biology/cdbfasta: Update to 2023.07.10

Upstreamed patches against 2018.10.05 commit

7 files changed, 6 insertions, 282 deletions

diff --git a/biology/cdbfasta/Makefile b/biology/cdbfasta/Makefile
index eea33d27211d..cca69dda1744 100644
--- a/biology/cdbfasta/Makefile
+++ b/biology/cdbfasta/Makefile
@@ -1,17 +1,17 @@
 PORTNAME=	cdbfasta
-PORTVERSION=	2018.10.05
+PORTVERSION=	2023.07.10
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Fast indexing and retrieval of FASTA records from flat file databases
-WWW=		https://sourceforge.net/projects/cdbfasta/
+WWW=		https://github.com/gpertea/cdbfasta
 
 LICENSE=	ART20
 
 USES=		gmake
 USE_GITHUB=	yes
 GH_ACCOUNT=	gpertea
-GH_TAGNAME=	014498c
+GH_TAGNAME=	da8f5ba
 
 PLIST_FILES=	bin/cdbfasta bin/cdbyank
 
diff --git a/biology/cdbfasta/distinfo b/biology/cdbfasta/distinfo
index 818a75e7dda8..88da9ca0f3f0 100644
--- a/biology/cdbfasta/distinfo
+++ b/biology/cdbfasta/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1689000001
-SHA256 (gpertea-cdbfasta-2018.10.05-014498c_GH0.tar.gz) = bba537d252b1ebcc60f91137c6d6924a4d36f024bc15fdb5de83d3f55332db8b
-SIZE (gpertea-cdbfasta-2018.10.05-014498c_GH0.tar.gz) = 63985
+TIMESTAMP = 1689089752
+SHA256 (gpertea-cdbfasta-2023.07.10-da8f5ba_GH0.tar.gz) = c32c1b09998ae24333dbf432740ef7d087d4c8987e8131363233242542d048ac
+SIZE (gpertea-cdbfasta-2023.07.10-da8f5ba_GH0.tar.gz) = 63949
diff --git a/biology/cdbfasta/files/patch-Makefile b/biology/cdbfasta/files/patch-Makefile
deleted file mode 100644
index 584928d0358f..000000000000
--- a/biology/cdbfasta/files/patch-Makefile
+++ /dev/null
@@ -1,62 +0,0 @@
---- Makefile.orig	2018-10-05 18:26:32 UTC
-+++ Makefile
-@@ -1,6 +1,8 @@ SEARCHDIRS := -I${GCLDIR}
- GCLDIR := ./gclib
- SEARCHDIRS := -I${GCLDIR}
--CC      := g++
-+# Use the correct compiler (CXX, not CC) and respect the environment
-+# by using ?=
-+CXX    ?= g++
- 
- BASEFLAGS  = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=1 -D_FILE_OFFSET_BITS=64 \
- -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing \
-@@ -9,39 +11,38 @@ ifeq ($(findstring debug,$(MAKECMDGOALS)),)
- 
- ifeq ($(findstring debug,$(MAKECMDGOALS)),)
-   DBGFLAGS = -O2 -g -DNDEBUG
--  LDFLAGS =
- else
-   DBGFLAGS = -g -DDEBUG -D_DEBUG
--  LDFLAGS = -g
-+  LDFLAGS += -g
- endif
- 
- ifeq ($(findstring nommap,$(MAKECMDGOALS)),)
--  CFLAGS = $(DBGFLAGS) $(BASEFLAGS)
-+  CXXFLAGS += $(DBGFLAGS) $(BASEFLAGS)
- else
--  CFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
-+  CXXFLAGS += $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
- endif
- 
- %.o : %.c
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cc
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.C
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cxx
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 
--LINKER    := g++
-+LINKER    := ${CXX}
- #LDFLAGS = 
- #uncomment this when ENABLE_COMPRESSION
--LDFLAGS    = -lz
-+LDFLAGS    += -lz
- 
- .PHONY : all
- all:    cdbfasta cdbyank 
diff --git a/biology/cdbfasta/files/patch-gclib_GBase.cpp b/biology/cdbfasta/files/patch-gclib_GBase.cpp
deleted file mode 100644
index 62cb518116f2..000000000000
--- a/biology/cdbfasta/files/patch-gclib_GBase.cpp
+++ /dev/null
@@ -1,40 +0,0 @@
---- gclib/GBase.cpp.orig	2023-07-10 09:56:17 UTC
-+++ gclib/GBase.cpp
-@@ -234,7 +234,7 @@ bool GstrEq(const char* a, const char* b) {
- 
- bool GstrEq(const char* a, const char* b) {
- 	 if (a==NULL || b==NULL) return false;
--	 register int i=0;
-+	 int i=0;
- 	 while (a[i]==b[i]) {
- 		 if (a[i]==0) return true;
- 		 ++i;
-@@ -244,7 +244,7 @@ bool GstriEq(const char* a, const char* b) {
- 
- bool GstriEq(const char* a, const char* b) {
- 	 if (a==NULL || b==NULL) return false;
--	 register int i=0;
-+	 int i=0;
- 	 while (tolower((unsigned char)a[i])==tolower((unsigned char)b[i])) {
- 		 if (a[i]==0) return true;
- 	 }
-@@ -253,7 +253,7 @@ int Gstricmp(const char* a, const char* b, int n) {
- 
- int Gstricmp(const char* a, const char* b, int n) {
-  if (a==NULL || b==NULL) return a==NULL ? -1 : 1;
-- register int ua, ub;
-+ int ua, ub;
-  if (n<0) {
-    while ((*a!=0) && (*b!=0)) {
-     ua=tolower((unsigned char)*a);
-@@ -662,8 +662,8 @@ int strhash(const char* str){
- 
- //hash function used for strings in GHash
- int strhash(const char* str){
--  register int h=0;
--  register int g;
-+  int h=0;
-+  int g;
-   while (*str) {
-     h=(h<<4)+*str++;
-     g=h&0xF0000000;
diff --git a/biology/cdbfasta/files/patch-gclib_GHash.hh b/biology/cdbfasta/files/patch-gclib_GHash.hh
deleted file mode 100644
index 1f3811b28546..000000000000
--- a/biology/cdbfasta/files/patch-gclib_GHash.hh
+++ /dev/null
@@ -1,65 +0,0 @@
---- gclib/GHash.hh.orig	2023-07-10 09:56:48 UTC
-+++ gclib/GHash.hh
-@@ -544,7 +544,7 @@ template <class OBJ> char* GHash<OBJ>::NextKey() {
- }
- 
- template <class OBJ> char* GHash<OBJ>::NextKey() {
-- register int pos=fCurrentEntry;
-+ int pos=fCurrentEntry;
-  while (pos<fCapacity && hash[pos].hash<0) pos++;
-  if (pos==fCapacity) {
-                  fCurrentEntry=fCapacity;
-@@ -557,7 +557,7 @@ template <class OBJ> OBJ* GHash<OBJ>::NextData() {
- }
- 
- template <class OBJ> OBJ* GHash<OBJ>::NextData() {
-- register int pos=fCurrentEntry;
-+ int pos=fCurrentEntry;
-  while (pos<fCapacity && hash[pos].hash<0) pos++;
-  if (pos==fCapacity) {
-                  fCurrentEntry=fCapacity;
-@@ -571,7 +571,7 @@ template <class OBJ> OBJ* GHash<OBJ>::NextData(char* &
- }
- 
- template <class OBJ> OBJ* GHash<OBJ>::NextData(char* &nextkey) {
-- register int pos=fCurrentEntry;
-+ int pos=fCurrentEntry;
-  while (pos<fCapacity && hash[pos].hash<0) pos++;
-  if (pos==fCapacity) {
-                  fCurrentEntry=fCapacity;
-@@ -589,7 +589,7 @@ template <class OBJ> int GHash<OBJ>::First() const {
- 
- // Get first non-empty entry
- template <class OBJ> int GHash<OBJ>::First() const {
--  register int pos=0;
-+  int pos=0;
-   while(pos<fCapacity){ if(0<=hash[pos].hash) break; pos++; }
-   GASSERT(fCapacity<=pos || 0<=hash[pos].hash);
-   return pos;
-@@ -597,7 +597,7 @@ template <class OBJ> int GHash<OBJ>::Last() const {
- 
- // Get last non-empty entry
- template <class OBJ> int GHash<OBJ>::Last() const {
--  register int pos=fCapacity-1;
-+  int pos=fCapacity-1;
-   while(0<=pos){ if(0<=hash[pos].hash) break; pos--; }
-   GASSERT(pos<0 || 0<=hash[pos].hash);
-   return pos;
-@@ -624,7 +624,7 @@ template <class OBJ> void GHash<OBJ>::Clear(){
- 
- // Remove all
- template <class OBJ> void GHash<OBJ>::Clear(){
--  register int i;
-+  int i;
-   for(i=0; i<fCapacity; i++){
-     if(hash[i].hash>=0){
-       if (hash[i].keyalloc) GFREE((hash[i].key));
-@@ -681,7 +681,7 @@ template <class OBJ> GHash<OBJ>::~GHash(){
- 
- // Destroy table
- template <class OBJ> GHash<OBJ>::~GHash(){
--  register int i;
-+  int i;
-   for(i=0; i<fCapacity; i++){
-     if(hash[i].hash>=0){
-       if (hash[i].keyalloc) GFREE((hash[i].key));
diff --git a/biology/cdbfasta/files/patch-gclib_GStr.cpp b/biology/cdbfasta/files/patch-gclib_GStr.cpp
deleted file mode 100644
index 1aa3a5f8f739..000000000000
--- a/biology/cdbfasta/files/patch-gclib_GStr.cpp
+++ /dev/null
@@ -1,98 +0,0 @@
---- gclib/GStr.cpp.orig	2023-07-10 09:57:46 UTC
-+++ gclib/GStr.cpp
-@@ -424,8 +424,8 @@ GStr& GStr::trim(char c) {
-   }
- 
- GStr& GStr::trim(char c) {
-- register int istart;
-- register int iend;
-+ int istart;
-+ int iend;
-  for (istart=0; istart<length() && my_data->chars[istart]==c;istart++) ;
-  if (istart==length()) {
-        make_unique(); //edit operation ahead
-@@ -444,8 +444,8 @@ GStr& GStr::trim(const char* c) {
-  }
- 
- GStr& GStr::trim(const char* c) {
-- register int istart;
-- register int iend;
-+ int istart;
-+ int iend;
-  for (istart=0; istart<length() && strchr(c, my_data->chars[istart])!=NULL ;istart++) ;
-  if (istart==length()) {
-         prep_data(0); //string was entirely trimmed
-@@ -464,8 +464,8 @@ GStr& GStr::trimR(char c) {
- 
- GStr& GStr::trimR(char c) {
-  //only trim the right end
-- //register int istart;
-- register int iend;
-+ //int istart;
-+ int iend;
-  for (iend=length()-1; iend>=0 && my_data->chars[iend]==c;iend--) ;
-  if (iend==-1) {
-        make_unique();
-@@ -488,7 +488,7 @@ GStr& GStr::trimR(const char* c) {
-  }
- 
- GStr& GStr::trimR(const char* c) {
-- register int iend;
-+ int iend;
-  for (iend=length()-1; iend>=0 && strchr(c,my_data->chars[iend])!=NULL;iend--) ;
-  if (iend==-1) {
-        make_unique();
-@@ -511,7 +511,7 @@ GStr& GStr::chomp(const char* cstr) {
- 
- 
- GStr& GStr::chomp(const char* cstr) {
-- register int iend;
-+ int iend;
-  if (cstr==NULL || *cstr==0) return *this;
-  //check if this ends with cstr
-  int cend=strlen(cstr)-1;
-@@ -537,7 +537,7 @@ GStr& GStr::trimL(char c) {
-  }
- 
- GStr& GStr::trimL(char c) {
-- register int istart;
-+ int istart;
-  for (istart=0; istart<length() && my_data->chars[istart]==c;istart++) ;
-  if (istart==length()) {
-        prep_data(0); //string was entirely trimmed
-@@ -554,7 +554,7 @@ GStr& GStr::trimL(const char* c) {
-  }
- 
- GStr& GStr::trimL(const char* c) {
-- register int istart;
-+ int istart;
-  for (istart=0; istart<length() && strchr(c,my_data->chars[istart])!=NULL;istart++) ;
-  if (istart==length()) {
-        prep_data(0); //string was entirely trimmed
-@@ -700,7 +700,7 @@ bool GStr::is_space() const {
-     if (my_data == &null_data)
-         return false;
- 
--    for (register const char *p = my_data->chars; *p; p++)
-+    for (const char *p = my_data->chars; *p; p++)
-         if (!isspace(*p))
-             return false;
- 
-@@ -1083,7 +1083,7 @@ GStr& GStr::upper() {
- 
- GStr& GStr::upper() {
-   make_unique(); //edit operation ahead
--  for (register char *p = chrs(); *p; p++)
-+  for (char *p = chrs(); *p; p++)
-             *p = (char) toupper(*p);
- 
-     return *this;
-@@ -1094,7 +1094,7 @@ GStr& GStr::lower() {
- GStr& GStr::lower() {
-     make_unique();
- 
--    for (register char *p = chrs(); *p; p++)
-+    for (char *p = chrs(); *p; p++)
-           *p = (char) tolower(*p);
- 
-     return *this;
diff --git a/biology/cdbfasta/files/patch-gclib_gcdb.cpp b/biology/cdbfasta/files/patch-gclib_gcdb.cpp
deleted file mode 100644
index 64b2e4aa1394..000000000000
--- a/biology/cdbfasta/files/patch-gclib_gcdb.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- gclib/gcdb.cpp.orig	2023-07-10 09:57:25 UTC
-+++ gclib/gcdb.cpp
-@@ -99,7 +99,7 @@ static unsigned int gcdb_strlen(const char *s) {
- #define gcdb_seek_begin(fd) (gcdb_seek_set((fd),(gcdb_seek_pos) 0))
- 
- static unsigned int gcdb_strlen(const char *s) {
--  register char *t;
-+  char *t;
-   t = (char*)s;
-   for (;;) {
-     if (!*t) return t - s;