Date: Mon, 10 Jul 2023 15:30:51 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: cc903ba09263 - main - biology/cdbfasta: Update to 2018.10.05 Message-ID: <202307101530.36AFUp9o066706@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=cc903ba092636e40c1f322c29a83447718dc7a39 commit cc903ba092636e40c1f322c29a83447718dc7a39 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-07-10 15:29:23 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2023-07-10 15:29:23 +0000 biology/cdbfasta: Update to 2018.10.05 Fix build for c++17 Improve pkg-descr Add license Reported by: pkg-fallout --- biology/cdbfasta/Makefile | 10 +-- biology/cdbfasta/distinfo | 5 +- biology/cdbfasta/files/patch-Makefile | 40 +++++++----- biology/cdbfasta/files/patch-gclib_GBase.cpp | 40 ++++++++++++ biology/cdbfasta/files/patch-gclib_GHash.hh | 65 ++++++++++++++++++ biology/cdbfasta/files/patch-gclib_GStr.cpp | 98 ++++++++++++++++++++++++++++ biology/cdbfasta/files/patch-gclib_gcdb.cpp | 11 ++++ biology/cdbfasta/pkg-descr | 3 +- 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.
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