From adc69bd4e1543a229fbee543940f8b92fd499682 Mon Sep 17 00:00:00 2001
From: Ranke Johannes <johannes.ranke@agroscope.admin.ch>
Date: Wed, 22 Oct 2025 10:35:37 +0200
Subject: Adapt to new SMILES names at PubChem

This may break some code using the old smiles names "PubChem_Canonical"
and "PubChem_Isomeric" instead of the new smiles names "PubChem"
(including isotopic and stereochemical information) and
"PubChem_Connectivity" (only containing connectivity, but still
canonical).

Further changes in this commit:
- A fix to the test target in the makefile
- Use markdown syntax for link to objects from other packages in the
  documentation
- Adapt the tests
- Increase test coverage a bit
---
 man/chent.Rd      | 4 ++--
 man/pai.Rd        | 2 +-
 man/plot.chent.Rd | 2 +-
 man/ppp.Rd        | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

(limited to 'man')

diff --git a/man/chent.Rd b/man/chent.Rd
index ba47feb..2da0169 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -4,7 +4,7 @@
 \alias{chent}
 \title{An R6 class for chemical entities with associated data}
 \format{
-An \code{\link{R6Class}} generator object
+An \link[R6:R6Class]{R6::R6Class} generator object
 }
 \description{
 The class is initialised with an identifier. Chemical
@@ -44,7 +44,7 @@ List of information retrieved from PubChem}
 
 \item{\code{svg}}{SVG code}
 
-\item{\code{Picture}}{Graph as a \code{\link{picture}} object obtained using grImport}
+\item{\code{Picture}}{Graph as a \link[grImport:Picture-class]{grImport::Picture} object obtained using the grImport package}
 
 \item{\code{Pict_font_size}}{Font size as extracted from the intermediate PostScript file}
 
diff --git a/man/pai.Rd b/man/pai.Rd
index d509af7..279dd24 100644
--- a/man/pai.Rd
+++ b/man/pai.Rd
@@ -4,7 +4,7 @@
 \alias{pai}
 \title{An R6 class for pesticidal active ingredients and associated data}
 \format{
-An \code{\link{R6Class}} generator object
+An \link[R6:R6Class]{R6::R6Class} generator object
 }
 \description{
 This class is derived from \link{chent}. It makes it easy
diff --git a/man/plot.chent.Rd b/man/plot.chent.Rd
index f2850fa..ecaa01b 100644
--- a/man/plot.chent.Rd
+++ b/man/plot.chent.Rd
@@ -9,7 +9,7 @@
 \arguments{
 \item{x}{The chent object to be plotted}
 
-\item{...}{Further arguments passed to \code{\link{grid.picture}}}
+\item{...}{Further arguments passed to \link[grImport:grid.picture]{grImport::grid.picture}}
 }
 \description{
 Plot method for chent objects
diff --git a/man/ppp.Rd b/man/ppp.Rd
index 4e456c4..a01b3bb 100644
--- a/man/ppp.Rd
+++ b/man/ppp.Rd
@@ -4,7 +4,7 @@
 \alias{ppp}
 \title{R6 class for a plant protection product with at least one active ingredient}
 \format{
-An \code{\link{R6Class}} generator object.
+An \link[R6:R6Class]{R6::R6Class} generator object.
 }
 \description{
 Contains basic information about the active ingredients in the
-- 
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