bump

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 ----