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biology/cdbfasta: Update to 2018.10.05

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

Reported by:    pkg-fallout
This commit is contained in:
Jason W. Bacon 2023-07-10 10:29:23 -05:00
parent 506e859aa1
commit cc903ba092
8 changed files with 248 additions and 24 deletions
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10
biology/cdbfasta/Makefile
View file

@ -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

5
biology/cdbfasta/distinfo
View file

@ -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

40
biology/cdbfasta/files/patch-Makefile
View file

@ -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

40
biology/cdbfasta/files/patch-gclib_GBase.cpp Normal file
View file

@ -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;

65
biology/cdbfasta/files/patch-gclib_GHash.hh Normal file
View file

@ -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));

98
biology/cdbfasta/files/patch-gclib_GStr.cpp Normal file
View file

@ -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;

11
biology/cdbfasta/files/patch-gclib_gcdb.cpp Normal file
View file

@ -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;

3
biology/cdbfasta/pkg-descr
View file

@ -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.