sparsevb 0.1.1__tar.gz

sparsevb-0.1.1/MANIFEST.in

@@ -0,0 +1,5 @@
+recursive-include sparsevb *.pyx *.cpp *.h
+recursive-include include *
+include setup.py
+include requirements.txt
+include README.md

sparsevb-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: sparsevb
+Version: 0.1.1
+Summary: Spike-and-Slab Variational Bayes for Linear and Logistic Regression
+Author-email: Gabriel Clara <gabriel.j.clara@gmail.com>
+License-Expression: GPL-3.0-or-later
+Project-URL: Repository, https://gitlab.com/gclara/varpack
+Keywords: variational-bayes,spike-and-slab,sparse-regression,bayesian,variable-selection
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Cython
+Classifier: Programming Language :: C++
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: scipy>=1.6.0
+Requires-Dist: scikit-learn>=1.0.0
+
+# sparsevb
+
+A Python package for Spike-and-Slab Variational Bayes for Linear and Logistic Regression.
+
+## Description
+
+This package provides variational Bayesian algorithms to perform scalable variable selection for sparse, high-dimensional linear and logistic regression models. The algorithms are implemented in C++ for performance and exposed to Python using Cython. 
+
+It is a direct port of the R `sparsevb` package, using the same underlying C++ logic but with a Pythonic API.
+
+## Installation
+
+To install the package from source:
+
+```bash
+pip install .
+```
+
+## Usage
+
+Here is a basic example of how to use the package:
+
+```python
+import numpy as np
+from sparsevb import svb_fit_linear, svb_fit_logit
+
+# Generate some synthetic data
+np.random.seed(42)
+n_samples, n_features = 200, 20
+X = np.random.randn(n_samples, n_features)
+beta_true = np.zeros(n_features)
+beta_true[:3] = [1.5, -2.0, 3.0]
+intercept_true = 5.0
+y = X.dot(beta_true) + intercept_true + 0.1 * np.random.randn(n_samples)
+
+# Fit a sparse linear regression model
+res = svb_fit_linear(X, y, intercept=True)
+print("Estimated coefficients (mu * gamma):", res['mu'] * res['gamma'])
+print("Estimated intercept:", res['intercept'])
+print("Estimated noise variance (noise_sd):", res['noise_sd'])
+
+# For logistic regression (binary classification)
+logits = X.dot(beta_true) + intercept_true
+probs = 1 / (1 + np.exp(-logits))
+y_binary = (np.random.rand(n_samples) < probs).astype(float)
+
+res_logit = svb_fit_logit(X, y_binary, intercept=True)
+print("Estimated logistic coefficients:", res_logit['mu'] * res_logit['gamma'])
+print("Estimated logistic intercept:", res_logit['intercept'])
+```
+
+## Features
+
+- **Prioritized Initialization**: Uses Ridge and Lasso (via `scikit-learn`) to provide robust starting points.
+- **Intercept Handling**: Built-in support for model intercepts.
+- **Noise Estimation**: Automatic estimation of residual noise for linear models.
+- **Same Core Logic**: Uses the exact same C++ algorithms as the original R package for reliable results.
+
+## Dependencies
+
+- Python >= 3.8
+- NumPy >= 1.20.0
+- SciPy >= 1.6.0
+- scikit-learn >= 1.0.0
+- Cython >= 0.29.0
+
+## License
+
+This project is licensed under the GNU General Public License v3.0.
+
+## References
+
+- Kolyan Ray and Botond Szabo (2020). "Scalable Spike-and-Slab Variational Bayes for Linear and Logistic Regression." [DOI:10.1080/01621459.2020.1847121](https://doi.org/10.1080/01621459.2020.1847121)

sparsevb-0.1.1/README.md

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+# sparsevb
+
+A Python package for Spike-and-Slab Variational Bayes for Linear and Logistic Regression.
+
+## Description
+
+This package provides variational Bayesian algorithms to perform scalable variable selection for sparse, high-dimensional linear and logistic regression models. The algorithms are implemented in C++ for performance and exposed to Python using Cython. 
+
+It is a direct port of the R `sparsevb` package, using the same underlying C++ logic but with a Pythonic API.
+
+## Installation
+
+To install the package from source:
+
+```bash
+pip install .
+```
+
+## Usage
+
+Here is a basic example of how to use the package:
+
+```python
+import numpy as np
+from sparsevb import svb_fit_linear, svb_fit_logit
+
+# Generate some synthetic data
+np.random.seed(42)
+n_samples, n_features = 200, 20
+X = np.random.randn(n_samples, n_features)
+beta_true = np.zeros(n_features)
+beta_true[:3] = [1.5, -2.0, 3.0]
+intercept_true = 5.0
+y = X.dot(beta_true) + intercept_true + 0.1 * np.random.randn(n_samples)
+
+# Fit a sparse linear regression model
+res = svb_fit_linear(X, y, intercept=True)
+print("Estimated coefficients (mu * gamma):", res['mu'] * res['gamma'])
+print("Estimated intercept:", res['intercept'])
+print("Estimated noise variance (noise_sd):", res['noise_sd'])
+
+# For logistic regression (binary classification)
+logits = X.dot(beta_true) + intercept_true
+probs = 1 / (1 + np.exp(-logits))
+y_binary = (np.random.rand(n_samples) < probs).astype(float)
+
+res_logit = svb_fit_logit(X, y_binary, intercept=True)
+print("Estimated logistic coefficients:", res_logit['mu'] * res_logit['gamma'])
+print("Estimated logistic intercept:", res_logit['intercept'])
+```
+
+## Features
+
+- **Prioritized Initialization**: Uses Ridge and Lasso (via `scikit-learn`) to provide robust starting points.
+- **Intercept Handling**: Built-in support for model intercepts.
+- **Noise Estimation**: Automatic estimation of residual noise for linear models.
+- **Same Core Logic**: Uses the exact same C++ algorithms as the original R package for reliable results.
+
+## Dependencies
+
+- Python >= 3.8
+- NumPy >= 1.20.0
+- SciPy >= 1.6.0
+- scikit-learn >= 1.0.0
+- Cython >= 0.29.0
+
+## License
+
+This project is licensed under the GNU General Public License v3.0.
+
+## References
+
+- Kolyan Ray and Botond Szabo (2020). "Scalable Spike-and-Slab Variational Bayes for Linear and Logistic Regression." [DOI:10.1080/01621459.2020.1847121](https://doi.org/10.1080/01621459.2020.1847121)

sparsevb-0.1.1/include/README

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+Procedure for updating the ensmallen library:
+
+- Download ensmallen from upstream
+- Copy and replace the ensmallen.hpp and ensmallen_bits found in this directory

sparsevb-0.1.1/include/RcppArmadillo/Alt_R_RNG.h

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+
+// This file support the legacy location and includes from the new location
+
+#include "RcppArmadillo/rng/Alt_R_RNG.h"

sparsevb-0.1.1/include/RcppArmadillo/Light

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+// Emacs, please make this  -*- mode: C++; -*-
+
+// RcppArmadillo: Rcpp/Armadillo glue
+//
+// Copyright (C)  2010 - 2022  Dirk Eddelbuettel, Romain Francois and Douglas Bates
+//
+// This file is part of RcppArmadillo.
+//
+// RcppArmadillo is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// RcppArmadillo is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef RcppArmadillo__RcppArmadillo
+#define RcppArmadillo__RcppArmadillo
+
+#if defined(Rcpp_hpp) && !defined(COMPILING_RCPPARMADILLO)
+    #error "The file 'Rcpp.h' should not be included. Please correct to include only 'RcppArmadillo.h'."
+#endif
+
+// We are undoing a design decision from early on by allowing vectors be returned
+// as standard 'one-dimension' objects -- as opposed to the matrix form we imposed
+#define RCPP_ARMADILLO_RETURN_ANYVEC_AS_VECTOR
+
+// Deal with Armadillo 14.6.3 (fallback) versus 15.0.* (or later, preference) selection
+#include <RcppArmadillo/version/arma.h>
+
+// Set up actual #include <armadillo> after first #include <RcppArmadilloConfig> and more config
+#include <RcppArmadillo/interface/RcppArmadilloForward.h>
+
+// Automatically include Rcpp as well -- but only the 'light' mode sans modules
+#include <Rcpp/Light>
+
+// Remaining RcppArmadillo code
+#include <RcppArmadillo/interface/RcppArmadilloWrap.h>
+#include <RcppArmadillo/interface/RcppArmadilloAs.h>
+#include <RcppArmadillo/interface/RcppArmadilloSugar.h>
+
+#endif

sparsevb-0.1.1/include/RcppArmadillo/Lighter

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+// Emacs, please make this  -*- mode: C++; -*-
+
+// RcppArmadillo: Rcpp/Armadillo glue
+//
+// Copyright (C)  2010 - 2022  Dirk Eddelbuettel, Romain Francois and Douglas Bates
+//
+// This file is part of RcppArmadillo.
+//
+// RcppArmadillo is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// RcppArmadillo is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef RcppArmadillo__RcppArmadillo
+#define RcppArmadillo__RcppArmadillo
+
+#if defined(Rcpp_hpp) && !defined(COMPILING_RCPPARMADILLO)
+    #error "The file 'Rcpp.h' should not be included. Please correct to include only 'RcppArmadillo.h'."
+#endif
+
+// We are undoing a design decision from early on by allowing vectors be returned
+// as standard 'one-dimension' objects -- as opposed to the matrix form we imposed
+#define RCPP_ARMADILLO_RETURN_ANYVEC_AS_VECTOR
+
+// Deal with Armadillo 14.6.3 (fallback) versus 15.0.* (or later, preference) selection
+#include <RcppArmadillo/version/arma.h>
+
+// Set up actual #include <armadillo> after first #include <RcppArmadilloConfig> and more config
+#include <RcppArmadillo/interface/RcppArmadilloForward.h>
+
+// Automatically include Rcpp as well -- but only the 'lighter' mode sans modules and rtti
+#include <Rcpp/Lighter>
+
+// Remaining RcppArmadillo code
+#include <RcppArmadillo/interface/RcppArmadilloWrap.h>
+#include <RcppArmadillo/interface/RcppArmadilloAs.h>
+#include <RcppArmadillo/interface/RcppArmadilloSugar.h>
+
+#endif

sparsevb-0.1.1/include/RcppArmadillo/Lightest

@@ -0,0 +1,47 @@
+// Emacs, please make this  -*- mode: C++; -*-
+
+// RcppArmadillo: Rcpp/Armadillo glue
+//
+// Copyright (C)  2010 - 2022  Dirk Eddelbuettel, Romain Francois and Douglas Bates
+//
+// This file is part of RcppArmadillo.
+//
+// RcppArmadillo is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// RcppArmadillo is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef RcppArmadillo__RcppArmadillo
+#define RcppArmadillo__RcppArmadillo
+
+#if defined(Rcpp_hpp) && !defined(COMPILING_RCPPARMADILLO)
+    #error "The file 'Rcpp.h' should not be included. Please correct to include only 'RcppArmadillo.h'."
+#endif
+
+// We are undoing a design decision from early on by allowing vectors be returned
+// as standard 'one-dimension' objects -- as opposed to the matrix form we imposed
+#define RCPP_ARMADILLO_RETURN_ANYVEC_AS_VECTOR
+
+// Deal with Armadillo 14.6.3 (fallback) versus 15.0.* (or later, preference) selection
+#include <RcppArmadillo/version/arma.h>
+
+// Set up actual #include <armadillo> after first #include <RcppArmadilloConfig> and more config
+#include <RcppArmadillo/interface/RcppArmadilloForward.h>
+
+// Automatically include Rcpp as well -- but only the 'lightest' mode sans modules, rtti, sugar
+#include <Rcpp/Lightest>
+
+// Remaining RcppArmadillo code
+#include <RcppArmadillo/interface/RcppArmadilloWrap.h>
+#include <RcppArmadillo/interface/RcppArmadilloAs.h>
+#include <RcppArmadillo/interface/RcppArmadilloSugar.h>
+
+#endif

sparsevb-0.1.1/include/RcppArmadillo/RcppArmadillo

@@ -0,0 +1,47 @@
+// Emacs, please make this  -*- mode: C++; -*-
+
+// RcppArmadillo: Rcpp/Armadillo glue
+//
+// Copyright (C)  2010 - 2022  Dirk Eddelbuettel, Romain Francois and Douglas Bates
+//
+// This file is part of RcppArmadillo.
+//
+// RcppArmadillo is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// RcppArmadillo is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef RcppArmadillo__RcppArmadillo
+#define RcppArmadillo__RcppArmadillo
+
+#if defined(Rcpp_hpp) && !defined(COMPILING_RCPPARMADILLO)
+    #error "The file 'Rcpp.h' should not be included. Please correct to include only 'RcppArmadillo.h'."
+#endif
+
+// We are undoing a design decision from early on by allowing vectors be returned
+// as standard 'one-dimension' objects -- as opposed to the matrix form we imposed
+#define RCPP_ARMADILLO_RETURN_ANYVEC_AS_VECTOR
+
+// Deal with Armadillo 14.6.3 (fallback) versus 15.0.* (or later, preference) selection
+#include <RcppArmadillo/version/arma.h>
+
+// Set up actual #include <armadillo> after first #include <RcppArmadilloConfig> and more config
+#include <RcppArmadillo/interface/RcppArmadilloForward.h>
+
+// Automatically include Rcpp as well -- full version
+#include <Rcpp/Rcpp>
+
+// Remaining RcppArmadillo code
+#include <RcppArmadillo/interface/RcppArmadilloWrap.h>
+#include <RcppArmadillo/interface/RcppArmadilloAs.h>
+#include <RcppArmadillo/interface/RcppArmadilloSugar.h>
+
+#endif

sparsevb-0.1.1/include/RcppArmadillo/config/RcppArmadilloConfig.h

@@ -0,0 +1,149 @@
+
+// RcppArmadilloConfig.h: Rcpp/Armadillo glue
+//
+// Copyright (C)  2010 - 2025  Dirk Eddelbuettel, Romain Francois and Douglas Bates
+// Copyright (C)  2016 - 2025  George G. Vega Yon
+// Copyright (C)  2017 - 2025  Serguei Sokol
+//
+// This file is part of RcppArmadillo.
+//
+// RcppArmadillo is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// RcppArmadillo is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef RcppArmadillo__RcppArmadilloConfig__h
+#define RcppArmadillo__RcppArmadilloConfig__h
+
+#if !defined(ARMA_USE_LAPACK)
+#define ARMA_USE_LAPACK
+#endif
+
+#if !defined(ARMA_USE_BLAS)
+#define ARMA_USE_BLAS
+#endif
+
+#define ARMA_HAVE_STD_ISFINITE
+#define ARMA_HAVE_STD_ISINF
+#define ARMA_HAVE_STD_ISNAN
+#define ARMA_HAVE_STD_SNPRINTF
+
+
+/* TODO: we might need to undef this on other platforms as well */
+#if defined(__GNUC__) && defined(_WIN64) || defined(__FreeBSD__)
+#undef ARMA_HAVE_STD_SNPRINTF
+#endif
+
+/*
+   suncc does not have std::isfinite (which is not standard)
+   so we tell armadillo not to use it, and comment out a few
+   others while we are at it
+*/
+#if defined(__SUNPRO_CC)
+#undef ARMA_HAVE_STD_ISFINITE
+#undef ARMA_HAVE_STD_SNPRINTF
+#undef ARMA_HAVE_LOG1P
+#undef ARMA_HAVE_STD_ISINF
+#undef ARMA_HAVE_STD_ISNAN
+#endif
+
+// Let's be careful for now and undef this as not all compilers support this
+//#if defined(ARMA_USE_CXX11)
+//#undef ARMA_USE_CXX11
+//#endif
+
+// If C++11 has been selected at the R package level, use it for Armadillo too
+// This is actually not needed, if the proper switch is set via -std=... then
+// Armadillo will know (cf compilation with -DARMA_EXTRA_DEBUG set)
+// #if defined(USE_CXX1X)
+// #define ARMA_USE_CXX11
+// #endif
+
+// We can use R as the RNG provider, see RcppArmadilloForward.h which
+// enables inclusion of the appropriate headers. Alternatively, the
+// C++11 RNG can be used by commenting out the current default and
+// selecting the C++11 RNG instead. Lastly, one could (but should not)
+// fall back to the C++98 RNG (often from the C library) by defining neither.
+
+// Rcpp has its own stream object which cooperates more nicely with R's i/o
+// And as of Armadillo 2.4.3, we can use this stream object as well
+//
+// As of Armadillo 8.100.1, this has been renamed to ARMA_COUT_STREAM and
+// ARMA_CERR_STREAM was added
+//
+#if !defined(ARMA_COUT_STREAM)
+#define ARMA_COUT_STREAM Rcpp::Rcout
+#endif
+#if !defined(ARMA_CERR_STREAM)
+#define ARMA_CERR_STREAM Rcpp::Rcerr
+#endif
+
+
+// R now defines NDEBUG which suppresses a number of useful Armadillo tests
+// Users can still defined it later, and/or define ARMA_NO_DEBUG
+// Updated 2022-Nov to only undefined if opt-in define has been set
+#if defined(RCPPARMADILLO_UNDEFINE_NDEBUG) && defined(NDEBUG)
+  #undef NDEBUG
+#endif
+
+// On Windows do not read autoconf-updated header
+#if defined(WIN32) || defined(_WIN32)
+  // R can be built with its own Rlapack library, or use an external
+  // one. Only the latter has zgesdd, a complex-valued SVD using divide-and-conquer
+  // on Windows we do not assume ZGESDD
+  //
+  // Update 2025-Nov: R now generally has good enough LAPACK/BLAS, and newer Arma
+  // versions whine so protecting this now for use with Armadillo older than 15.*
+  #if defined(ARMA_SELECTED_LEGACY_VERSION)
+    #define ARMA_CRIPPLED_LAPACK 1
+  #endif
+  // on Windows we can now assume OpenMP with Rtools / gcc 4.9.3
+  // note that performance is said to still be poor
+  // cf https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#The-MinGW_002dw64-toolchain
+  #define ARMA_USE_OPENMP
+#else
+  // on the other OSs we test via LAPACK_LIBS (in configure) which
+  // updates this include file
+  #include <RcppArmadillo/config/RcppArmadilloConfigGenerated.h>
+#endif
+
+// Many client packages do not set the OpenMP compiler flag in their src/Makevars
+// (ie add $(SHLIB_OPENMP_CXXFLAGS) to the PKG_CXXFLAGS line as we do) so to tone
+// down the line noise we ask Armadillo not to print the warning
+#if defined(ARMA_USE_OPENMP)
+  //#if !defined(_OPENMP)
+  //  #pragma message("NOTE: To enable OpenMP-based speedups, add -fopenmp to the compiler flags. See Writing R Extension (Sec 1.2.1) and R Inst. + Admin. (Sec 6.3.3) for details.")
+  //#endif
+  #define ARMA_DONT_PRINT_OPENMP_WARNING 1
+#endif
+
+
+// Under C++11 and C++14, Armadillo now defaults to using int64_t for
+// integers.  This prevents us from passing integer vectors to R as
+// only used int32_t -- so we select the shorter representation here.
+// Unless int64_t is explicitly required during compilation.
+#if !defined(ARMA_64BIT_WORD)
+  #define ARMA_32BIT_WORD 1
+#endif
+
+// To return arma::vec or arma::rowvec as R vector (i.e. dimensionless),
+// one of the following macro can be defined before including
+// RcppArmadillo.h. "ANYVEC" applys for both col- and row-vec.
+//#define RCPP_ARMADILLO_RETURN_COLVEC_AS_VECTOR
+//#define RCPP_ARMADILLO_RETURN_ROWVEC_AS_VECTOR
+//#define RCPP_ARMADILLO_RETURN_ANYVEC_AS_VECTOR
+
+// To preserve all dims of arma::field when passing objects to or from R
+// the following macro can be defined before including RcppArmadillo.h.
+// see https://github.com/RcppCore/RcppArmadillo/pull/352
+// #define RCPP_ARMADILLO_FIX_Field
+
+#endif

sparsevb-0.1.1/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h

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+
+// RcppArmadilloConfigGenerated.h: Autoconf-updated file for LAPACK and OpenMP choices
+//
+// Copyright (C)  2013 - 2025  Dirk Eddelbuettel
+//                       2025  James J. Balamuta
+//
+// This file is part of RcppArmadillo.
+//
+// RcppArmadillo is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// RcppArmadillo is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef RcppArmadillo__RcppArmadilloConfigGenerated__h
+#define RcppArmadillo__RcppArmadilloConfigGenerated__h
+
+// macOS special case as discussed in https://github.com/RcppCore/RcppArmadillo/issues/493
+#if !defined(ARMA_USE_OPENMP)
+  #if defined(__APPLE__) && defined(_OPENMP)
+    // User has OpenMP available, but check if they want it disabled
+    #ifndef RCPPARMADILLO_MACOS_DISABLE_OPENMP
+      #define ARMA_USE_OPENMP 1
+    #else
+      #define ARMA_DONT_USE_OPENMP 1
+    #endif
+  #else
+    // from configure test for OpenMP based on how R is configured
+    #define ARMA_USE_OPENMP 1
+  #endif
+#endif
+
+#endif

sparsevb-0.1.1/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h.in

@@ -0,0 +1,40 @@
+
+// RcppArmadilloConfigGenerated.h: Autoconf-updated file for LAPACK and OpenMP choices
+//
+// Copyright (C)  2013 - 2025  Dirk Eddelbuettel
+//                       2025  James J. Balamuta
+//
+// This file is part of RcppArmadillo.
+//
+// RcppArmadillo is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// RcppArmadillo is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef RcppArmadillo__RcppArmadilloConfigGenerated__h
+#define RcppArmadillo__RcppArmadilloConfigGenerated__h
+
+// macOS special case as discussed in https://github.com/RcppCore/RcppArmadillo/issues/493
+#if !defined(ARMA_USE_OPENMP)
+  #if defined(__APPLE__) && defined(_OPENMP)
+    // User has OpenMP available, but check if they want it disabled
+    #ifndef RCPPARMADILLO_MACOS_DISABLE_OPENMP
+      #define ARMA_USE_OPENMP 1
+    #else
+      #define ARMA_DONT_USE_OPENMP 1
+    #endif
+  #else
+    // from configure test for OpenMP based on how R is configured
+    @ARMA_HAVE_OPENMP@
+  #endif
+#endif
+
+#endif