zlib 1.3

chrchang · Sep 6, 2023 · 5e9f5cb · 5e9f5cb
1 parent fddc1bd
commit 5e9f5cb
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Showing 13 changed files with 25 additions and 240 deletions.
diff --git a/1.9/Makefile b/1.9/Makefile
@@ -47,7 +47,7 @@ ifeq ($(SYS), MAC)
   CXXFLAGS += $(MACFLAGS)
   BLASFLAGS ?= -framework Accelerate
   LDFLAGS ?= -ldl
-  ZLIB ?= -L. ../zlib-1.2.13/libz.a
+  ZLIB ?= -L. ../zlib-1.3/libz.a
 endif
 
 ifeq ($(SYS), WIN)
@@ -58,13 +58,13 @@ ifeq ($(SYS), WIN)
 # NO_LAPACK.
   BLASFLAGS ?= -L. lapack/liblapack.a -L. lapack/librefblas.a
   LDFLAGS ?= -lm -static-libgcc
-  ZLIB ?= -L. ../zlib-1.2.13/libz.a
+  ZLIB ?= -L. ../zlib-1.3/libz.a
 endif
 
 # These must appear after the MAC/WIN-specific ?= statements.
 BLASFLAGS ?=	-L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
 LDFLAGS ?=	-lm -lpthread -ldl
-ZLIB ?=		-L. ../zlib-1.2.13/libz.so.1.2.13
+ZLIB ?=		-L. ../zlib-1.3/libz.so.1.3
 
 ifdef NO_LAPACK
   BLASFLAGS=

diff --git a/1.9/Makefile.old b/1.9/Makefile.old
diff --git a/1.9/Makefile.std b/1.9/Makefile.std
diff --git a/1.9/build_mac/Makefile b/1.9/build_mac/Makefile
@@ -25,8 +25,8 @@ ifeq ($(SYS), MAC)
   CXXFLAGS += $(MACFLAGS)
   BLASFLAGS ?= -framework Accelerate
   LDFLAGS ?= -ldl
-  ZLIB_AMD ?= -L. ../../zlib-1.2.13/libz-amd64.a
-  ZLIB_ARM ?= -L. ../../zlib-1.2.13/libz-arm64.a
+  ZLIB_AMD ?= -L. ../../zlib-1.3/libz-amd64.a
+  ZLIB_ARM ?= -L. ../../zlib-1.3/libz-arm64.a
 endif
 
 CCSRC = plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c

diff --git a/1.9/dose2plink.c b/1.9/dose2plink.c
@@ -96,7 +96,7 @@
   #endif
 #endif
 
-#include "../zlib-1.2.13/zlib.h"
+#include "../zlib-1.3/zlib.h"
 
 #ifdef __APPLE__
   #include <sys/sysctl.h>

diff --git a/1.9/pigz.c b/1.9/pigz.c
@@ -300,7 +300,7 @@
 #ifdef DYNAMIC_ZLIB
   #include <zlib.h>
 #else
-  #include "../zlib-1.2.13/zlib.h"
+  #include "../zlib-1.3/zlib.h"
 #endif
 
 #include "pigz.h"
@@ -526,7 +526,7 @@ int32_t flex_pzwrite_close_null(Pigz_state* ps_ptr, char* writep) {
 #ifdef DYNAMIC_ZLIB
   #include <zlib.h>
 #else
-  #include "../zlib-1.2.13/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
+  #include "../zlib-1.3/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
                         /* deflateEnd(), deflateSetDictionary(), crc32(),
                            inflateBackInit(), inflateBack(), inflateBackEnd(),
                            Z_DEFAULT_COMPRESSION, Z_DEFAULT_STRATEGY,

diff --git a/1.9/plink.c b/1.9/plink.c
@@ -105,10 +105,10 @@ static const char ver_str[] =
 #else
   " 32-bit"
 #endif
-  " (13 Feb 2023)";
+  " (6 Sep 2023)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
-  ""
+  " "
 #ifdef STABLE_BUILD
   " " // (don't want this when version number has two trailing digits)
 #else

diff --git a/1.9/plink_calc.c b/1.9/plink_calc.c
@@ -5442,7 +5442,6 @@ int32_t rel_cutoff_batch(uint32_t load_grm_bin, char* grmname, char* outname, ch
   uint32_t uii;
   uint32_t row;
   uint32_t col;
-  uint32_t new_row;
   uint32_t pct;
   uintptr_t sample_idx;
   int32_t* rel_ct_arr;
@@ -5862,7 +5861,6 @@ int32_t rel_cutoff_batch(uint32_t load_grm_bin, char* grmname, char* outname, ch
       pct = 1;
       row = 0;
       col = 0;
-      new_row = 1;
       progress = 0;
       hundredth = 1 + ((((uint64_t)sample_ct) * (sample_ct - 1)) / 200);
       memcpy(outname_end, ".grm.N.bin", 11);
@@ -5923,7 +5921,6 @@ int32_t rel_cutoff_batch(uint32_t load_grm_bin, char* grmname, char* outname, ch
 	      }
 	    }
 	  }
-	  new_row++;
 	}
 	row++;
 	progress += row;
@@ -6700,7 +6697,7 @@ int32_t calc_rel(pthread_t* threads, uint32_t parallel_idx, uint32_t parallel_to
       }
       strcpy(outname_end, ".rel.bin");
       if (parallel_tot > 1) {
-	sprintf(&(outname_end[8]), ".%u", parallel_idx + 1);
+	snprintf(&(outname_end[8]), MAX_POST_EXT - 8, ".%u", parallel_idx + 1);
       }
       if (fopen_checked(outname, FOPEN_WB, &outfile)) {
 	goto calc_rel_ret_OPEN_FAIL;
@@ -6793,7 +6790,7 @@ int32_t calc_rel(pthread_t* threads, uint32_t parallel_idx, uint32_t parallel_to
       // make this .rel.bin4?
       strcpy(outname_end, ".rel.bin");
       if (parallel_tot > 1) {
-	sprintf(&(outname_end[8]), ".%u", parallel_idx + 1);
+	snprintf(&(outname_end[8]), MAX_POST_EXT - 8, ".%u", parallel_idx + 1);
       }
       if (fopen_checked(outname, FOPEN_WB, &outfile)) {
 	goto calc_rel_ret_OPEN_FAIL;
@@ -6857,7 +6854,7 @@ int32_t calc_rel(pthread_t* threads, uint32_t parallel_idx, uint32_t parallel_to
 	} else {
 	  strcpy(outname_end, ".grm");
 	  if (parallel_tot > 1) {
-	    sprintf(&(outname_end[4]), ".%u", parallel_idx + 1);
+	    snprintf(&(outname_end[4]), MAX_POST_EXT - 4, ".%u", parallel_idx + 1);
 	  }
 	  retval = write_uncompressed(outname, overflow_buf, 0, calc_rel_grm_emitn);
 	  if (retval) {
@@ -6874,7 +6871,7 @@ int32_t calc_rel(pthread_t* threads, uint32_t parallel_idx, uint32_t parallel_to
 	} else {
 	  strcpy(outname_end, ".rel");
 	  if (parallel_tot > 1) {
-	    sprintf(&(outname_end[4]), ".%u", parallel_idx + 1);
+	    snprintf(&(outname_end[4]), MAX_POST_EXT - 4, ".%u", parallel_idx + 1);
 	  }
 	}
 	if (rel_shape == REL_CALC_TRI) {
@@ -6938,7 +6935,7 @@ int32_t calc_rel(pthread_t* threads, uint32_t parallel_idx, uint32_t parallel_to
       if (retval) {
 	goto calc_rel_ret_1;
       }
-      sprintf(wptr, " , and IDs written to %s .\n", outname);
+      snprintf(wptr, LOGBUFLEN - (wptr - g_logbuf), " , and IDs written to %s .\n", outname);
     } else {
       snprintf(g_logbuf, LOGBUFLEN, "Relationship matrix component written to %s .\n", outname);
     }
@@ -8066,7 +8063,7 @@ int32_t calc_distance(pthread_t* threads, uint32_t parallel_idx, uint32_t parall
       if (retval) {
 	goto calc_distance_ret_1;
       }
-      sprintf(wptr, " , and IDs to %s .\n", outname);
+      snprintf(wptr, LOGBUFLEN - (wptr - g_logbuf), " , and IDs to %s .\n", outname);
     } else {
       snprintf(g_logbuf, LOGBUFLEN, "Distances (proportions) written to %s .\n", outname);
     }

diff --git a/1.9/plink_common.h b/1.9/plink_common.h
@@ -265,7 +265,7 @@
     #error "zlib version 1.2.4 or later required."
   #endif
 #else
-  #include "../zlib-1.2.13/zlib.h"
+  #include "../zlib-1.3/zlib.h"
 #endif
 #include "SFMT.h"