Makefile

@@ -31,9 +31,6 @@ CC ?=		gcc
 CXX ?=		g++
 CFLAGS ?=	-Wall -O2
 CXXFLAGS ?=	-Wall -O2
-BLASFLAGS ?=	-L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
-LDFLAGS ?=	-lm -lpthread -ldl
-ZLIB ?=		../zlib-1.2.11/libz.so.1.2.11
 
 PREFIX ?=	/usr/local
 DESTDIR ?=	.
@@ -61,6 +58,11 @@ ifeq ($(SYS), WIN)
   ZLIB ?= ../zlib-1.2.11/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 ?=		../zlib-1.2.11/libz.so.1.2.11
+
 ifdef NO_LAPACK
   BLASFLAGS=
 endif

Makefile.std

@@ -31,9 +31,6 @@ CC ?=		gcc
 CXX ?=		g++
 CFLAGS ?=	-Wall -O2
 CXXFLAGS ?=	-Wall -O2
-BLASFLAGS ?=	-L/usr/lib64/atlas -llapack -lblas -lcblas -latlas
-LDFLAGS ?=	-lm -lpthread -ldl
-ZLIB ?=		../zlib-1.2.11/libz.so.1.2.11
 
 PREFIX ?=	/usr/local
 DESTDIR ?=	.
@@ -61,6 +58,11 @@ ifeq ($(SYS), WIN)
   ZLIB ?= ../zlib-1.2.11/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 ?=		../zlib-1.2.11/libz.so.1.2.11
+
 ifdef NO_LAPACK
   BLASFLAGS=
 endif

plink.c

@@ -93,7 +93,7 @@
 static const char ver_str[] =
 #ifdef STABLE_BUILD
-  "PLINK v1.90b6.10"
+  "PLINK v1.90b6.11"
 #else
   "PLINK v1.90p"
 #endif
@@ -105,7 +105,7 @@ static const char ver_str[] =
 #else
   " 32-bit"
 #endif
-  " (17 Jun 2019)";
+  " (24 Oct 2019)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""
@@ -7531,7 +7531,7 @@ int32_t main(int32_t argc, char** argv) {
 	  goto main_ret_INVALID_CMDLINE_2A;
 	}
 	// may want to permit decimal here
-	if (scan_posint_defcapx(argv[cur_arg + 1], &ld_info.prune_window_size) || ((ld_info.prune_window_size == 1) && (param_ct == 3))) {
+	if (scan_posint_defcap(argv[cur_arg + 1], &ld_info.prune_window_size) || ((ld_info.prune_window_size == 1) && (param_ct == 3))) {
 	  sprintf(g_logbuf, "Error: Invalid --%s window size '%s'.\n", argptr, argv[cur_arg + 1]);
 	  goto main_ret_INVALID_CMDLINE_WWA;
 	}
@@ -8218,6 +8218,10 @@ int32_t main(int32_t argc, char** argv) {
 	  goto main_ret_NOMEM;
 	}
       } else if (!memcmp(argptr2, "d-snps", 7)) {
+        if (ld_info.snpstr) {
+          logerrprint("Error: --ld-snps cannot be used with --ld-snp or --ld-snp-list.\n");
+          goto main_ret_INVALID_CMDLINE_A;
+        }
         if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 0x7fffffff)) {
 	  goto main_ret_INVALID_CMDLINE_2A;
 	}
@@ -8226,6 +8230,10 @@ int32_t main(int32_t argc, char** argv) {
 	  goto main_ret_1;
 	}
       } else if (!memcmp(argptr2, "d-snp-list", 11)) {
+        if (ld_info.snpstr) {
+          logerrprint("Error: --ld-snp cannot be used with --ld-snp-list.\n");
+          goto main_ret_INVALID_CMDLINE_A;
+        }
         if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 1)) {
 	  goto main_ret_INVALID_CMDLINE_2A;
 	}
@@ -10756,6 +10764,7 @@ int32_t main(int32_t argc, char** argv) {
           ld_info.modifier |= LD_R2;
 	} else if (ld_info.window_r2 != 0.2) {
 	  logerrprint("Error: --ld-window-r2 flag cannot be used with --r.\n");
+          goto main_ret_INVALID_CMDLINE_A;
 	}
 	if (matrix_flag_state) {
 	  matrix_flag_state = 2;

plink_calc.c

@@ -7121,6 +7121,11 @@ int32_t calc_pca(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outna
   }
   fill_int_zero(liwork * (sizeof(__CLPK_integer) / sizeof(int32_t)), (int32_t*)iwork);
   dsyevr_(&jobz, &range, &uplo, &mdim, main_matrix, &mdim, &nz, &nz, &i1, &i2, &zz, &out_m, out_w, out_z, &ldz, isuppz, work, &lwork, iwork, &liwork, &info);
+  if ((info != 0) || (out_w[0] != out_w[0])) {
+    logprint("\n");
+    logerrprint("Error: Failed to extract eigenvector(s) from GRM.\n");
+    goto calc_pca_ret_DEGENERATE_DATA;
+  }
 
   // * out_w[0..(pc_ct-1)] contains eigenvalues
   // * out_z[(ii*ulii)..(ii*ulii + ulii - 1)] is eigenvector corresponding to
@@ -7437,6 +7442,9 @@ int32_t calc_pca(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outna
   calc_pca_ret_WRITE_FAIL:
     retval = RET_WRITE_FAIL;
     break;
+  calc_pca_ret_DEGENERATE_DATA:
+    retval = RET_DEGENERATE_DATA;
+    break;
   }
   return retval;
 }

plink_common.h

@@ -319,6 +319,7 @@
 #define RET_ALL_SAMPLES_EXCLUDED 11
 #define RET_ALL_MARKERS_EXCLUDED 12
 #define RET_NETWORK 13
+#define RET_DEGENERATE_DATA 14
 #define LOAD_PHENO_LAST_COL 127
 
 // for 2.0 -> 1.9 backports

plink_dosage.c

@@ -1135,10 +1135,12 @@ int32_t plink1_dosage(Dosage_info* doip, char* famname, char* mapname, char* out
       goto plink1_dosage_ret_1;
     }
     if (qrange_ct) {
+      // bugfix (24 Oct 2019): score_range_obs_cts and score_miss_cts need to
+      // be zero-initialized
       if (bigstack_calloc_d(sample_ct * qrange_ct, &cur_scores) ||
           bigstack_calloc_d(qrange_ct, &score_bases) ||
-          bigstack_alloc_ui(qrange_ct, &score_range_obs_cts) ||
-          bigstack_alloc_ui(sample_ct * qrange_ct, &score_miss_cts)) {
+          bigstack_calloc_ui(qrange_ct, &score_range_obs_cts) ||
+          bigstack_calloc_ui(sample_ct * qrange_ct, &score_miss_cts)) {
 	goto plink1_dosage_ret_NOMEM;
       }
       *outname_end = '.';