbe95d0991c35 *DESCRIPTION
-35bd8606c71dfbfad3ad27387e177ad4 *LICENSE
-3b12101fc5adac1a1a94c2046b4b4f74 *NAMESPACE
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-c4f534dd388e0482cdd8aee612728d24 *tests/fixtures/ncbi_children_id_class_check.yml
-52ad77ec6cf5b0f47386d98bbd8d4afc *tests/fixtures/ncbi_downstream.yml
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-c17d80c9f590fa90c3c898f3d30a4f74 *tests/fixtures/ncbi_downstream_ambiguous_true.yml
-8d8fed9fde948e5322cda992cb52bd49 *tests/fixtures/ncbi_downstream_handles_self_ids.yml
-2e113872bf2b98aed8be608438472213 *tests/fixtures/ncbi_downstream_intermediate.yml
-04050ec7b30fd278cbdda2028e066ff6 *tests/fixtures/ncbi_get_taxon_summary.yml
-ee8045d0e02d4ea702655a137bab766a *tests/fixtures/ncbi_get_taxon_summary_many_ids_long.yml
-68d23e6247750314d5fe16fc0c1d906a *tests/fixtures/ncbi_get_taxon_summary_many_ids_short.yml
-df20fc764653c8230cd493f36dbd7442 *tests/fixtures/ncbi_ping.yml
-b6b22281a9ad99b6b528f161c454f1c9 *tests/fixtures/plantminer.yml
-c404a0ecadd1f211390bfba8c50150f6 *tests/fixtures/plantminer_not_found.yml
-6b54dbf7f8f57ac9ed4f3a7da5a3d17e *tests/fixtures/pow_lookup.yml
-a9098f86b11c5718c1a8b47ede5de0e0 *tests/fixtures/pow_lookup_include_param.yml
-a36d6e31010090aeaa5988574eee06b4 *tests/fixtures/pow_search.yml
-f171460b789bfde859531703fee4c127 *tests/fixtures/sci2comm.yml
-22b1ede91a2eea012492559cb8903a68 *tests/fixtures/sci2comm_warn_on_db_mismatch.yml
-8375aa0cce645516722eca86ec205bb9 *tests/fixtures/synonyms_itis.yml
-9f2dbe90c66b1dc5af944c7d40e7af39 *tests/fixtures/synonyms_name_found_but_no_synonyms.yml
-1422fe43a3e59bee3b44d6ef3a9b6102 *tests/fixtures/synonyms_name_found_but_no_synonyms_redlist.yml
-459d03162e8482d6f18fcb74f1b5ea8f *tests/fixtures/synonyms_name_not_found.yml
-84d21c506d92542ef43d92bbf40d4669 *tests/fixtures/synonyms_name_not_found_redlist.yml
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-e638e74c1119cea5fec699112c85c7c4 *tests/fixtures/synonyms_worms.yml
-46683c593bbc91cddac4b680b7393898 *tests/fixtures/tax_name_arg_arg.yml
-2ebd8f067f28f6e5cb549b9b1afc9a33 *tests/fixtures/tax_name_itis.yml
-211e791694f23d886bf98446dd899a9d *tests/fixtures/tax_name_na.yml
-e5bf4cbb857c16c329fd8b27c7db5a99 *tests/fixtures/tax_name_ncbi.yml
-b439a64c57e11ee4760308910e075b4e *tests/fixtures/tax_name_no_data.yml
-a87e0b6295620ee8590aec326118f954 *tests/fixtures/tax_name_rows_Arg.yml
-d0f250e0383e6b67f1a03665d31dab6f *tests/fixtures/tax_name_throws_warning.yml
-2b69d75db61902aabf41ec5eed6c85f7 *tests/fixtures/tax_rank.yml
-7bb7b40d1ededf07b9c9f624f31efc81 *tests/fixtures/tax_rank_get_star_input.yml
-45f9c65d1c2f6679214326bf89761881 *tests/fixtures/taxon_state_get_gbifid.yml
-fb15315f303348f4b2a75bba93577434 *tests/fixtures/taxon_state_get_uid.yml
-195b0f78e3ac428a76a59583ac0c25e8 *tests/fixtures/tnrs.yml
-6dd6fd054272cba5c9e57efaab15cf15 *tests/fixtures/tnrs_order_row_names.yml
-7846c64e002e3b231ff752666ebfc8d3 *tests/fixtures/tnrs_sources.yml
-0eb1cc850a519f8808fa20f7738f7b01 *tests/fixtures/tol_resolve.yml
-1c4c41021e99cd84a7c8f4daa2380043 *tests/fixtures/tol_resolve_context_name.yml
-b4b72feabee45c4c7edfeda70e4a32e0 *tests/fixtures/tol_resolve_do_approximate_matching.yml
-d5bda26b9f7adb1b0deb5e4bb64f8424 *tests/fixtures/tol_resolve_do_approximate_matching_false.yml
-5cedbb646fbb87dce31aefa97661daa8 *tests/fixtures/tp_accnames.yml
-14ed3ab413d255dbab240194772e7da3 *tests/fixtures/tp_dist.yml
-d1de81b8349d6b27d2634103e1d2a6ea *tests/fixtures/tp_refs.yml
-5f653a034df855c2b88d6a071154953c *tests/fixtures/tp_search.yml
-7943c0a9239272772f6efbc696b691a7 *tests/fixtures/tp_search_warnings_dots.yml
-f72bf80d18e1f9d74b34bad913e819cd *tests/fixtures/tp_search_warnings_subspecific.yml
-039dcdcaa316e57479ffa91903abcd92 *tests/fixtures/tp_summary.yml
-ecd12829096374a4d2b641623f88c2e0 *tests/fixtures/tp_synonyms.yml
-b5052adb10762c73cd13912082d915f5 *tests/fixtures/trpicos_ping.yml
-fddaf6f59208d3b03e46fff0fce90438 *tests/fixtures/upstream.yml
-f99d2e6a5d9af1d3cb44bf28d331bbad *tests/fixtures/vascan_ping.yml
-ba3e99f3f597e13f5ffe4ba33eb77ff1 *tests/fixtures/vascan_search.yml
-a30737a0903a1d0850c94d7612bcd90c *tests/fixtures/worms_downstream.yml
-405f51ea335fc5f14f42519137b07b3b *tests/fixtures/worms_downstream_intermediate_param.yml
-485de10720aa0bc41fe07da2916bd3a3 *tests/fixtures/worms_downstream_marine_only_para.yml
-961738d3fb08a33f36196291e55cf775 *tests/fixtures/worms_downstream_previously_unaccounted_for_ranks.yml
-1c965222ee7561fcbd5f50f83c6d020b *tests/fixtures/worms_downstream_start_param.yml
-265c6f13798f3db6770e9265dd5c0665 *tests/test-all.R
-b953369962945db1cff1f25655e17789 *tests/testthat/Rplots.pdf
-6b7302ed33c17aa39c611d309ed72955 *tests/testthat/helper-taxize.R
-88c361a06ab441183fe01013f09ef519 *tests/testthat/test-apgscraping.R
-1a78ed1c210d9a8270b12e32b502018c *tests/testthat/test-bold_children.R
-1c9950e3415d5fdd4d9b0b5b343b60c7 *tests/testthat/test-bold_downstream.R
-41e6b82ad9cf848d76c791e072ba825f *tests/testthat/test-bold_search.R
-76d515a92c0b7b676b8ee4ee46adad38 *tests/testthat/test-children.R
-5ac0134aa095b6fd3a9956a7511b0fb3 *tests/testthat/test-class2tree.R
-a8ebb4377f926a8a8effc4e37def24c4 *tests/testthat/test-classification-gbif.R
-a861b7e54c88efbeffbd0882877ee9e0 *tests/testthat/test-classification-pow.R
-ad612947eb3a560717f3287ee050e5ff *tests/testthat/test-classification.R
-977f4dce43c1ef7db9884ad866d79da8 *tests/testthat/test-comm2sci.R
-6f46392451136de1b5d53b114d63cf66 *tests/testthat/test-dataset_rank_ref.R
-fc26abcc67128c2572141c607cc06757 *tests/testthat/test-downstream.R
-09b8521eb0afa8e001451f8c7fcc8eae *tests/testthat/test-eol_dataobjects.R
-0a84b740eebb9ad5c97ddea3d85bb73e *tests/testthat/test-eol_pages.R
-9666d3e2116c36f19169b04ad30c95b0 *tests/testthat/test-eol_ping.R
-f759911230a22e269dbf1305b3f9305b *tests/testthat/test-eol_search.R
-2654d4f1abb7764996dfe21c47a828a3 *tests/testthat/test-eubon.R
-c4d045a0e4bbfc1c8750f5202342da65 *tests/testthat/test-fungorum.R
-92496aac06d4acfc54f3add25cd7e4ed *tests/testthat/test-gbif_downstream.R
-6bc5cd413b03c5facb15cf8c744e6231 *tests/testthat/test-gbif_parse.R
-b68398cfd271eb14603ebf08f0830391 *tests/testthat/test-genbank2uid.R
-e7a8a69fb1d41ff3f4adfb57ffa6cddc *tests/testthat/test-get_boldid.R
-f10830c9e5e5723f47074d9428e3552a *tests/testthat/test-get_eolid.R
-c9663ed6dc2f8079f5e84c0a5a5c1ef3 *tests/testthat/test-get_gbifid.R
-31114955cbac2cf05b74423dc7cb5901 *tests/testthat/test-get_ids.R
-c7d975e56ec5fa9ea12a9ba3475e85ef *tests/testthat/test-get_natservid.R
-2d98fb0f94c94c45a2cdf05115b2d43b *tests/testthat/test-get_pow.R
-6aa8c13282a641adbcb426c1d6c22f13 *tests/testthat/test-get_tolid.R
-e0340a7edcfff0e47985dc79029b3147 *tests/testthat/test-get_tpsid.R
-de14841a555d434c6263cefa31fabe68 *tests/testthat/test-get_tsn.R
-ef1ca526b9c1f384bbe36a0d1d2244fa *tests/testthat/test-get_uid.R
-ab5fc40e9128cb68c86e20692f026621 *tests/testthat/test-get_wormsid.R
-3075054226a147ebf89b53cfc1fdea9d *tests/testthat/test-gn_parse.R
-a858181305c1937a23f86e5b4729d003 *tests/testthat/test-gni_details.R
-c3ff57f0c84c36363a350c3fd5bc82f2 *tests/testthat/test-gni_parse.R
-6b9bd0a925beb7da330c4cf2df477309 *tests/testthat/test-gni_search.R
-9409b5ac6d31914cbd19d07e9740e8e9 *tests/testthat/test-gnr_datasources.R
-d70ec39e9871aa559810f8b6f8709e95 *tests/testthat/test-gnr_resolve.R
-dedbcdb5bc2f184f29a52eeeb8170d4d *tests/testthat/test-id2name.R
-28805309c85db2d5ab8dab5c76c64340 *tests/testthat/test-ion.R
-35830ae9ed762ed3bca5b87a1a1ab51d *tests/testthat/test-ipni_search.R
-3e7c8fb6352aa71c04026814186a6fda *tests/testthat/test-itis_acceptname.R
-1d34d16a9b13d1ab04371f8dd70dbb22 *tests/testthat/test-itis_downstream.R
-575f2d07d4ff2390b290470aca2a68b7 *tests/testthat/test-itis_getrecord.R
-1ee6ea92e60fb695a8983b8a6e5a45b4 *tests/testthat/test-itis_hierarchy.R
-35d73c353738f6e80f5c67d0a5001334 *tests/testthat/test-itis_kingdomnames.R
-8e5c44f4bf6910429d38cdc2411986c6 *tests/testthat/test-itis_lsid.R
-5edec2e15cb26c60c9db3f8fad550d70 *tests/testthat/test-itis_native.R
-208ee4bf9e41d560081288c6d818bb2a *tests/testthat/test-itis_ping.R
-bdb07f096ea4de66d8f0199428cced53 *tests/testthat/test-itis_refs.R
-dbbeed57925eb538693d1b7a9425f459 *tests/testthat/test-itis_taxrank.R
-f4b245ee3d8a4a07147ce3caf3268888 *tests/testthat/test-itis_terms.R
-ed0fdae8d88c2fde430b6e08ba9227f6 *tests/testthat/test-iucn_getname.R
-a641ca0e511edb9caa2a642d35de4bc1 *tests/testthat/test-iucn_id.R
-3fbdf0c3f042d563fd15d684be18f8aa *tests/testthat/test-iucn_summary.R
-982668e1e9569e007d31e0b17855e1e4 *tests/testthat/test-key_helpers.R
-1488364b138bcba2aa7588bb7908cfb9 *tests/testthat/test-lowest_common.R
-1100aebc2134b941951e69dc3a4bf084 *tests/testthat/test-names_list.R
-87fab7070b22a728fea6931c7ae99eac *tests/testthat/test-ncbi_children.R
-f3d88302289de8a42dadb94346ec67a5 *tests/testthat/test-ncbi_downstream.R
-e4363d22d45b4a0ff915746cf0694c87 *tests/testthat/test-ncbi_get_taxon_summary.R
-8496f16f8f00800637999f51ae7c0fe8 *tests/testthat/test-ncbi_rate_limit_pause.R
-653697042fff4743a63e800470b9258d *tests/testthat/test-ping.R
-667a6896f05e2f23772a23b1dc3950f8 *tests/testthat/test-plantminer.R
-a7e1d884cc6aa3543b58e03710f4b24d *tests/testthat/test-pow_search.R
-ecc968ad1f6dcfbe0642460c5ae855a2 *tests/testthat/test-progressor.R
-727d343232826ac774531426087b7aff *tests/testthat/test-rankagg.R
-ddefc41178da3210cd763517a6e05212 *tests/testthat/test-sci2comm.R
-1560ab20d6c5fbcb989981ab1a6297ac *tests/testthat/test-synonyms.R
-a159ac415ab9f50bc029a15d7c10a2f6 *tests/testthat/test-tax_agg.R
-6f88bf477275f7791138750f59afd2db *tests/testthat/test-tax_name.R
-597efd0a0195b98392308285edeafa1e *tests/testthat/test-tax_rank.R
-33d1095541756b42931541699f7d6f62 *tests/testthat/test-taxize_options.R
-1cfebfa274bdca144ec0657f8c46128d *tests/testthat/test-taxon_state.R
-f76b2837d20f61b0b3e3d96106c34ced *tests/testthat/test-tol_resolve.R
-7f39580ed7b6eb0e736111b82ffbeace *tests/testthat/test-tp_accnames.R
-68d9620cd9ce7c99d3dda012d2d50faf *tests/testthat/test-tp_dist.R
-f6f24189125053561f64ff7b85d3750a *tests/testthat/test-tp_refs.R
-ca64f4f31ca85d33a9b7e68eaad4d3ce *tests/testthat/test-tp_search.R
-516559142dcef0daf6ee9a216589766d *tests/testthat/test-tp_summary.R
-0401de2a5fe080ba39a3e5761108ce6e *tests/testthat/test-tp_synonyms.R
-f6baec6ab2742444392e47b839a71d9d *tests/testthat/test-upstream.R
-1f991db984a2b4fd5e1798e9683a1d63 *tests/testthat/test-utils.R
-d61ec55fbd68cbeb21451751ae3d4c4c *tests/testthat/test-vascan_search.r
-8f8236563b63f36f5796db5bc02dfe95 *tests/testthat/test-worms_downstream.R
-7988b4cbd9f330a8aa0cb8c96576356b *tools/screencast.png
diff --git a/R/classification.R b/R/classification.R
index ced17e68..a7ddaed4 100644
--- a/R/classification.R
+++ b/R/classification.R
@@ -365,31 +365,33 @@ classification.uid <- function(id, callopts = list(), return_id = TRUE,
tries <- 1
while (success == FALSE && tries <= max_tries) {
res <- cli$get("entrez/eutils/efetch.fcgi", query = query)
- res$raise_for_status()
- tt <- res$parse("UTF-8")
- ttp <- xml2::read_xml(tt)
- out <- lapply(xml2::xml_find_all(ttp, '//TaxaSet/Taxon'),
- function(tax_node) {
- lin <- data.frame(
- name = xml_text_all(tax_node,
- ".//LineageEx/Taxon/ScientificName"),
- rank = xml_text_all(tax_node, ".//LineageEx/Taxon/Rank"),
- id = xml_text_all(tax_node, ".//LineageEx/Taxon/TaxId"),
- stringsAsFactors = FALSE)
- targ_tax <- data.frame(
- name = xml_text_all(tax_node, "./ScientificName"),
- rank = xml_text_all(tax_node, "./Rank"),
- id = xml_text_all(tax_node, "./TaxId"),
- stringsAsFactors = FALSE)
- rbind(lin, targ_tax)
- })
- # Is not directly below root and no lineage info
- parent_id <- xml_text_all(ttp, "//TaxaSet/Taxon/ParentTaxId") %||% ""
- out[vapply(out, NROW, numeric(1)) == 0 & parent_id != "1"] <- NA
- # Add NA where the taxon ID was not found
- names(out) <- xml_text(xml2::xml_find_all(ttp,
- '//TaxaSet/Taxon/TaxId'))
- success <- ! grepl(tt, pattern = 'error', ignore.case = TRUE)
+ try({
+ res$raise_for_status()
+ tt <- res$parse("UTF-8")
+ ttp <- xml2::read_xml(tt)
+ out <- lapply(xml2::xml_find_all(ttp, '//TaxaSet/Taxon'),
+ function(tax_node) {
+ lin <- data.frame(
+ name = xml_text_all(tax_node,
+ ".//LineageEx/Taxon/ScientificName"),
+ rank = xml_text_all(tax_node, ".//LineageEx/Taxon/Rank"),
+ id = xml_text_all(tax_node, ".//LineageEx/Taxon/TaxId"),
+ stringsAsFactors = FALSE)
+ targ_tax <- data.frame(
+ name = xml_text_all(tax_node, "./ScientificName"),
+ rank = xml_text_all(tax_node, "./Rank"),
+ id = xml_text_all(tax_node, "./TaxId"),
+ stringsAsFactors = FALSE)
+ rbind(lin, targ_tax)
+ })
+ # Is not directly below root and no lineage info
+ parent_id <- xml_text_all(ttp, "//TaxaSet/Taxon/ParentTaxId") %||% ""
+ out[vapply(out, NROW, numeric(1)) == 0 & parent_id != "1"] <- NA
+ # Add NA where the taxon ID was not found
+ names(out) <- xml_text(xml2::xml_find_all(ttp,
+ '//TaxaSet/Taxon/TaxId'))
+ success <- ! grepl(tt, pattern = 'error', ignore.case = TRUE)
+ }, silent=FALSE)
tries <- tries + 1
# NCBI limits requests to three per second without key or 10 per
# second with key
diff --git a/README.md b/README.md
index 2d85dc02..9d93d396 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
state and is being actively
developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[](https://cranchecks.info/pkgs/taxize)
+checks](https://badges.cranchecks.info/worst/taxize.svg)](https://cran.r-project.org/web/checks/check_results_taxize.html)
[](https://github.com/ropensci/taxize/actions/)
[](https://app.codecov.io/gh/ropensci/taxize)
[.
-- License: MIT
-- Get citation information for `taxize` in R doing
- `citation(package = 'taxize')`
-- Please note that this package is released with a [Contributor Code
- of Conduct](https://ropensci.org/code-of-conduct/). By contributing
- to this project, you agree to abide by its terms.
+- Please [report any issues or
+ bugs](https://github.com/ropensci/taxize/issues).
+- License: MIT
+- Get citation information for `taxize` in R doing
+ `citation(package = 'taxize')`
+- Please note that this package is released with a [Contributor Code of
+ Conduct](https://ropensci.org/code-of-conduct/). By contributing to
+ this project, you agree to abide by its terms.
[](https://ropensci.org)
diff --git a/debian/changelog b/debian/changelog
index 4ca7ac68..fc9da5f3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+r-cran-taxize (0.9.100+git20230103.0.d04e35d+ds-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Thu, 19 Jan 2023 14:02:19 -0000
+
r-cran-taxize (0.9.100-1) unstable; urgency=medium
* Team upload.
diff --git a/man/progressor.Rd b/man/progressor.Rd
index 80c00dae..b3e7249d 100644
--- a/man/progressor.Rd
+++ b/man/progressor.Rd
@@ -56,21 +56,21 @@ methods for preparing/printing info for prompts for \verb{get_*} functions
\section{Methods}{
\subsection{Public methods}{
\itemize{
-\item \href{#method-new}{\code{progressor$new()}}
-\item \href{#method-completed}{\code{progressor$completed()}}
-\item \href{#method-completed_found}{\code{progressor$completed_found()}}
-\item \href{#method-completed_not_found}{\code{progressor$completed_not_found()}}
-\item \href{#method-prog_start}{\code{progressor$prog_start()}}
-\item \href{#method-prog}{\code{progressor$prog()}}
-\item \href{#method-prog_found}{\code{progressor$prog_found()}}
-\item \href{#method-prog_not_found}{\code{progressor$prog_not_found()}}
-\item \href{#method-prog_summary}{\code{progressor$prog_summary()}}
-\item \href{#method-clone}{\code{progressor$clone()}}
+\item \href{#method-progressor-new}{\code{progressor$new()}}
+\item \href{#method-progressor-completed}{\code{progressor$completed()}}
+\item \href{#method-progressor-completed_found}{\code{progressor$completed_found()}}
+\item \href{#method-progressor-completed_not_found}{\code{progressor$completed_not_found()}}
+\item \href{#method-progressor-prog_start}{\code{progressor$prog_start()}}
+\item \href{#method-progressor-prog}{\code{progressor$prog()}}
+\item \href{#method-progressor-prog_found}{\code{progressor$prog_found()}}
+\item \href{#method-progressor-prog_not_found}{\code{progressor$prog_not_found()}}
+\item \href{#method-progressor-prog_summary}{\code{progressor$prog_summary()}}
+\item \href{#method-progressor-clone}{\code{progressor$clone()}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\if{html}{\out{<a id="method-progressor-new"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-new}{}}}
\subsection{Method \code{new()}}{
Create a new \code{progressor} object
\subsection{Usage}{
@@ -91,8 +91,8 @@ A new \code{progressor} object
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-completed"></a>}}
-\if{latex}{\out{\hypertarget{method-completed}{}}}
+\if{html}{\out{<a id="method-progressor-completed"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-completed}{}}}
\subsection{Method \code{completed()}}{
add results to found or not found
\subsection{Usage}{
@@ -113,8 +113,8 @@ nothing returned; adds to \verb{$found} or \verb{$not_found}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-completed_found"></a>}}
-\if{latex}{\out{\hypertarget{method-completed_found}{}}}
+\if{html}{\out{<a id="method-progressor-completed_found"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-completed_found}{}}}
\subsection{Method \code{completed_found()}}{
add to found results
\subsection{Usage}{
@@ -133,8 +133,8 @@ nothing returned; adds to \verb{$found}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-completed_not_found"></a>}}
-\if{latex}{\out{\hypertarget{method-completed_not_found}{}}}
+\if{html}{\out{<a id="method-progressor-completed_not_found"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-completed_not_found}{}}}
\subsection{Method \code{completed_not_found()}}{
add to not found results
\subsection{Usage}{
@@ -153,8 +153,8 @@ nothing returned; adds to \verb{$not_found}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-prog_start"></a>}}
-\if{latex}{\out{\hypertarget{method-prog_start}{}}}
+\if{html}{\out{<a id="method-progressor-prog_start"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-prog_start}{}}}
\subsection{Method \code{prog_start()}}{
print messages of total queries to do, and
percent completed
@@ -164,8 +164,8 @@ percent completed
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-prog"></a>}}
-\if{latex}{\out{\hypertarget{method-prog}{}}}
+\if{html}{\out{<a id="method-progressor-prog"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-prog}{}}}
\subsection{Method \code{prog()}}{
prints message of found or not found using packages
cli and crayon
@@ -185,8 +185,8 @@ messages
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-prog_found"></a>}}
-\if{latex}{\out{\hypertarget{method-prog_found}{}}}
+\if{html}{\out{<a id="method-progressor-prog_found"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-prog_found}{}}}
\subsection{Method \code{prog_found()}}{
prints found message using packages cli and crayon
\subsection{Usage}{
@@ -198,8 +198,8 @@ messages
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-prog_not_found"></a>}}
-\if{latex}{\out{\hypertarget{method-prog_not_found}{}}}
+\if{html}{\out{<a id="method-progressor-prog_not_found"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-prog_not_found}{}}}
\subsection{Method \code{prog_not_found()}}{
prints not found message using packages cli and crayon
\subsection{Usage}{
@@ -211,8 +211,8 @@ messages
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-prog_summary"></a>}}
-\if{latex}{\out{\hypertarget{method-prog_summary}{}}}
+\if{html}{\out{<a id="method-progressor-prog_summary"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-prog_summary}{}}}
\subsection{Method \code{prog_summary()}}{
prints summary at end of result with total found and
not found
@@ -225,8 +225,8 @@ messages
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-clone}{}}}
+\if{html}{\out{<a id="method-progressor-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-progressor-clone}{}}}
\subsection{Method \code{clone()}}{
The objects of this class are cloneable with this method.
\subsection{Usage}{
diff --git a/man/taxon_state.Rd b/man/taxon_state.Rd
index 867a5648..2dfae504 100644
--- a/man/taxon_state.Rd
+++ b/man/taxon_state.Rd
@@ -86,20 +86,20 @@ ts$count
\section{Methods}{
\subsection{Public methods}{
\itemize{
-\item \href{#method-new}{\code{taxon_state$new()}}
-\item \href{#method-print}{\code{taxon_state$print()}}
-\item \href{#method-add}{\code{taxon_state$add()}}
-\item \href{#method-get}{\code{taxon_state$get()}}
-\item \href{#method-remove}{\code{taxon_state$remove()}}
-\item \href{#method-purge}{\code{taxon_state$purge()}}
-\item \href{#method-taxa_remaining}{\code{taxon_state$taxa_remaining()}}
-\item \href{#method-taxa_completed}{\code{taxon_state$taxa_completed()}}
-\item \href{#method-clone}{\code{taxon_state$clone()}}
+\item \href{#method-taxon_state-new}{\code{taxon_state$new()}}
+\item \href{#method-taxon_state-print}{\code{taxon_state$print()}}
+\item \href{#method-taxon_state-add}{\code{taxon_state$add()}}
+\item \href{#method-taxon_state-get}{\code{taxon_state$get()}}
+\item \href{#method-taxon_state-remove}{\code{taxon_state$remove()}}
+\item \href{#method-taxon_state-purge}{\code{taxon_state$purge()}}
+\item \href{#method-taxon_state-taxa_remaining}{\code{taxon_state$taxa_remaining()}}
+\item \href{#method-taxon_state-taxa_completed}{\code{taxon_state$taxa_completed()}}
+\item \href{#method-taxon_state-clone}{\code{taxon_state$clone()}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\if{html}{\out{<a id="method-taxon_state-new"></a>}}
+\if{latex}{\out{\hypertarget{method-taxon_state-new}{}}}
\subsection{Method \code{new()}}{
Create a new \code{taxon_state} object
\subsection{Usage}{
@@ -120,8 +120,8 @@ A new \code{taxon_state} object
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-print"></a>}}
-\if{latex}{\out{\hypertarget{method-print}{}}}
+\if{html}{\out{<a id="method-taxon_state-print"></a>}}
+\if{latex}{\out{\hypertarget{method-taxon_state-print}{}}}
\subsection{Method \code{print()}}{
print method for the \code{taxon_state} class
\subsection{Usage}{
@@ -139,8 +139,8 @@ print method for the \code{taxon_state} class
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add"></a>}}
-\if{latex}{\out{\hypertarget{method-add}{}}}
+\if{html}{\out{<a id="method-taxon_state-add"></a>}}
+\if{latex}{\out{\hypertarget{method-taxon_state-add}{}}}
\subsection{Method \code{add()}}{
add a record with it's result; duplicates allowed
\subsection{Usage}{
@@ -161,8 +161,8 @@ nothing returned; sets only
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-get"></a>}}
-\if{latex}{\out{\hypertarget{method-get}{}}}
+\if{html}{\out{<a id="method-taxon_state-get"></a>}}
+\if{latex}{\out{\hypertarget{method-taxon_state-get}{}}}
\subsection{Method \code{get()}}{
get all records matching 'query'
\subsection{Usage}{
@@ -182,8 +182,8 @@ named by the taxon name
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-remove"></a>}}
-\if{latex}{\out{\hypertarget{method-remove}{}}}
+\if{html}{\out{<a id="method-taxon_state-remove"></a>}}
+\if{latex}{\out{\hypertarget{method-taxon_state-remove}{}}}
\subsection{Method \code{remove()}}{
remove's all records matching 'query'
\subsection{Usage}{
@@ -202,8 +202,8 @@ nothing, removes records matching query
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-purge"></a>}}
-\if{latex}{\out{\hypertarget{method-purge}{}}}
+\if{html}{\out{<a id="method-taxon_state-purge"></a>}}
+\if{latex}{\out{\hypertarget{method-taxon_state-purge}{}}}
\subsection{Method \code{purge()}}{
removes all records
\subsection{Usage}{
@@ -215,8 +215,8 @@ nothing returned; sets only
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-taxa_remaining"></a>}}
-\if{latex}{\out{\hypertarget{method-taxa_remaining}{}}}
+\if{html}{\out{<a id="method-taxon_state-taxa_remaining"></a>}}
+\if{latex}{\out{\hypertarget{method-taxon_state-taxa_remaining}{}}}
\subsection{Method \code{taxa_remaining()}}{
get remaining taxa
\subsection{Usage}{
@@ -228,8 +228,8 @@ sorted taxon names
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-taxa_completed"></a>}}
-\if{latex}{\out{\hypertarget{method-taxa_completed}{}}}
+\if{html}{\out{<a id="method-taxon_state-taxa_completed"></a>}}
+\if{latex}{\out{\hypertarget{method-taxon_state-taxa_completed}{}}}
\subsection{Method \code{taxa_completed()}}{
get completed taxa
\subsection{Usage}{
@@ -241,8 +241,8 @@ sorted taxon names
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-clone}{}}}
+\if{html}{\out{<a id="method-taxon_state-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-taxon_state-clone}{}}}
\subsection{Method \code{clone()}}{
The objects of this class are cloneable with this method.
\subsection{Usage}{
diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
deleted file mode 100644
index b57660bd..00000000
Binary files a/tests/testthat/Rplots.pdf and /dev/null differ
Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in first set of .debs but not in second
-rw-r--r-- root/root /usr/share/doc/r-cran-taxize/tests/testthat/Rplots.pdf.gz
Control files: lines which differ (wdiff format)
Depends: r-base-core (>= 4.2.2.20221110-2), 4.2.2.20221110-1), r-api-4.0, r-cran-crul (>= 0.7.0), r-cran-xml2 (>= 1.2.0), r-cran-jsonlite, r-cran-foreach, r-cran-ape, r-cran-zoo, r-cran-data.table, r-cran-tibble (>= 1.2), r-cran-bold (>= 0.8.6), r-cran-rredlist, r-cran-rotl (>= 3.0.0), r-cran-ritis (>= 0.7.6), r-cran-worrms (>= 0.4.0), r-cran-natserv (>= 1.0.0), r-cran-wikitaxa (>= 0.3.0), r-cran-r6, r-cran-crayon, r-cran-cli, r-cran-phangorn, r-cran-conditionz