fix intel compiler build break

Illumina#48
bioinformaticsorphanage · Dec 7, 2023 · b8f8016 · b8f8016
1 parent 022704e
commit b8f8016
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Showing 13 changed files with 37 additions and 38 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -4,7 +4,6 @@ on:
   push:
     branches: [ "master" ]
   pull_request:
-    branches: [ "master" ]
 
 jobs:
   build:

diff --git a/config.mk b/config.mk
@@ -140,7 +140,7 @@ endif
 VERSION_STRING?=$(shell git describe --tags --always --abbrev=8 2> /dev/null || echo "UNKNOWN")
 
 CXXWARNINGS=-Werror -Wno-unused-variable -Wno-free-nonheap-object -Wno-parentheses
-CWARNINGS?=-Werror -Wno-unused-variable -Wno-unused-function -Wno-format-truncation
+CWARNINGS?=-Werror -Wno-unused-variable -Wno-unused-function -Wno-format-truncation -Wno-unknown-warning-option -Wno-unused-but-set-variable
 CXXSTD?=-std=c++17
 
 

diff --git a/src/include/align/Aligner.hpp b/src/include/align/Aligner.hpp
@@ -141,8 +141,8 @@ class Aligner {
   const map::Mapper         mapper_;
   const SimilarityScores    similarity_;
   const ScoreType           gapInit_;
-  const ScoreType           gapExtend_;
-  const ScoreType           unclipScore_;
+  // const ScoreType           gapExtend_;
+  // const ScoreType           unclipScore_;
   const ScoreType           alnMinScore_;
   const int                 aln_cfg_mapq_min_len_;
   const int                 aln_cfg_unpaired_pen_;

diff --git a/src/include/map/ChainBuilder.hpp b/src/include/map/ChainBuilder.hpp
@@ -77,7 +77,7 @@ class ChainBuilder {
   size_t                 seedChainCount_;
   double                 chainFilterRatio_    = 2.0;
   double                 chainFilterConstant_ = 0.0;
-  int                    numRandomSampleHits_ = 0;
+  // int                    numRandomSampleHits_ = 0;
 };
 
 }  // namespace map

diff --git a/src/lib/align/Aligner.cpp b/src/lib/align/Aligner.cpp
@@ -56,8 +56,8 @@ Aligner::Aligner(
     mapper_(&hashtable),
     similarity_(similarity),
     gapInit_(gapInit),
-    gapExtend_(gapExtend),
-    unclipScore_(unclipScore),
+    // gapExtend_(gapExtend),
+    // unclipScore_(unclipScore),
     alnMinScore_(alnMinScore),
     aln_cfg_mapq_min_len_(aln_cfg_mapq_min_len),
     aln_cfg_unpaired_pen_(aln_cfg_unpaired_pen),

diff --git a/src/lib/align/AlignmentGenerator.cpp b/src/lib/align/AlignmentGenerator.cpp
@@ -141,7 +141,7 @@ bool AlignmentGenerator::generateAlignment(
       1,
       (seedChain.isReverseComplement() ? (read.getLength() - seedChain.lastReadBase() - 1)
                                        : seedChain.firstReadBase()));  //10;//1;
-  static constexpr size_t forcedHorizontalMotion = smithWaterman_.width;
+  static const size_t forcedHorizontalMotion = smithWaterman_.width;
   // initialize the query from the base and the orientation of the seedChain
   const auto& query = read.getBases();
   int         move  = 0;

diff --git a/src/lib/align/SmithWaterman.cpp b/src/lib/align/SmithWaterman.cpp
@@ -58,7 +58,7 @@ void SmithWatermanT<C, T, WIDTH, ALIGN, STEERING_DELAY>::buildWavefronts(
 
   // dragen thing...
   setDatabaseSize(std::min(getDatabaseOffset() + 1 + 2 * width + 1, getDatabaseSize()));
-  for (unsigned i = 0; (getDatabaseOffset() < getDatabaseSize() - 1); ++i) {
+  while (getDatabaseOffset() < getDatabaseSize() - 1) {
     moveRight();
   }
 

diff --git a/src/lib/reference/ExtendTableInterval.cpp b/src/lib/reference/ExtendTableInterval.cpp
@@ -30,11 +30,11 @@ ExtendTableInterval::ExtendTableInterval(I begin, I end)
 }
 
 // explicit instantiation for vectors and pointers
-template ExtendTableInterval::ExtendTableInterval<const HashRecord*>(
+template ExtendTableInterval::ExtendTableInterval(
     const HashRecord* begin, const HashRecord* end);
-template ExtendTableInterval::ExtendTableInterval<std::vector<HashRecord>::const_iterator>(
+template ExtendTableInterval::ExtendTableInterval(
     std::vector<HashRecord>::const_iterator begin, std::vector<HashRecord>::const_iterator end);
-template ExtendTableInterval::ExtendTableInterval<std::vector<HashRecord>::iterator>(
+template ExtendTableInterval::ExtendTableInterval(
     std::vector<HashRecord>::iterator begin, std::vector<HashRecord>::iterator end);
 
 template <typename I>

diff --git a/src/lib/reference/ReferenceDir.cpp b/src/lib/reference/ReferenceDir.cpp
@@ -52,7 +52,7 @@ typename ReferenceDir7::UcharPtr ReferenceDir7::ReadFileIntoBuffer(
   size = file.tellg();
   file.seekg(0, file.beg);
 
-  UcharPtr bufPtr(new uint8_t[size], [this](uint8_t* p) -> void { delete [](p); });
+  UcharPtr bufPtr(new uint8_t[size], [](uint8_t* p) -> void { delete [](p); });
   file.read(reinterpret_cast<char*>(bufPtr.get()), size);
   if (!file) {
     //    THROW(DragenException, "Could not load reference - could not read ", path);
@@ -119,9 +119,9 @@ ReferenceDir7::ReferenceDir7(const boost::filesystem::path& path, bool mmap, boo
     dup2(stdoutori, 1);
 
     hashtableData_ =
-        Uint64Ptr(reinterpret_cast<uint64_t*>(hashbuf), [this](uint64_t* p) -> void { free(p); });
+        Uint64Ptr(reinterpret_cast<uint64_t*>(hashbuf), [](uint64_t* p) -> void { free(p); });
     extendTableData_ =
-        Uint64Ptr(reinterpret_cast<uint64_t*>(extendTableBuf), [this](uint64_t* p) -> void { free(p); });
+        Uint64Ptr(reinterpret_cast<uint64_t*>(extendTableBuf), [](uint64_t* p) -> void { free(p); });
   }
 
   referenceSequencePtr_ = std::unique_ptr<ReferenceSequence>(new ReferenceSequence(
@@ -251,7 +251,7 @@ std::unique_ptr<T, std::function<void(T*)>> ReferenceDir7::readData(
             " error: " + std::strerror(errno)));
   }
   return std::unique_ptr<T, std::function<void(T*)>>(
-      reinterpret_cast<T*>(table), [this](T* p) -> void { free(p); });
+      reinterpret_cast<T*>(table), [](T* p) -> void { free(p); });
 }
 
 size_t ReferenceDir7::getHashtableConfigSize() const

diff --git a/stubs/bamtools/bamtools-2.4.1/include/api/BamConstants.h b/stubs/bamtools/bamtools-2.4.1/include/api/BamConstants.h
@@ -129,15 +129,15 @@ const char BAM_DNA_DEL   = '-';
 const char BAM_DNA_PAD   = '*';
 
 // zlib & BGZF constants
-const char GZIP_ID1   = 31;
-const char GZIP_ID2   = 139;
-const char CM_DEFLATE = 8;
-const char FLG_FEXTRA = 4;
-const char OS_UNKNOWN = 255;
-const char BGZF_XLEN  = 6;
-const char BGZF_ID1   = 66;
-const char BGZF_ID2   = 67;
-const char BGZF_LEN   = 2;
+const uint8_t GZIP_ID1   = 31;
+const uint8_t GZIP_ID2   = 139;
+const uint8_t CM_DEFLATE = 8;
+const uint8_t FLG_FEXTRA = 4;
+const uint8_t OS_UNKNOWN = 255;
+const uint8_t BGZF_XLEN  = 6;
+const uint8_t BGZF_ID1   = 66;
+const uint8_t BGZF_ID2   = 67;
+const uint8_t BGZF_LEN   = 2;
 
 const int8_t   GZIP_WINDOW_BITS          = -15;
 //--START EDICO EDITED

diff --git a/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp b/stubs/dragen/src/host/infra/linux/infra_linux_utils.cpp
@@ -39,15 +39,15 @@ namespace infra {
 static std::string g_kernelVersionStr;
 static int         g_kernelVersion;
 
-static constexpr int MKVER(const int major, const int minor, const int patch)
-{
-  return major * 10000 + minor * 100 + patch;
-}
-
-static constexpr int MKVER(const int major, const int minor)
-{
-  return major * 10000 + minor * 100;
-}
+// static constexpr int MKVER(const int major, const int minor, const int patch)
+// {
+//   return major * 10000 + minor * 100 + patch;
+// }
+
+// static constexpr int MKVER(const int major, const int minor)
+// {
+//   return major * 10000 + minor * 100;
+// }
 
 //------------------------------------------------------------------------alain
 int GetDmiValue(const std::string& label, std::string& value)

diff --git a/stubs/dragen/src/host/infra/public/infra_compiler.h b/stubs/dragen/src/host/infra/public/infra_compiler.h
@@ -153,7 +153,7 @@ static inline int atomic16_cmpset(uint16_t volatile *ptr, const uint16_t exp,
 }
 static inline uint32_t atomic16_xchg(uint16_t volatile *ptr,
                                      const uint16_t val) {
-  return __atomic_exchange_2(ptr, val, __ATOMIC_SEQ_CST);
+  return __atomic_exchange_n(ptr, val, __ATOMIC_SEQ_CST);
 }
 static inline int32_t atomic16_read(int16_t volatile *ptr) { return *ptr; }
 static inline void atomic16_write(int16_t volatile *ptr, const int16_t val) {
@@ -191,7 +191,7 @@ static inline int atomic32_cmpset(uint32_t volatile *ptr, const uint32_t exp,
 }
 static inline uint32_t atomic32_xchg(uint32_t volatile *ptr,
                                      const uint32_t val) {
-  return __atomic_exchange_4(ptr, val, __ATOMIC_SEQ_CST);
+  return __atomic_exchange_n(ptr, val, __ATOMIC_SEQ_CST);
 }
 static inline int32_t atomic32_read(int32_t volatile *ptr) { return *ptr; }
 static inline void atomic32_write(int32_t volatile *ptr, const int32_t val) {
@@ -229,7 +229,7 @@ static inline int atomic64_cmpset(uint64_t volatile *ptr, const uint64_t exp,
 }
 static inline uint64_t atomic64_xchg(uint64_t volatile *ptr,
                                      const uint64_t val) {
-  return __atomic_exchange_8(ptr, val, __ATOMIC_SEQ_CST);
+  return __atomic_exchange_n(ptr, val, __ATOMIC_SEQ_CST);
 }
 static inline int64_t atomic64_read(int64_t volatile *ptr) { return *ptr; }
 static inline void atomic64_write(int64_t volatile *ptr, const int64_t val) {

diff --git a/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c b/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c
@@ -249,7 +249,7 @@ void setDefaultHashParams(hashTableConfig_t* defConfig, const char* destDir, Has
     free(dir);
   }
 
-  defConfig->hostVersion = (char*)getHostVersion(0);
+  defConfig->hostVersion = (char*)getHostVersion();
 }
 
 //-------------------------------------------------------------------------------swhitmore
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,7 +4,6 @@ on: @@
       push:
         branches: [ "master" ]
       pull_request:
-        branches: [ "master" ]
     jobs:
       build:
@@ Expand Down @@