From 46da413cf7c9c995842a83cd54b02a17cd9c7289 Mon Sep 17 00:00:00 2001 From: Nicholas Noll Date: Wed, 6 May 2020 20:39:55 -0700 Subject: bump --- .gitignore | 10 +-- compile_commands.json | 164 ++++++++++++++++++++++---------------------------- sys/libbio/simulate.c | 2 + sys/libn/rules.mk | 2 +- 4 files changed, 76 insertions(+), 102 deletions(-) diff --git a/.gitignore b/.gitignore index 941439d..d92c655 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,4 @@ lib/ -dep/ build/ data/ share/ @@ -10,10 +9,5 @@ sys/nixos bin/fasttree bin/mafft -GRTAGS -GTAGS -GPATH - -.cscope -cscope.out -tags +.dep/ +.clangd diff --git a/compile_commands.json b/compile_commands.json index fac553e..acb788e 100644 --- a/compile_commands.json +++ b/compile_commands.json @@ -4,7 +4,6 @@ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -12,23 +11,25 @@ "-fms-extensions", "-Wno-microsoft-anon-tag", "-Wno-incompatible-function-pointer-types", + "-ffreestanding", + "-fno-builtin", + "-nostdlib", "-isystem", "include/vendor/libc", "-I", "include", "-o", - "build/libbio/io/newick.o", - "sys/libbio/io/newick.c" + "build/libc/string.o", + "sys/libc/string.c" ], "directory": "/home/nolln/root", - "file": "sys/libbio/io/newick.c" + "file": "sys/libc/string.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -36,24 +37,22 @@ "-fms-extensions", "-Wno-microsoft-anon-tag", "-Wno-incompatible-function-pointer-types", - "-D_GNU_SOURCE", "-isystem", "include/vendor/libc", "-I", "include", "-o", - "build/libmath/test.o", - "sys/libmath/test.c" + "build/libn/bufio.o", + "sys/libn/bufio.c" ], "directory": "/home/nolln/root", - "file": "sys/libmath/test.c" + "file": "sys/libn/bufio.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -66,18 +65,17 @@ "-I", "include", "-o", - "build/libn/flate.o", - "sys/libn/flate.c" + "build/libbio/phylo.o", + "sys/libbio/phylo.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/flate.c" + "file": "sys/libbio/phylo.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -90,18 +88,17 @@ "-I", "include", "-o", - "build/libn/gz.o", - "sys/libn/gz.c" + "build/libn/flate.o", + "sys/libn/flate.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/gz.c" + "file": "sys/libn/flate.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -114,18 +111,17 @@ "-I", "include", "-o", - "build/libn/mmap.o", - "sys/libn/mmap.c" + "build/libn/sort.o", + "sys/libn/sort.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/mmap.c" + "file": "sys/libn/sort.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -133,24 +129,22 @@ "-fms-extensions", "-Wno-microsoft-anon-tag", "-Wno-incompatible-function-pointer-types", - "-D_GNU_SOURCE", "-isystem", "include/vendor/libc", "-I", "include", "-o", - "build/libmath/blas.o", - "sys/libmath/blas.c" + "build/libbio/test.o", + "sys/libbio/test.c" ], "directory": "/home/nolln/root", - "file": "sys/libmath/blas.c" + "file": "sys/libbio/test.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -163,18 +157,17 @@ "-I", "include", "-o", - "build/libbio/test.o", - "sys/libbio/test.c" + "build/libbio/align.o", + "sys/libbio/align.c" ], "directory": "/home/nolln/root", - "file": "sys/libbio/test.c" + "file": "sys/libbio/align.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -182,26 +175,23 @@ "-fms-extensions", "-Wno-microsoft-anon-tag", "-Wno-incompatible-function-pointer-types", - "-ffreestanding", - "-fno-builtin", - "-nostdlib", + "-D_GNU_SOURCE", "-isystem", "include/vendor/libc", "-I", "include", "-o", - "build/libc/string.o", - "sys/libc/string.c" + "build/libmath/blas.o", + "sys/libmath/blas.c" ], "directory": "/home/nolln/root", - "file": "sys/libc/string.c" + "file": "sys/libmath/blas.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -209,26 +199,22 @@ "-fms-extensions", "-Wno-microsoft-anon-tag", "-Wno-incompatible-function-pointer-types", - "-ffreestanding", - "-fno-builtin", - "-nostdlib", "-isystem", "include/vendor/libc", "-I", "include", "-o", - "build/libc/stdio.o", - "sys/libc/stdio.c" + "build/libn/memory.o", + "sys/libn/memory.c" ], "directory": "/home/nolln/root", - "file": "sys/libc/stdio.c" + "file": "sys/libn/memory.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -241,18 +227,17 @@ "-I", "include", "-o", - "build/libn/error.o", - "sys/libn/error.c" + "build/libn/mmap.o", + "sys/libn/mmap.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/error.c" + "file": "sys/libn/mmap.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -265,18 +250,17 @@ "-I", "include", "-o", - "build/libbio/align.o", - "sys/libbio/align.c" + "build/libbio/io/fasta.o", + "sys/libbio/io/fasta.c" ], "directory": "/home/nolln/root", - "file": "sys/libbio/align.c" + "file": "sys/libbio/io/fasta.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -289,18 +273,17 @@ "-I", "include", "-o", - "build/libn/random.o", - "sys/libn/random.c" + "build/libbio/simulate.o", + "sys/libbio/simulate.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/random.c" + "file": "sys/libbio/simulate.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -313,18 +296,17 @@ "-I", "include", "-o", - "build/libbio/phylo.o", - "sys/libbio/phylo.c" + "build/libn/random.o", + "sys/libn/random.c" ], "directory": "/home/nolln/root", - "file": "sys/libbio/phylo.c" + "file": "sys/libn/random.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -332,23 +314,23 @@ "-fms-extensions", "-Wno-microsoft-anon-tag", "-Wno-incompatible-function-pointer-types", + "-D_GNU_SOURCE", "-isystem", "include/vendor/libc", "-I", "include", "-o", - "build/libn/memory.o", - "sys/libn/memory.c" + "build/libmath/test.o", + "sys/libmath/test.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/memory.c" + "file": "sys/libmath/test.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -361,18 +343,17 @@ "-I", "include", "-o", - "build/libn/io.o", - "sys/libn/io.c" + "build/libbio/io/newick.o", + "sys/libbio/io/newick.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/io.c" + "file": "sys/libbio/io/newick.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -396,7 +377,6 @@ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -404,23 +384,25 @@ "-fms-extensions", "-Wno-microsoft-anon-tag", "-Wno-incompatible-function-pointer-types", + "-ffreestanding", + "-fno-builtin", + "-nostdlib", "-isystem", "include/vendor/libc", "-I", "include", "-o", - "build/libn/coro.o", - "sys/libn/coro.c" + "build/libc/stdio.o", + "sys/libc/stdio.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/coro.c" + "file": "sys/libc/stdio.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -433,18 +415,17 @@ "-I", "include", "-o", - "build/libn/sort.o", - "sys/libn/sort.c" + "build/libn/test.o", + "sys/libn/test.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/sort.c" + "file": "sys/libn/test.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -457,18 +438,17 @@ "-I", "include", "-o", - "build/libn/bufio.o", - "sys/libn/bufio.c" + "build/libn/gz.o", + "sys/libn/gz.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/bufio.c" + "file": "sys/libn/gz.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -481,18 +461,17 @@ "-I", "include", "-o", - "build/libbio/io/fasta.o", - "sys/libbio/io/fasta.c" + "build/libn/coro.o", + "sys/libn/coro.c" ], "directory": "/home/nolln/root", - "file": "sys/libbio/io/fasta.c" + "file": "sys/libn/coro.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -505,18 +484,17 @@ "-I", "include", "-o", - "build/libbio/simulate.o", - "sys/libbio/simulate.c" + "build/libn/io.o", + "sys/libn/io.c" ], "directory": "/home/nolln/root", - "file": "sys/libbio/simulate.c" + "file": "sys/libn/io.c" }, { "arguments": [ "clang", "-c", "-g", - "-O0", "-march=native", "-ffast-math", "-fno-strict-aliasing", @@ -529,10 +507,10 @@ "-I", "include", "-o", - "build/libn/test.o", - "sys/libn/test.c" + "build/libn/error.o", + "sys/libn/error.c" ], "directory": "/home/nolln/root", - "file": "sys/libn/test.c" + "file": "sys/libn/error.c" } ] \ No newline at end of file diff --git a/sys/libbio/simulate.c b/sys/libbio/simulate.c index f5489b6..0f5a97e 100644 --- a/sys/libbio/simulate.c +++ b/sys/libbio/simulate.c @@ -115,4 +115,6 @@ main() for (n = 0; n < aln·N; n++) { aln·sort(NSEQS, aln·L, (uint64*)vals[n]); } + + return 0; } diff --git a/sys/libn/rules.mk b/sys/libn/rules.mk index 19e4c50..a60a3d5 100644 --- a/sys/libn/rules.mk +++ b/sys/libn/rules.mk @@ -37,7 +37,7 @@ $(LIBS_$(d)): $(OBJS_$(d)) $(ARCHIVE) $(BINS_$(d)): TCLIBS := $(LIBS_$(d)) $(LIB_DIR)/vendor/libz.a -$(BINS_$(d)): $(OBJ_DIR)/libn/test.o +$(BINS_$(d)): $(OBJ_DIR)/libn/test.o $(LIBS_$(d)) $(LINK) # ---- Pop off stack ---- -- cgit v1.2.1