From 1eccfbd2f1b63fe956127e5d82e96bedab338414 Mon Sep 17 00:00:00 2001
From: Arshammik <79arsham@gmail.com>
Date: Tue, 18 Nov 2025 20:51:37 -0500
Subject: [PATCH] fixing the issue with openMP detection on linux

---
 DESCRIPTION         | 7 +++----
 src/Makevars        | 3 +++
 src/Makevars.linux  | 4 ----
 src/Makevars.mac    | 4 ----
 src/Makevars.win    | 4 ++--
 src/RcppExports.cpp | 1 -
 6 files changed, 8 insertions(+), 15 deletions(-)
 delete mode 100644 src/Makevars.linux
 delete mode 100644 src/Makevars.mac

diff --git a/DESCRIPTION b/DESCRIPTION
index 3892b16..bbab603 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: splikit
 Title: A toolkit for analysing RNA splicing in scRNA-seq data
-Version: 1.0.5
+Version: 1.0.6
 Authors@R: 
     person("Arsham", "Mikaeili Namini", , "arsham.mikaeilinamini@mail.mcgill.ca", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9453-6951"))
@@ -16,9 +16,8 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Imports: Matrix, data.table, methods, stats, Rcpp, RcppArmadillo,
-        RcppEigen
-LinkingTo: Rcpp, RcppArmadillo, RcppEigen
+Imports: Matrix, data.table, methods, stats, Rcpp, RcppArmadillo
+LinkingTo: Rcpp, RcppArmadillo
 Suggests: testthat (>= 3.0.0)
 Config/testthat/edition: 3
 NeedsCompilation: yes
diff --git a/src/Makevars b/src/Makevars
index e69de29..6660c7f 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -0,0 +1,3 @@
+CXX_STD = CXX14
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/Makevars.linux b/src/Makevars.linux
deleted file mode 100644
index a02c158..0000000
--- a/src/Makevars.linux
+++ /dev/null
@@ -1,4 +0,0 @@
-## src/Makevars (Linux)
-CXX_STD = CXX14
-PKG_CXXFLAGS += -O3 -pipe -fopenmp
-PKG_LIBS += -fopenmp $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/Makevars.mac b/src/Makevars.mac
deleted file mode 100644
index 466d00c..0000000
--- a/src/Makevars.mac
+++ /dev/null
@@ -1,4 +0,0 @@
-## src/Makevars.mac (macOS)
-CXX_STD = CXX14
-PKG_CXXFLAGS += -O3 -pipe
-PKG_LIBS += $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/Makevars.win b/src/Makevars.win
index 5d5b5e5..85d1c66 100644
--- a/src/Makevars.win
+++ b/src/Makevars.win
@@ -1,4 +1,4 @@
 ## src/Makevars.win (Windows)
 CXX_STD = CXX14
-PKG_CXXFLAGS += -O2 -fopenmp
-PKG_LIBS     += -fopenmp $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 0990146..ce1a11d 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -2,7 +2,6 @@
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 #include <RcppArmadillo.h>
-#include <RcppEigen.h>
 #include <Rcpp.h>
 
 using namespace Rcpp;