Fix R stuff

Author: michalsta

src/IsoSpec++/cwrapper.h

@@ -16,6 +16,8 @@
 
 #pragma once
 
+#include "platform.h"
+
 #define ISOSPEC_ALGO_LAYERED 0
 #define ISOSPEC_ALGO_ORDERED 1
 #define ISOSPEC_ALGO_THRESHOLD_ABSOLUTE 2

src/IsoSpec++/element_tables.cpp

@@ -23,7 +23,7 @@ namespace IsoSpec
 extern "C" {
 #endif
 
-const size_t isospec_number_of_isotopic_entries = ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES;
+const ::size_t isospec_number_of_isotopic_entries = ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES;
 
 const int elem_table_ID [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {
 1,

src/IsoSpec++/element_tables.h

@@ -18,6 +18,8 @@
 
 #include <stddef.h>
 
+#include "platform.h"
+
 namespace IsoSpec
 {
 

src/IsoSpec++/fixedEnvelopes.cpp

@@ -16,6 +16,7 @@
 
 #include "fixedEnvelopes.h"
 #include <limits>
+#include <cassert>
 #include "isoMath.h"
 
 namespace IsoSpec

src/IsoSpec++/marginalTrek++.cpp

@@ -737,4 +737,7 @@ SingleAtomMarginal<add_guards>::SingleAtomMarginal(Marginal&& m, int, int)
         guarded_lProbs = lProbs.data();
 }
 
+template class SingleAtomMarginal<true>;
+template SingleAtomMarginal<false>::SingleAtomMarginal(IsoSpec::Marginal&&, int, int);
+
 }  // namespace IsoSpec

src/IsoSpecR/DESCRIPTION

@@ -2,9 +2,18 @@ Encoding: UTF-8
 Package: IsoSpecR
 Type: Package
 Title: The IsoSpec Algorithm
-Version: 2.2.0
-Date: 2021-07-01
-Author: Mateusz Krzysztof Lacki and Michal Startek
+Version: 2.3.0
+Date: 2025-10-25
+Authors@R: c(person(given = c("Mateusz", "Krzysztof"),
+                      family = "Lacki",
+                      role = "aut"),
+               person(given = "Michal",
+                      family = "Startek",
+                      role = "aut"),
+               person(given = "Matteo",
+                      family = "Lacki",
+                      role = "cre",
+                      email = "matteo.lacki@gmail.com"))
 Maintainer: Matteo Lacki <matteo.lacki@gmail.com>
 Description: IsoSpec is a fine structure calculator used for obtaining the most
     probable masses of a chemical compound given the frequencies of the composing
@@ -27,5 +36,5 @@ Suggests:
 LazyData: no
 LinkingTo: Rcpp
 NeedsCompilation: yes
-SystemRequirements: C++14
+SystemRequirements: C++17
 RoxygenNote: 7.1.1

src/IsoSpecR/LICENCE

@@ -1,3 +1,3 @@
-YEAR: 2015-2018
+YEAR: 2015-2025
 COPYRIGHT HOLDER: Michał Startek, Mateusz Łącki
 

src/IsoSpecR/inst/CITATION

@@ -1,38 +1,35 @@
 citHeader("To cite IsoSpecR in publications use:")
 
-citEntry(entry = "Article",
-title          = "{IsoSpec2}: Ultrafast Fine Structure Calculator",
-author         = personList(as.person("Mateusz K. Łącki"), as.person("Dirk Valkenborg"), as.person("Michał Startek")),
-year           = "2020",
-journal        = "Analytical Chemistry",
-volume         = "92",
-number         = "14",
-pages          = "9472-9475",
-doi            = "10.1021/acs.analchem.0c00959",
-url            = "https://doi.org/10.1021/acs.analchem.0c00959",
-
-textVersion = paste("Mateusz K. Łącki, Dirk Valkenborg, Michał Startek (2020).",
-                    "IsoSpec2: Ultrafast Fine Structure Calculator",
-                    "Analytical Chemistry, Published online ahead of print",
-                    "URL https://doi.org/10.1021/acs.analchem.0c00959")
+bibentry(
+  bibtype = "Article",
+  title   = "{IsoSpec2}: Ultrafast Fine Structure Calculator",
+  author  = c(person("Mateusz K. Łącki"), person("Dirk Valkenborg"), person("Michał Startek")),
+  year    = "2020",
+  journal = "Analytical Chemistry",
+  volume  = "92",
+  number  = "14",
+  pages   = "9472-9475",
+  doi     = "10.1021/acs.analchem.0c00959",
+  url     = "https://doi.org/10.1021/acs.analchem.0c00959",
+  note    = paste("Mateusz K. Łącki, Dirk Valkenborg, Michał Startek (2020).",
+                  "IsoSpec2: Ultrafast Fine Structure Calculator",
+                  "Analytical Chemistry, Published online ahead of print",
+                  "URL https://doi.org/10.1021/acs.analchem.0c00959")
 )
 
-citEntry(entry = "Article",
-  title        = "{IsoSpec}: Hyperfast Fine Structure Calculator",
-  author       = personList(as.person("Mateusz K. Łącki"),
-                   as.person("Michał Startek"),
-                   as.person("Dirk Valkenborg"),
-                   as.person("Anna Gambin")),
-  journal      = "Analytical Chemistry",
-  year         = "2017",
-  volume       = "89",
-  number       = "6",
-  pages        = "3272-3277",
-  url          = "https://doi.org/10.1021/acs.analchem.6b01459",
-
-  textVersion  =
-  paste("Mateusz K. Łącki, Michał Startek, Dirk Valkenborg, Anna Gambin (2017).",
-        "IsoSpec: Hyperfast Fine Structure Calculator.",
-        "Analytical Chemistry 89(6), 3272-3277.",
-        "URL https://doi.org/10.1021/acs.analchem.6b01459")
+bibentry(
+  bibtype = "Article",
+  title   = "{IsoSpec}: Hyperfast Fine Structure Calculator",
+  author  = c(person("Mateusz K. Łącki"), person("Michał Startek"),
+              person("Dirk Valkenborg"), person("Anna Gambin")),
+  journal = "Analytical Chemistry",
+  year    = "2017",
+  volume  = "89",
+  number  = "6",
+  pages   = "3272-3277",
+  url     = "https://doi.org/10.1021/acs.analchem.6b01459",
+  note    = paste("Mateusz K. Łącki, Michał Startek, Dirk Valkenborg, Anna Gambin (2017).",
+                  "IsoSpec: Hyperfast Fine Structure Calculator.",
+                  "Analytical Chemistry 89(6), 3272-3277.",
+                  "URL https://doi.org/10.1021/acs.analchem.6b01459")
 )