fixed build error on Solaris: _X is a reserved keyword

gagolews · Jan 7, 2021 · b29cf21 · b29cf21
1 parent ae7c36e
commit b29cf21
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: genieclust
 Type: Package
 Title: The Genie++ Hierarchical Clustering Algorithm with Noise Points Detection
 Version: 0.9.8
-Date: 2021-01-07
+Date: 2021-01-08
 Authors@R: c(
     person("Marek", "Gagolewski",
         role = c("aut", "cre", "cph"),

diff --git a/Makefile b/Makefile
@@ -24,6 +24,9 @@ rd2rst:
 	# https://github.com/gagolews/Rd2rst
 	cd devel/sphinx && Rscript -e "Rd2rst::Rd2rst('genieclust')" && cd ../../
 
+news:
+	cd devel/sphinx && pandoc ../../NEWS -f markdown -t rst -o news.rst
+
 #rapiold:
 	#Rscript -e "Rd2md::ReferenceManual()"
 	#Rscript -e "f <- readLines('Reference_Manual_genieclust.md');" \
@@ -36,7 +39,7 @@ rd2rst:
 	##rstlisttable --in-place devel/sphinx/r.rst
 	#rm -f Reference_Manual_genieclust.md r.md
 
-sphinx: python r weave rd2rst
+sphinx: python r weave rd2rst news
 	rm -rf devel/sphinx/_build/
 	cd devel/sphinx && make html && cd ../../
 	rm -rf docs/
@@ -67,7 +70,7 @@ r-build:
 
 r-check: r-build
 	#Rscript -e 'devtools::check(cran=TRUE, remote=TRUE, manual=TRUE)'  # avoid redundant dependencies
-	cd .. && R CMD check `ls -t genieclust*.tar.gz | head -1` --no-manual #  --as-cran
+	cd .. && R CMD check `ls -t genieclust*.tar.gz | head -1` --no-manual --as-cran
 
 clean:
 	python3 setup.py clean

diff --git a/NEWS b/NEWS
@@ -1,9 +1,9 @@
-# `genieclust` Package NEWS
+# What's New in *genieclust*
 
 
-## genieclust 0.9.8 (2021-xx-xx)
+## genieclust 0.9.8 (2021-01-08)
 
--   ...
+-   [Bugfix] [R] Fixed build errors on Solaris: `_X` is a reserved identifier.
 
 
 ## genieclust 0.9.7 (2021-01-07)
@@ -22,50 +22,50 @@
 
 -   [Python] `nmslib` is now required.
 
--   [R] switched to `tinytest` for unit testing.
+-   [R] Switched to `tinytest` for unit testing.
 
--   [R] fixed the examples that relied on a now-changed API of `emstreeR`.
+-   [R] Fixed the examples that relied on the amended API of `emstreeR`.
 
 
 ## genieclust 0.9.4 (2020-07-31)
 
--   [BUGFIX] [R] Fix build on Solaris.
+-   [Bugfix] [R] Fix build on Solaris.
 
 
 ## genieclust 0.9.3 (2020-07-25)
 
--   [BUGFIX] [PYTHON] Code coverage CI added. Fixed some minor inconsistencies.
+-   [Bugfix] [Python] Code coverage CI added. Fixed some minor inconsistencies.
     Automated the `bdist` build chain.
 
 -   [R] Updated DESCRIPTION to meet the CRAN policies.
 
 
 ## genieclust 0.9.2 (2020-07-22)
 
--   [BUGFIX] [PYTHON] Fixed broken build script for OS X with no OpenMP.
+-   [BUGFIX] [Python] Fixed broken build script for OS X with no OpenMP.
 
 
 ## genieclust 0.9.1 (2020-07-18)
 
--   [GENERAL] The package has been completely rewritten.
+-   [General] The package has been completely rewritten.
     The core functionality is now implemented in C++ (with OpenMP).
 
--   [GENERAL] Clustering with respect to HDBSCAN*-like
+-   [General] Clustering with respect to HDBSCAN*-like
     mutual reachability distances is supported.
 
--   [GENERAL] The parallelised Jarnik-Prim algorithm now supports on-the-fly
+-   [General] The parallelised Jarnik-Prim algorithm now supports on-the-fly
     distance computations. Euclidean minimum spanning tree can be
     determined with `mlpack`, which is much faster in low-dimensional spaces.
 
 -   [R] R version is now available.
 
--   [PYTHON] [EXPERIMENTAL] The GIc algorithm proposed by Anna Cena
+-   [Python] [Experimental] The GIc algorithm proposed by Anna Cena
     in her 2018 PhD thesis was added.
 
--   [PYTHON] Approximate version based on nearest neighbour graphs produced
+-   [Python] Approximate version based on nearest neighbour graphs produced
     by `nmslib` was added.
 
 
 ## genieclust 0.1a2 (2018-05-23)
 
--   [PYTHON] Initial PyPI release.
+-   [Python] Initial PyPI release.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -150,23 +150,23 @@ pair_sets_index <- function(x, y = NULL) {
 }
 
 .emst_mlpack <- function(X) {
-    .Call(`_genieclust___emst_mlpack`, X)
+    .Call(`_genieclust_dot_emst_mlpack`, X)
 }
 
-.gclust <- function(mst, gini_threshold, verbose) {
-    .Call(`_genieclust___gclust`, mst, gini_threshold, verbose)
+.mst.default <- function(X, distance = "euclidean", M = 1L, cast_float32 = TRUE, verbose = FALSE) {
+    .Call(`_genieclust_dot_mst_default`, X, distance, M, cast_float32, verbose)
 }
 
-.genie <- function(mst, k, gini_threshold, postprocess, detect_noise, verbose) {
-    .Call(`_genieclust___genie`, mst, k, gini_threshold, postprocess, detect_noise, verbose)
+.mst.dist <- function(d, M = 1L, verbose = FALSE) {
+    .Call(`_genieclust_dot_mst_dist`, d, M, verbose)
 }
 
-.mst.default <- function(X, distance = "euclidean", M = 1L, cast_float32 = TRUE, verbose = FALSE) {
-    .Call(`_genieclust_mst_default`, X, distance, M, cast_float32, verbose)
+.genie <- function(mst, k, gini_threshold, postprocess, detect_noise, verbose) {
+    .Call(`_genieclust_dot_genie`, mst, k, gini_threshold, postprocess, detect_noise, verbose)
 }
 
-.mst.dist <- function(d, M = 1L, verbose = FALSE) {
-    .Call(`_genieclust_mst_dist`, d, M, verbose)
+.gclust <- function(mst, gini_threshold, verbose) {
+    .Call(`_genieclust_dot_gclust`, mst, gini_threshold, verbose)
 }
 
 #' @title Inequity (Inequality) Measures

diff --git a/devel/sphinx/index.rst b/devel/sphinx/index.rst
@@ -95,6 +95,7 @@ any contributions are welcome.
 
     genieclust
     rapi
+    news
 
 .. toctree::
     :maxdepth: 2

diff --git a/devel/sphinx/news.rst b/devel/sphinx/news.rst
@@ -0,0 +1,76 @@
+What’s New in *genieclust*
+==========================
+
+genieclust 0.9.8 (2021-01-08)
+-----------------------------
+
+-  [Bugfix] [R] Fixed build errors on Solaris: ``_X`` is a reserved
+   identifier.
+
+genieclust 0.9.7 (2021-01-07)
+-----------------------------
+
+-  [Python] Python >= 3.7 is now required (implied by ``numpy``).
+
+-  [R] Use ``RcppMLPACK`` directly instead of via a wrapper,
+   ``emstreeR``.
+
+genieclust 0.9.6 (2021-01-05)
+-----------------------------
+
+-  [Python] Python >= 3.7 is now required (implied by ``numpy``).
+
+genieclust 0.9.5 (2021-01-04)
+-----------------------------
+
+-  [Python] ``nmslib`` is now required.
+
+-  [R] Switched to ``tinytest`` for unit testing.
+
+-  [R] Fixed the examples that relied on the amended API of
+   ``emstreeR``.
+
+genieclust 0.9.4 (2020-07-31)
+-----------------------------
+
+-  [Bugfix] [R] Fix build on Solaris.
+
+genieclust 0.9.3 (2020-07-25)
+-----------------------------
+
+-  [Bugfix] [Python] Code coverage CI added. Fixed some minor
+   inconsistencies. Automated the ``bdist`` build chain.
+
+-  [R] Updated DESCRIPTION to meet the CRAN policies.
+
+genieclust 0.9.2 (2020-07-22)
+-----------------------------
+
+-  [BUGFIX] [Python] Fixed broken build script for OS X with no OpenMP.
+
+genieclust 0.9.1 (2020-07-18)
+-----------------------------
+
+-  [General] The package has been completely rewritten. The core
+   functionality is now implemented in C++ (with OpenMP).
+
+-  [General] Clustering with respect to HDBSCAN*-like mutual
+   reachability distances is supported.
+
+-  [General] The parallelised Jarnik-Prim algorithm now supports
+   on-the-fly distance computations. Euclidean minimum spanning tree can
+   be determined with ``mlpack``, which is much faster in
+   low-dimensional spaces.
+
+-  [R] R version is now available.
+
+-  [Python] [Experimental] The GIc algorithm proposed by Anna Cena in
+   her 2018 PhD thesis was added.
+
+-  [Python] Approximate version based on nearest neighbour graphs
+   produced by ``nmslib`` was added.
+
+genieclust 0.1a2 (2018-05-23)
+-----------------------------
+
+-  [Python] Initial PyPI release.
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -95,6 +95,7 @@ any contributions are welcome.
 
     genieclust
     rapi
+    news
 
 .. toctree::
     :maxdepth: 2

diff --git a/docs/_sources/news.rst.txt b/docs/_sources/news.rst.txt
@@ -0,0 +1,76 @@
+What’s New in *genieclust*
+==========================
+
+genieclust 0.9.8 (2021-01-08)
+-----------------------------
+
+-  [Bugfix] [R] Fixed build errors on Solaris: ``_X`` is a reserved
+   identifier.
+
+genieclust 0.9.7 (2021-01-07)
+-----------------------------
+
+-  [Python] Python >= 3.7 is now required (implied by ``numpy``).
+
+-  [R] Use ``RcppMLPACK`` directly instead of via a wrapper,
+   ``emstreeR``.
+
+genieclust 0.9.6 (2021-01-05)
+-----------------------------
+
+-  [Python] Python >= 3.7 is now required (implied by ``numpy``).
+
+genieclust 0.9.5 (2021-01-04)
+-----------------------------
+
+-  [Python] ``nmslib`` is now required.
+
+-  [R] Switched to ``tinytest`` for unit testing.
+
+-  [R] Fixed the examples that relied on the amended API of
+   ``emstreeR``.
+
+genieclust 0.9.4 (2020-07-31)
+-----------------------------
+
+-  [Bugfix] [R] Fix build on Solaris.
+
+genieclust 0.9.3 (2020-07-25)
+-----------------------------
+
+-  [Bugfix] [Python] Code coverage CI added. Fixed some minor
+   inconsistencies. Automated the ``bdist`` build chain.
+
+-  [R] Updated DESCRIPTION to meet the CRAN policies.
+
+genieclust 0.9.2 (2020-07-22)
+-----------------------------
+
+-  [BUGFIX] [Python] Fixed broken build script for OS X with no OpenMP.
+
+genieclust 0.9.1 (2020-07-18)
+-----------------------------
+
+-  [General] The package has been completely rewritten. The core
+   functionality is now implemented in C++ (with OpenMP).
+
+-  [General] Clustering with respect to HDBSCAN*-like mutual
+   reachability distances is supported.
+
+-  [General] The parallelised Jarnik-Prim algorithm now supports
+   on-the-fly distance computations. Euclidean minimum spanning tree can
+   be determined with ``mlpack``, which is much faster in
+   low-dimensional spaces.
+
+-  [R] R version is now available.
+
+-  [Python] [Experimental] The GIc algorithm proposed by Anna Cena in
+   her 2018 PhD thesis was added.
+
+-  [Python] Approximate version based on nearest neighbour graphs
+   produced by ``nmslib`` was added.
+
+genieclust 0.1a2 (2018-05-23)
+-----------------------------
+
+-  [Python] Initial PyPI release.
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.9.6',
+    VERSION: '0.9.8',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/genieclust.html b/docs/genieclust.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Python Package genieclust Reference &mdash; genieclust 0.9.6 documentation</title>
+  <title>Python Package genieclust Reference &mdash; genieclust 0.9.8 documentation</title>
 
 
 
@@ -66,7 +66,7 @@
 
 
               <div class="version">
-                0.9.6
+                0.9.8
               </div>
 
 
@@ -114,6 +114,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="rapi.html">R Package <em>genieclust</em> Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="news.html">What’s New in <em>genieclust</em></a></li>
 </ul>
 <p class="caption"><span class="caption-text">External Links</span></p>
 <ul>

diff --git a/docs/genieclust_compare_partitions.html b/docs/genieclust_compare_partitions.html
@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>genieclust.compare_partitions &mdash; genieclust 0.9.6 documentation</title>
+  <title>genieclust.compare_partitions &mdash; genieclust 0.9.8 documentation</title>
 
 
 
@@ -66,7 +66,7 @@
 
 
               <div class="version">
-                0.9.6
+                0.9.8
               </div>
 
 
@@ -114,6 +114,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="rapi.html">R Package <em>genieclust</em> Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="news.html">What’s New in <em>genieclust</em></a></li>
 </ul>
 <p class="caption"><span class="caption-text">External Links</span></p>
 <ul>
-Original file line number
+Diff line change
@@ Expand Up / @@ -95,6 +95,7 @@ any contributions are welcome. @@
         genieclust
         rapi
+        news
     .. toctree::
         :maxdepth: 2
@@ Expand Down @@