fix -Wvla

zhengxwen · Apr 11, 2024 · 5cdff0e · 5cdff0e
1 parent aaa253c
commit 5cdff0e
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Showing 5 changed files with 12 additions and 12 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: HIBAG
 Type: Package
 Title: HLA Genotype Imputation with Attribute Bagging
-Version: 1.39.4
-Date: 2024-03-14
+Version: 1.39.5
+Date: 2024-04-11
 Depends: R (>= 3.2.0)
 Imports: methods, RcppParallel
 Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr,

diff --git a/NEWS b/NEWS
@@ -1,4 +1,4 @@
-CHANGES IN VERSION 1.39.4
+CHANGES IN VERSION 1.40.0
 -------------------------
 
     o new option 'all' in `hlaUniqueAllele()`

diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@ HIBAG is a state of the art software package for imputing HLA types using SNP da
 
 ## Bioconductor Package
 
-Release Version: 1.38.3
+Release Version: 1.40.0
 
 [http://www.bioconductor.org/packages/HIBAG/](http://www.bioconductor.org/packages/HIBAG/)
 

diff --git a/src/LibHLA.cpp b/src/LibHLA.cpp
@@ -981,11 +981,12 @@ void CAlg_EM::PrepareHaplotypes(const CHaplotypeList &CurHaplo,
 
 	// the number of in-bag samples
 	const size_t n_samp_ib = vs.idx_inbag.size();
+	vector<int> StartIdx(nhla);
+	int st = 0;
 
 	if (GPUExtProcPtr && *GPUExtProcPtr->build_haplomatch)
 	{
 		// prepare data and check
-		int StartIdx[nhla], st=0;
 		for (int i=0; i < nhla; i++)
 		{
 			if (CurHaplo.LenPerHLA[i] > 65535)
@@ -1046,7 +1047,6 @@ void CAlg_EM::PrepareHaplotypes(const CHaplotypeList &CurHaplo,
 	} else {
 
 		// prepare data
-		int StartIdx[nhla], st=0;
 		for (int i=0; i < nhla; i++)
 		{
 			StartIdx[i] = st;
@@ -2471,9 +2471,9 @@ void CAttrBag_Model::_Init_GPU_PredHLA()
 	{
 		// prepare data structure for GPU
 		const size_t n_classifier = _ClassifierList.size();
-		THaplotype* haplo[n_classifier];
-		int p_n_haplo[n_classifier];
-		int p_n_snp[n_classifier];
+		vector<THaplotype*> haplo(n_classifier);
+		vector<int> p_n_haplo(n_classifier);
+		vector<int> p_n_snp(n_classifier);
 
 		gpu_geno_buf.resize(n_classifier);
 		vector<CAttrBag_Classifier>::iterator p = _ClassifierList.begin();
@@ -2487,8 +2487,8 @@ void CAttrBag_Model::_Init_GPU_PredHLA()
 		}
 
 		// call the external function
-		(*GPUExtProcPtr->predict_init)(nHLA(), n_classifier, haplo,
-			p_n_haplo, p_n_snp);
+		(*GPUExtProcPtr->predict_init)(nHLA(), n_classifier, &haplo[0],
+			&p_n_haplo[0], &p_n_snp[0]);
 	}
 }
 

diff --git a/src/samtools_ext.c b/src/samtools_ext.c
@@ -44,7 +44,7 @@ static int (*bgzf_close)(BGZF *fp) = NULL;
 static ssize_t (*bgzf_write)(BGZF *fp, const void *data, ssize_t length) = NULL;
 
 
-static void init_bgzf()
+static void init_bgzf(void)
 {
 	PKG_LOAD(bgzf_open);
 	PKG_LOAD(bgzf_close);