spooles: fix compiler errors and link properly; fix darwin build

pkgs/development/libraries/science/math/spooles/allocate.patch

@@ -0,0 +1,38 @@
+From cc153b180829c6b561765cbbb9b621d1142ff1cd Mon Sep 17 00:00:00 2001
+From: annalee <[email protected]>
+Date: Tue, 28 Nov 2023 13:13:44 +0000
+Subject: [PATCH] use proper format specifier for size_t
+
+---
+ Utilities/MM.h | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Utilities/MM.h b/Utilities/MM.h
+index 11e86c5..301c3ec 100644
+--- a/Utilities/MM.h
++++ b/Utilities/MM.h
+@@ -33,18 +33,18 @@ if ( (count) > 0 ) { \
+    if ( (ptr = (type *)malloc((unsigned long)((count)*sizeof(type)))) \
+         == NULL ) {\
+       fprintf(stderr, \
+-              "\n ALLOCATE failure : bytes %d, line %d, file %s", \
++              "\n ALLOCATE failure : bytes %zu, line %d, file %s", \
+               (count)*sizeof(type), __LINE__, __FILE__) ; \
+       exit(-1) ; } \
+    else if ( MEMORY_DEBUG > 0 ) { \
+       fprintf(stderr, \
+-              "\n ALLOCATE : address %p, bytes %d, line %d, file %s", \
++              "\n ALLOCATE : address %p, bytes %zu, line %d, file %s", \
+               ptr, (count)*sizeof(type), __LINE__, __FILE__) ; } } \
+ else if ( (count) == 0 ) { \
+    ptr = NULL ; } \
+ else { \
+    fprintf(stderr, \
+-           "\n ALLOCATE error : bytes %d, line %d, file %s", \
++           "\n ALLOCATE error : bytes %zu, line %d, file %s", \
+            (count)*sizeof(type), __LINE__, __FILE__) ; \
+    exit(-1) ; }
+ /*
+-- 
+2.42.0
+

pkgs/development/libraries/science/math/spooles/default.nix

@@ -13,10 +13,14 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./spooles.patch
+    # fix compiler error where NULL is used as a zero parameter
+    ./transform.patch
+    # use proper format specifier for size_t
+    ./allocate.patch
   ];
 
   postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
-    substituteInPlace makefile --replace '-Wl,-soname' '-Wl,-install_name'
+    substituteInPlace makefile --replace "-Wl,-soname," "-Wl,-install_name,$out/lib/"
   '';
 
   buildPhase = ''

pkgs/development/libraries/science/math/spooles/transform.patch

@@ -0,0 +1,43 @@
+From c5d0574182d76af3bf286dce0bb147ae3f098916 Mon Sep 17 00:00:00 2001
+From: annalee <[email protected]>
+Date: Tue, 28 Nov 2023 12:57:18 +0000
+Subject: [PATCH] fix compiler error: use zero, not NULL, in calls to IVinit
+
+---
+ ETree/src/transform.c | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/ETree/src/transform.c b/ETree/src/transform.c
+index 1e36981..dbdfc70 100644
+--- a/ETree/src/transform.c
++++ b/ETree/src/transform.c
+@@ -291,7 +291,7 @@ etree2 = ETree_compress(etree, mapIV) ;
+    remap the nzeros[] vector
+    -------------------------
+ */
+-temp = IVinit(nfront, NULL) ;
++temp = IVinit(nfront, 0) ;
+ IVcopy(nfront, temp, nzeros) ;
+ IV_setSize(nzerosIV, nnew) ;
+ nzeros = IV_entries(nzerosIV) ;
+@@ -453,7 +453,7 @@ etree2 = ETree_compress(etree, mapIV) ;
+    remap the nzeros[] vector
+    -------------------------
+ */
+-temp = IVinit(nfront, NULL) ;
++temp = IVinit(nfront, 0) ;
+ IVcopy(nfront, temp, nzeros) ;
+ IV_setSize(nzerosIV, nnew) ;
+ nzeros = IV_entries(nzerosIV) ;
+@@ -614,7 +614,7 @@ etree2 = ETree_compress(etree, mapIV) ;
+    remap the nzeros[] vector
+    -------------------------
+ */
+-temp = IVinit(nfront, NULL) ;
++temp = IVinit(nfront, 0) ;
+ IVcopy(nfront, temp, nzeros) ;
+ IV_setSize(nzerosIV, nnew) ;
+ nzeros = IV_entries(nzerosIV) ;
+-- 
+2.42.0
+