From e6ff82c785d36c2d6717ae7b48b536b33c5f2f7f Mon Sep 17 00:00:00 2001
From: Milot Mirdita <milot@mirdita.de>
Date: Thu, 14 Nov 2024 00:20:19 +0900
Subject: [PATCH] Fix warnings

---
 src/commons/Sequence.cpp           | 1 -
 src/commons/SubstitutionMatrix.cpp | 8 ++++++--
 src/test/TestUngappedCpuPerf.cpp   | 1 -
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/commons/Sequence.cpp b/src/commons/Sequence.cpp
index a92bd1da..127e428d 100644
--- a/src/commons/Sequence.cpp
+++ b/src/commons/Sequence.cpp
@@ -225,7 +225,6 @@ void Sequence::mapSequence(size_t id, unsigned int dbKey, const char *sequence,
 void Sequence::mapSequence(size_t id, unsigned int dbKey, std::pair<const unsigned char *,const unsigned int> data){
     this->id = id;
     this->dbKey = dbKey;
-    const int alphabetSize = subMat->alphabetSize;
     if (Parameters::isEqualDbtype(this->seqType, Parameters::DBTYPE_AMINO_ACIDS)
         || Parameters::isEqualDbtype( this->seqType,Parameters::DBTYPE_NUCLEOTIDES)){
         this->L = data.second;
diff --git a/src/commons/SubstitutionMatrix.cpp b/src/commons/SubstitutionMatrix.cpp
index d223fb53..3130a86c 100644
--- a/src/commons/SubstitutionMatrix.cpp
+++ b/src/commons/SubstitutionMatrix.cpp
@@ -57,8 +57,12 @@ SubstitutionMatrix::SubstitutionMatrix(const char *filename, float bitFactor, fl
 }
 
 
-bool SubstitutionMatrix::estimateLambdaAndBackground(const double **scoreMatrix,
-                                                     int alphabetSize, double *pBack, double &lambda) {
+bool SubstitutionMatrix::estimateLambdaAndBackground(
+        const double** MAYBE_UNUSED(scoreMatrix),
+        int MAYBE_UNUSED(alphabetSize),
+        double* MAYBE_UNUSED(pBack),
+        double& MAYBE_UNUSED(lambda)
+    ) {
     Debug(Debug::ERROR) << "Custom Substitution Matrix not supported in the release. Please use previous release\n";
     return false;
     // We need to pass the parameters as 1-based pointers, hence the +1s and -1s.
diff --git a/src/test/TestUngappedCpuPerf.cpp b/src/test/TestUngappedCpuPerf.cpp
index cecffbe3..accfc340 100644
--- a/src/test/TestUngappedCpuPerf.cpp
+++ b/src/test/TestUngappedCpuPerf.cpp
@@ -41,7 +41,6 @@ int main (int, const char**) {
         }
     }
 
-    size_t seqLen = 32;
     size_t targets = 5000000;
 
     std::vector<int> benchSizes = {