biology/cdbfasta: Update to 2018.10.05

Fix build for c++17
Improve pkg-descr
Add license

Reported by:    pkg-fallout

8 files changed, 248 insertions, 24 deletions

diff --git a/biology/cdbfasta/Makefile b/biology/cdbfasta/Makefile
index 8a30ab65ee8d..eea33d27211d 100644
--- a/biology/cdbfasta/Makefile
+++ b/biology/cdbfasta/Makefile
@@ -1,17 +1,17 @@
 PORTNAME=	cdbfasta
-PORTVERSION=	2010.07.22
+PORTVERSION=	2018.10.05
 CATEGORIES=	biology
-MASTER_SITES=	http://acadix.biz/Ports/distfiles/
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Fast indexing and retrieval of FASTA records from flat file databases
 WWW=		https://sourceforge.net/projects/cdbfasta/
 
-# LICENSE=	unspecified
-
-WRKSRC=		${WRKDIR}/${PORTNAME}
+LICENSE=	ART20
 
 USES=		gmake
+USE_GITHUB=	yes
+GH_ACCOUNT=	gpertea
+GH_TAGNAME=	014498c
 
 PLIST_FILES=	bin/cdbfasta bin/cdbyank
 
diff --git a/biology/cdbfasta/distinfo b/biology/cdbfasta/distinfo
index 0d3ec1700289..818a75e7dda8 100644
--- a/biology/cdbfasta/distinfo
+++ b/biology/cdbfasta/distinfo
@@ -1,2 +1,3 @@
-SHA256 (cdbfasta-2010.07.22.tar.gz) = 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c
-SIZE (cdbfasta-2010.07.22.tar.gz) = 59735
+TIMESTAMP = 1689000001
+SHA256 (gpertea-cdbfasta-2018.10.05-014498c_GH0.tar.gz) = bba537d252b1ebcc60f91137c6d6924a4d36f024bc15fdb5de83d3f55332db8b
+SIZE (gpertea-cdbfasta-2018.10.05-014498c_GH0.tar.gz) = 63985
diff --git a/biology/cdbfasta/files/patch-Makefile b/biology/cdbfasta/files/patch-Makefile
index c062b13bf9eb..584928d0358f 100644
--- a/biology/cdbfasta/files/patch-Makefile
+++ b/biology/cdbfasta/files/patch-Makefile
@@ -1,26 +1,32 @@
---- Makefile.orig	2009-12-03 20:17:51 UTC
+--- Makefile.orig	2018-10-05 18:26:32 UTC
 +++ Makefile
-@@ -18,7 +18,10 @@ else
-     MARCH = 
- endif    
- 
+@@ -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=0 -D_FILE_OFFSET_BITS=64 \
++CXX    ?= g++
+ 
+ BASEFLAGS  = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=1 -D_FILE_OFFSET_BITS=64 \
  -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing \
- -D_REENTRANT 
-@@ -33,30 +36,30 @@ else
+@@ -9,39 +11,38 @@ ifeq ($(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)
++  CXXFLAGS += $(DBGFLAGS) $(BASEFLAGS)
  else
 -  CFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
-+  CXXFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
++  CXXFLAGS += $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
  endif
  
  %.o : %.c
@@ -46,9 +52,11 @@
  # C/C++ linker
  
 -LINKER    := g++
++LINKER    := ${CXX}
+ #LDFLAGS = 
+ #uncomment this when ENABLE_COMPRESSION
 -LDFLAGS    = -lz
-+LINKER	:= ${CXX}
-+LDFLAGS	= -lz
- #if ENABLE_COMPRESSION is not needed,
- # LDFLAGS = 
++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
new file mode 100644
index 000000000000..62cb518116f2
--- /dev/null
+++ b/biology/cdbfasta/files/patch-gclib_GBase.cpp
@@ -0,0 +1,40 @@
+--- 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
new file mode 100644
index 000000000000..1f3811b28546
--- /dev/null
+++ b/biology/cdbfasta/files/patch-gclib_GHash.hh
@@ -0,0 +1,65 @@
+--- 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
new file mode 100644
index 000000000000..1aa3a5f8f739
--- /dev/null
+++ b/biology/cdbfasta/files/patch-gclib_GStr.cpp
@@ -0,0 +1,98 @@
+--- 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
new file mode 100644
index 000000000000..64b2e4aa1394
--- /dev/null
+++ b/biology/cdbfasta/files/patch-gclib_gcdb.cpp
@@ -0,0 +1,11 @@
+--- 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;
diff --git a/biology/cdbfasta/pkg-descr b/biology/cdbfasta/pkg-descr
index c0ef25c244ec..71336f98157f 100644
--- a/biology/cdbfasta/pkg-descr
+++ b/biology/cdbfasta/pkg-descr
@@ -1 +1,2 @@
-Fast indexing and retrieval of FASTA records from flat file data bases.
+Cdbfasta creates an index file for a multi-FASTA file to facilitate
+fast retrieval of any sequence using cdbyank.