Type changes required for LTO (#479)

* disable deprecated error and change type * add tlo flags * azure: test export * Update azure-pipelines.yml * Update azure-pipelines.yml * Update azure-pipelines.yml * test dialign.h * azure: revert test changes * azure: test * azure: test no distcheck * azure: test flags * Update azure-pipelines.yml * azure: export path * Update azure-pipelines.yml * Makefile.am: remove lto flag * azure: revert test changes * azure: test mac with gcc14 * azure: clang error test * azure: full test * azure: remove frozen compilers version * azure: install btllib via conda * CI fixes * Revert btllib version for gcc-8 --------- Co-authored-by: lcoombe <lauren.e.coombe@gmail.com>
bcgsc · Jul 18, 2024 · 4906b99 · 4906b99
1 parent 6548e04
commit 4906b99
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Showing 25 changed files with 82 additions and 87 deletions.
diff --git a/ABYSS/Makefile.am b/ABYSS/Makefile.am
@@ -10,3 +10,5 @@ ABYSS_LDADD = \
 	$(top_builddir)/Common/libcommon.a
 
 ABYSS_SOURCES = abyss.cc
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/AdjList/Makefile.am b/AdjList/Makefile.am
@@ -23,3 +23,5 @@ AdjList_LDADD += \
 
 AdjList_SOURCES = \
 	AdjList.cpp
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/Align/dialign.h b/Align/dialign.h
@@ -20,7 +20,7 @@ struct alignment* guided_aligner(struct alignment *palgn,
 	struct prob_dist *pdist,
 	struct gt_node *gtn,
 	int round);
-char simple_aligner(struct seq_col *scol, struct diag_col *dcol,
+int simple_aligner(struct seq_col *scol, struct diag_col *dcol,
 	struct scr_matrix* smatrix,
 	struct prob_dist *pdist,
 	struct alignment *algn, int round);

diff --git a/Bloom/Makefile.am b/Bloom/Makefile.am
@@ -21,3 +21,5 @@ abyss_bloom_SOURCES = bloom.cc \
 	CascadingBloomFilterWindow.h \
 	RollingBloomDBGVisitor.h \
 	HashAgnosticCascadingBloom.h
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/BloomDBG/Makefile.am b/BloomDBG/Makefile.am
@@ -25,3 +25,5 @@ abyss_bloom_dbg_SOURCES = \
 	RollingHash.h \
 	RollingHashIterator.h \
 	SpacedSeed.h
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/FMIndex/Makefile.am b/FMIndex/Makefile.am
@@ -21,3 +21,4 @@ abyss_count_LDADD = libfmindex.a \
 	$(top_builddir)/Common/libcommon.a
 abyss_count_CPPFLAGS = -I$(top_srcdir) \
 	-I$(top_srcdir)/Common
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/FilterGraph/Makefile.am b/FilterGraph/Makefile.am
@@ -11,3 +11,5 @@ abyss_filtergraph_LDADD = \
 	$(top_builddir)/Common/libcommon.a
 
 abyss_filtergraph_SOURCES = FilterGraph.cc
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/Graph/Makefile.am b/Graph/Makefile.am
@@ -41,3 +41,5 @@ EXTRA_DIST = \
 abyss_gc_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
 abyss_gc_LDADD = $(top_builddir)/Common/libcommon.a
 abyss_gc_SOURCES = gc.cc
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/KAligner/Makefile.am b/KAligner/Makefile.am
@@ -11,3 +11,5 @@ KAligner_LDADD = \
 
 KAligner_SOURCES = KAligner.cpp Aligner.cpp Aligner.h Options.h \
 	Pipe.h PipeMux.h Semaphore.h
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/Konnector/Makefile.am b/Konnector/Makefile.am
@@ -15,3 +15,5 @@ konnector_SOURCES = konnector.cc \
 	DBGBloom.h \
 	DBGBloomAlgorithms.h \
 	konnector.h
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/Layout/Makefile.am b/Layout/Makefile.am
@@ -3,3 +3,5 @@ bin_PROGRAMS = abyss-layout
 abyss_layout_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
 abyss_layout_LDADD = $(top_builddir)/Common/libcommon.a
 abyss_layout_SOURCES = layout.cc
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/Map/Makefile.am b/Map/Makefile.am
@@ -50,3 +50,5 @@ abyss_overlap_LDADD = \
 	$(top_builddir)/Common/libcommon.a
 
 abyss_overlap_SOURCES = overlap.cc
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/MergePaths/Makefile.am b/MergePaths/Makefile.am
@@ -45,3 +45,5 @@ PathConsensus_LDADD = \
 
 PathConsensus_SOURCES = \
 	PathConsensus.cpp
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/Overlap/Makefile.am b/Overlap/Makefile.am
@@ -10,3 +10,5 @@ Overlap_LDADD = \
 
 Overlap_SOURCES = \
 	Overlap.cpp
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/PairedDBG/Makefile.am b/PairedDBG/Makefile.am
@@ -24,3 +24,5 @@ abyss_paired_dbg_SOURCES = \
 	SequenceCollection.h
 
 libpaireddbg_a_SOURCES = KmerPair.cc KmerPair.h
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/Parallel/CommLayer.cpp b/Parallel/CommLayer.cpp
@@ -247,6 +247,7 @@ void CommLayer::receiveBufferedMessage(MessagePtrVector& outmessages)
 				pNewMessage = new SetBaseMessage();
 				break;
 			default:
+				pNewMessage = new SeqDataRequest();
 				assert(false);
 				break;
 		}

diff --git a/Parallel/Makefile.am b/Parallel/Makefile.am
@@ -27,3 +27,5 @@ abyss_paired_dbg_mpi_CPPFLAGS = $(ABYSS_P_CPPFLAGS) -DPAIRED_DBG
 abyss_paired_dbg_mpi_LDADD = $(ABYSS_P_LDADD)
 
 abyss_paired_dbg_mpi_SOURCES = $(ABYSS_P_SOURCES)
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/PathOverlap/Makefile.am b/PathOverlap/Makefile.am
@@ -12,3 +12,5 @@ PathOverlap_LDADD = \
 
 PathOverlap_SOURCES = \
 	PathOverlap.cpp
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/PopBubbles/Makefile.am b/PopBubbles/Makefile.am
@@ -14,3 +14,5 @@ PopBubbles_LDADD = \
 	$(top_builddir)/dialign/libdialign.a
 
 PopBubbles_SOURCES = PopBubbles.cpp
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/Scaffold/Makefile.am b/Scaffold/Makefile.am
@@ -33,6 +33,8 @@ abyss_junction_LDADD = \
 
 abyss_junction_SOURCES = junction.cc
 
+CXXFLAGS += -Wno-deprecated-declarations
+
 #abyss_drawgraph_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
 #abyss_drawgraph_LDADD = $(top_builddir)/Common/libcommon.a
 #abyss_drawgraph_SOURCES = drawgraph.cc
diff --git a/Sealer/Makefile.am b/Sealer/Makefile.am
@@ -27,3 +27,5 @@ abyss_sealer_SOURCES = sealer.cc \
 # Convert the README.md to a man page using Pandoc
 abyss-sealer.1: README.md
 	pandoc -s -o $@ $<
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/SimpleGraph/Makefile.am b/SimpleGraph/Makefile.am
@@ -12,3 +12,5 @@ SimpleGraph_LDADD = \
 	-lpthread
 
 SimpleGraph_SOURCES = SimpleGraph.cpp
+
+CXXFLAGS += -Wno-deprecated-declarations
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -9,14 +9,14 @@ jobs:
       brew install --force python3 node@18 && brew unlink python3 node@18 && brew unlink python3 node@18 && brew link --overwrite python3 node@18
       find /usr/local/Cellar/python* -name EXTERNALLY-MANAGED -print0 | xargs -0 rm -vf
       brew update
-      brew install automake boost openmpi google-sparsehash make pandoc ghc gcc@13 llvm
+      brew install automake boost openmpi google-sparsehash make pandoc ghc gcc@14 llvm
     displayName: Install common
   - script: |
-      wget https://github.com/bcgsc/btllib/releases/download/v1.5.1/btllib-1.5.1.tar.gz
-      export CC=gcc-13
-      export CXX=g++-13
-      tar xzf btllib-1.5.1.tar.gz
-      cd btllib-1.5.1
+      wget https://github.com/bcgsc/btllib/releases/download/v1.5.0/btllib-1.5.0.tar.gz
+      export CC=gcc-14
+      export CXX=g++-14
+      tar xzf btllib-1.5.0.tar.gz
+      cd btllib-1.5.0
       ./compile
     displayName: Install btllib
   - script: |
@@ -26,10 +26,10 @@ jobs:
       export CFLAGS="$CFLAGS -fuse-ld=lld"
       export OBJCFLAGS="$OBJCFLAGS -fuse-ld=lld"
       export OBJCXXFLAGS="$OBJCXXFLAGS -fuse-ld=lld"
-      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-13 CXX=g++-13 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.1/install"
-      ./configure CC=gcc-13 CXX=g++-13 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.1/install
+      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-14 CXX=g++-14 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.0/install"
+      ./configure CC=gcc-14 CXX=g++-14 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.0/install
       make -j12 distcheck AM_CXXFLAGS=-Wno-error=dangling-reference
-    displayName: Compiling ABySS with gcc-13
+    displayName: Compiling ABySS with gcc-14
 
 - job:
   displayName: mac_latest-compilers-clang
@@ -43,24 +43,12 @@ jobs:
   - script: |
       source activate abyss_CI
       conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi automake perl pandoc meson ninja
+      mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi automake perl pandoc meson ninja btllib
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
-      wget https://github.com/bcgsc/btllib/releases/download/v1.7.0/btllib-1.7.0.tar.gz
-      tar xzf btllib-1.7.0.tar.gz
-      cd btllib-1.7.0
-      export CC=clang
-      export CXX=clang++
-      ./compile
-    displayName: Install btllib
-  - script: |
-      source activate abyss_CI
-      export CC=clang
-      export CXX=clang++
-      export DISTCHECK_CONFIGURE_FLAGS="CC=clang CXX=clang++  --with-btllib=/Users/runner/work/1/s/btllib-1.7.0/install"
       ./autogen.sh
-      ./configure  --with-btllib=/Users/runner/work/1/s/btllib-1.7.0/install
+      ./configure
       make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
     displayName: Compiling ABySS
 
@@ -76,24 +64,12 @@ jobs:
   - script: |
       source activate abyss_CI
       conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc
+      mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
-      wget https://github.com/bcgsc/btllib/releases/download/v1.7.0/btllib-1.7.0.tar.gz
-      tar xzf btllib-1.7.0.tar.gz
-      cd btllib-1.7.0
-      export CC=clang
-      export CXX=clang++
-      ./compile
-    displayName: Install btllib
-  - script: |
-      source activate abyss_CI
-      export CC=clang
-      export CXX=clang++
-      export DISTCHECK_CONFIGURE_FLAGS="CC=clang CXX=clang++ --with-btllib=/Users/runner/work/1/s/btllib-1.7.0/install"
       ./autogen.sh
-      ./configure --with-btllib=/Users/runner/work/1/s/btllib-1.7.0/install
+      ./configure
       make -j12 distcheck
     displayName: Compiling ABySS
 
@@ -109,24 +85,12 @@ jobs:
   - script: |
       source activate abyss_CI
       conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc
+      mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
-      wget https://github.com/bcgsc/btllib/releases/download/v1.7.0/btllib-1.7.0.tar.gz
-      tar xzf btllib-1.7.0.tar.gz
-      cd btllib-1.7.0
-      export CC=clang
-      export CXX=clang++
-      ./compile
-    displayName: Install btllib
-  - script: |
-      source activate abyss_CI
-      export CC=clang
-      export CXX=clang++
-      export DISTCHECK_CONFIGURE_FLAGS="CC=clang CXX=clang++ --with-btllib=/Users/runner/work/1/s/btllib-1.7.0/install"
       ./autogen.sh
-      ./configure --with-btllib=/Users/runner/work/1/s/btllib-1.7.0/install
+      ./configure
       make -j12 distcheck
     displayName: Compiling ABySS with clang 13
 
@@ -142,27 +106,16 @@ jobs:
   - script: |
       source activate abyss_CI
       conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.4.0 make boost-cpp sparsehash openmpi automake perl pandoc llvm-openmp
+      mamba install --yes -c conda-forge -c bioconda compilers=1.4.0 make boost-cpp sparsehash openmpi automake perl pandoc llvm-openmp btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
-      wget https://github.com/bcgsc/btllib/releases/download/v1.7.0/btllib-1.7.0.tar.gz
-      tar xzf btllib-1.7.0.tar.gz
-      cd btllib-1.7.0
-      export CC=clang
-      export CXX=clang++
-      ./compile
-    displayName: Install btllib
-  - script: |
-      source activate abyss_CI
-      export CC=clang
-      export CXX=clang++
-      export DISTCHECK_CONFIGURE_FLAGS="CC=clang CXX=clang++ --with-btllib=/Users/runner/work/1/s/btllib-1.7.0/install"
       ./autogen.sh
-      ./configure --with-btllib=/Users/runner/work/1/s/btllib-1.7.0/install
+      ./configure
       make -j12 distcheck
     displayName: Compiling ABySS with clang 12
 
+
 - job: linux_gcc12
   pool:
     vmImage: ubuntu-latest
@@ -178,17 +131,17 @@ jobs:
   - script: sudo apt-get install -qq gcc-12 g++-12
     displayName: Install gcc-12
   - script: |
-      wget https://github.com/bcgsc/btllib/releases/download/v1.7.0/btllib-1.7.0.tar.gz
-      tar xzf btllib-1.7.0.tar.gz
-      cd btllib-1.7.0
+      wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
+      tar xzf btllib-1.7.2.tar.gz
+      cd btllib-1.7.2
       export CC=gcc-12
       export CXX=g++-12
       ./compile
     displayName: Install btllib
   - script: |
       ./autogen.sh
-      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-12 CXX=g++-12 --with-btllib=/home/vsts/work/1/s/btllib-1.7.0/install"
-      ./configure CC=gcc-12 CXX=g++-12 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.0/install
+      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-12 CXX=g++-12 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
+      ./configure CC=gcc-12 CXX=g++-12 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
       make -j12 distcheck
     displayName: Compiling ABySS with gcc-12
 
@@ -208,17 +161,17 @@ jobs:
   - script: sudo apt-get install -qq gcc-11 g++-11
     displayName: Install gcc-11
   - script: |
-      wget https://github.com/bcgsc/btllib/releases/download/v1.7.0/btllib-1.7.0.tar.gz
-      tar xzf btllib-1.7.0.tar.gz
-      cd btllib-1.7.0
+      wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
+      tar xzf btllib-1.7.2.tar.gz
+      cd btllib-1.7.2
       export CC=gcc-11
       export CXX=g++-11
       ./compile
     displayName: Install btllib
   - script: |
       ./autogen.sh
-      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-11 CXX=g++-11 --with-btllib=/home/vsts/work/1/s/btllib-1.7.0/install"
-      ./configure CC=gcc-11 CXX=g++-11 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.0/install
+      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-11 CXX=g++-11 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
+      ./configure CC=gcc-11 CXX=g++-11 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
       make -j12 distcheck
     displayName: Compiling ABySS with gcc-11
 
@@ -237,17 +190,17 @@ jobs:
   - script: sudo apt-get install -qq gcc-10 g++-10
     displayName: Install gcc-10
   - script: |
-      wget https://github.com/bcgsc/btllib/releases/download/v1.7.0/btllib-1.7.0.tar.gz
-      tar xzf btllib-1.7.0.tar.gz
-      cd btllib-1.7.0
+      wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
+      tar xzf btllib-1.7.2.tar.gz
+      cd btllib-1.7.2
       export CC=gcc-10
       export CXX=g++-10
       ./compile
     displayName: Install btllib
   - script: |
       ./autogen.sh
-      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-10 CXX=g++-10 --with-btllib=/home/vsts/work/1/s/btllib-1.7.0/install"
-      ./configure CC=gcc-10 CXX=g++-10 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.0/install
+      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-10 CXX=g++-10 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
+      ./configure CC=gcc-10 CXX=g++-10 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
       make -j12 distcheck
     displayName: Compiling ABySS with gcc-10
   - script: |
@@ -275,17 +228,17 @@ jobs:
   - script: sudo apt-get install -qq gcc-9 g++-9
     displayName: Install gcc-9
   - script: |
-      wget https://github.com/bcgsc/btllib/releases/download/v1.7.0/btllib-1.7.0.tar.gz
-      tar xzf btllib-1.7.0.tar.gz
-      cd btllib-1.7.0
+      wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
+      tar xzf btllib-1.7.2.tar.gz
+      cd btllib-1.7.2
       export CC=gcc-9
       export CXX=g++-9
       ./compile
     displayName: Install btllib
   - script: |
       ./autogen.sh
-      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-9 CXX=g++-9 --with-btllib=/home/vsts/work/1/s/btllib-1.7.0/install"
-      ./configure CC=gcc-9 CXX=g++-9 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.0/install
+      export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-9 CXX=g++-9 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
+      ./configure CC=gcc-9 CXX=g++-9 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
       make -j12 distcheck
     displayName: Compiling ABySS with gcc-9
 

diff --git a/dialign/assemble.c b/dialign/assemble.c
@@ -395,7 +395,7 @@ void heapify_diag_array(struct diag **diags, int pos, int length, int up) {
  *
  * Returns whether something new could be aligned
  */
-char simple_aligner(struct seq_col *scol, struct diag_col *dcol, 
+int simple_aligner(struct seq_col *scol, struct diag_col *dcol, 
 			    struct scr_matrix* smatrix, 
 			    struct prob_dist *pdist, 
 			    struct alignment *algn, int round) {

diff --git a/kmerprint/Makefile.am b/kmerprint/Makefile.am
@@ -11,3 +11,5 @@ kmerprint_LDADD = \
 	$(top_builddir)/Common/libcommon.a
 
 kmerprint_SOURCES = kmerprint.cc
+
+CXXFLAGS += -Wno-deprecated-declarations