pkgdown update

Author: rfhb

.github/workflows/check-standard.yml

@@ -95,12 +95,12 @@ jobs:
 
       # for nodbi:
 
-      - name: Install duckdb extension library
+      - name: Try installing duckdb extension library
         run: |
           library(duckdb)
           drv <- duckdb()
           con <- dbConnect(drv)
-          dbExecute(con, 'INSTALL json;')
+          try(dbExecute(con, 'INSTALL json;'), silent = TRUE)
           dbDisconnect(con)
           duckdb_shutdown(drv)
         shell: Rscript {0}

DESCRIPTION

@@ -1,19 +1,15 @@
 Package: nodbi
-Title: 'NoSQL' Database Connector
-Description: Simplified JSON document database access and manipulation,
-     providing a common API across supported 'NoSQL' databases 
-     'Elasticsearch', 'CouchDB', 'MongoDB' as well as 
-     'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
+Title: 'NoSQL' Database Interface
+Description: R database interface for creating, reading (querying and listing 
+     fields), updating and deleting of individual or many JSON documents, 
+     providing a common API across supported databases ('SQLite', 'PostgreSQL', 
+     'DuckDB' and 'NoSQL' databases 'MongoDB', 'CouchDB' and 'Elasticsearch').
 Version: 0.14.0.9000
 Authors@R: c(
-    person(given = "Ralf",
-           family = "Herold",
-           role = c("aut", "cre"),
+    person("Ralf", "Herold", role = c("aut", "cre"),
            email = "ralf.herold@mailbox.org",
            comment = c(ORCID = "0000-0002-8148-6748")),
-    person(given = "Scott", 
-           family = "Chamberlain", 
-           role = "aut",
+    person("Scott", "Chamberlain", role = "aut",
            comment = c(ORCID = "0000-0003-1444-9135")),
     person("Rich", "FitzJohn", role = "aut"),
     person("Jeroen", "Ooms", role = "aut"),

NEWS.md

@@ -1,6 +1,6 @@
 # nodbi 0.14.0.9000
 
-* Changes to address that package elastic was archived
+* Changes to address that package elastic was archived (CI, documentation)
 
 # nodbi 0.14.0
 

R/src_elastic.R

@@ -28,7 +28,12 @@
 #' document ID `_id`, otherwise a UUID is created as document ID `_id`.
 #' Only lowercase is accepted for container names (in parameter `key`).
 #' Opensearch can equally be used.
-#' For a benchmark, see <https://github.com/ropensci/nodbi#benchmark>
+#' For a benchmark, see <https://github.com/ropensci/nodbi#benchmark>.
+#'
+#' As of 2026-01-17, the future availability and development of package elastic
+#' is not clear after it was recently archived, see also
+#' <https://github.com/opensci-archive/elastic>; at this time, it can still be
+#' installed by calling `remotes::install_github("ropensci-archive/elastic")`
 #'
 #' @return A `nodbi` source object
 #'

README.Rmd

@@ -108,6 +108,16 @@ src <- nodbi::src_mongo(
 src <- nodbi::src_sqlite(dbname = ":memory:", ...)
 ```
 
+### PostgreSQL
+
+"Container" refers to a PostgreSQL table, with columns `_id` and `json` created and used by package `nodbi`, applying SQL functions and functions as per <https://www.postgresql.org/docs/current/functions-json.html> to the `json` column. With PostgreSQL, a custom `plpgsql` function [jsonb_merge_patch()](https://github.com/ropensci/nodbi/blob/master/R/src_postgres.R#L60) is used for `docdb_update()`. The order of variables in data frames returned by `docdb_get()` and `docdb_query()` can differ from their order the input to `docdb_create()`. 
+
+```{r}
+src <- nodbi::src_postgres(
+  dbname = "my_database", host = "127.0.0.1", port = 5432L, ...
+)
+```
+
 ### CouchDB
 
 "Container" refers to a CouchDB database, in which `nodbi` creates JSON documents. See also <https://CRAN.R-project.org/package=sofa>. With CouchDB, function `docdb_update()` uses [jqr](https://cran.r-project.org/package=jqr) to implement patching JSON, in analogy to functions available for the other databases. 
@@ -136,16 +146,6 @@ As of 2026-01-17, the future availability and development of package elastic is
 remotes::install_github("ropensci-archive/elastic")
 ```
 
-### PostgreSQL
-
-"Container" refers to a PostgreSQL table, with columns `_id` and `json` created and used by package `nodbi`, applying SQL functions and functions as per <https://www.postgresql.org/docs/current/functions-json.html> to the `json` column. With PostgreSQL, a custom `plpgsql` function [jsonb_merge_patch()](https://github.com/ropensci/nodbi/blob/master/R/src_postgres.R#L60) is used for `docdb_update()`. The order of variables in data frames returned by `docdb_get()` and `docdb_query()` can differ from their order the input to `docdb_create()`. 
-
-```{r}
-src <- nodbi::src_postgres(
-  dbname = "my_database", host = "127.0.0.1", port = 5432L, ...
-)
-```
-
 ## Walk-through {#walk-through}
 
 This example is to show how functional `nodbi` is at this time: With any of the six database backends, the functions work in the same way and return the same values. 

README.md

@@ -125,6 +125,24 @@ indexed on `_id`. See also <https://CRAN.R-project.org/package=RSQLite>.
 src <- nodbi::src_sqlite(dbname = ":memory:", ...)
 ```
 
+### PostgreSQL
+
+“Container” refers to a PostgreSQL table, with columns `_id` and `json`
+created and used by package `nodbi`, applying SQL functions and
+functions as per
+<https://www.postgresql.org/docs/current/functions-json.html> to the
+`json` column. With PostgreSQL, a custom `plpgsql` function
+[jsonb_merge_patch()](https://github.com/ropensci/nodbi/blob/master/R/src_postgres.R#L60)
+is used for `docdb_update()`. The order of variables in data frames
+returned by `docdb_get()` and `docdb_query()` can differ from their
+order the input to `docdb_create()`.
+
+``` r
+src <- nodbi::src_postgres(
+  dbname = "my_database", host = "127.0.0.1", port = 5432L, ...
+)
+```
+
 ### CouchDB
 
 “Container” refers to a CouchDB database, in which `nodbi` creates JSON
@@ -163,24 +181,6 @@ be installed as follows.
 remotes::install_github("ropensci-archive/elastic")
 ```
 
-### PostgreSQL
-
-“Container” refers to a PostgreSQL table, with columns `_id` and `json`
-created and used by package `nodbi`, applying SQL functions and
-functions as per
-<https://www.postgresql.org/docs/current/functions-json.html> to the
-`json` column. With PostgreSQL, a custom `plpgsql` function
-[jsonb_merge_patch()](https://github.com/ropensci/nodbi/blob/master/R/src_postgres.R#L60)
-is used for `docdb_update()`. The order of variables in data frames
-returned by `docdb_get()` and `docdb_query()` can differ from their
-order the input to `docdb_create()`.
-
-``` r
-src <- nodbi::src_postgres(
-  dbname = "my_database", host = "127.0.0.1", port = 5432L, ...
-)
-```
-
 ## Walk-through
 
 This example is to show how functional `nodbi` is at this time: With any

codemeta.json

@@ -2,8 +2,8 @@
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@type": "SoftwareSourceCode",
   "identifier": "nodbi",
-  "description": "Simplified JSON document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.",
-  "name": "nodbi: 'NoSQL' Database Connector",
+  "description": "R database interface for creating, reading (querying and listing fields), updating and deleting of individual or many JSON documents, providing a common API across supported databases ('SQLite', 'PostgreSQL', 'DuckDB' and 'NoSQL' databases 'MongoDB', 'CouchDB' and 'Elasticsearch').",
+  "name": "nodbi: 'NoSQL' Database Interface",
   "relatedLink": ["https://docs.ropensci.org/nodbi/", "https://CRAN.R-project.org/package=nodbi"],
   "codeRepository": "https://github.com/ropensci/nodbi",
   "issueTracker": "https://github.com/ropensci/nodbi/issues",
@@ -316,7 +316,7 @@
   "applicationCategory": "Databases",
   "isPartOf": "https://ropensci.org",
   "keywords": ["database", "MongoDB", "Elasticsearch", "CouchDB", "SQLite", "PostgreSQL", "DuckDB", "NoSQL", "JSON", "documents", "rstats", "nosql", "couchdb", "mongodb", "elasticsearch", "r", "r-package", "sqlite", "postgresql"],
-  "fileSize": "669.266KB",
+  "fileSize": "676.108KB",
   "releaseNotes": "https://github.com/ropensci/nodbi/blob/main/NEWS.md",
   "readme": "https://github.com/ropensci/nodbi/blob/master/README.md",
   "contIntegration": ["https://github.com/ropensci/nodbi/actions?query=workflow%3AR-CMD-check", "https://app.codecov.io/gh/rfhb/nodbi"],