From nobody Tue Jul 11 15:41:53 2023 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4R0lV95ZNPz4dQWV; Tue, 11 Jul 2023 15:41:53 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4R0lV94vc6z3LRT; Tue, 11 Jul 2023 15:41:53 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689090113; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=N1FiVXbnts9NTRubmnvPW6ybTzxUXrga9jhFL6GHan8=; b=i7bF+uPNSxy62tZ+7fCpI00IZDcmrUxDDGJQzIXXDTzXTZrsVYdJJbIkX4yjo3/SU4ua54 ajy97ZD21yjwOc96WzYpZemkuvT/OhUlO3D+utFf64Aq01yaqgv2v3n3pqQB3zFtZuCRlJ DUARRopiPw+zLOQ5UT9pIpLaHi4he71CgMTzeMItsONDBFiOI8Luh9JwRBk65+CDI08JCN nLyYwMM3UHRUcnzbr1g5QYcHJT45gBgmQulcWmNiEVSdm1HVbWxhbdSLbGIUAxEGGcf8Fw Sku+16U+yc8wIneDGf0A1bs8NrullZtmkAkCk9cjU7p2zbB2DV7TUCNEZmDnxg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689090113; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=N1FiVXbnts9NTRubmnvPW6ybTzxUXrga9jhFL6GHan8=; b=E6R9Y0TQaWPTl8fhfTsW4CF1PBi48TxEN52O1Zt7oWqqVnwYIVVD2208tJZrimF3olKYYw 7xdYWE7yVSNjjvY09QjR5sdGspiR7gStZWVgDDflcWGz8B+ZRtEUV0X/VF0ItoQEwqpB2j /cr8WxRgZcRoHYKC0aIr6d0ZaBMY5yX6yxFnOHEa65hTpq1hudD+jAmbqCrN6t8O2kOJ7c 4SoYhJAlpyRKdAvKiIQoYQrVoAkuXuX3skt4AtPHeaeHN8vjoPo8kVdkBhtcn1nuHlZ92X oW95GIGfbnxAD58tFD26gHaUTkMnk2e/hPnLA4qanShfSWFc3oJLU8ZXqg9Nig== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1689090113; a=rsa-sha256; cv=none; b=fMaNVfBt8NkI/7SBa7lG+3T3VYXo6FmHg84TonHETfiBqtB06Iud9DzBgnNtIfvwVUZcdq tOhUF9N9gnTSZLvmJFJje12NW0dvqgoFlPJLkKfAIG/wtWSIUzO0XWFCvjQf0lQ6prlsWC 6wloiGf5gztmVZNjAbAv+6F+XbM5entR+5S+HkEG68ajojI4oEoZLm0ITsxahEFlmwGiHA q9Y5ypKyrIJ9W/fi96IQiKJiqzdhxF5guAiI0Gpwv/l/Yvn2N6X62P2Fb9DE/lYh6nLvlL /6aB+gUbEUYgCY2ZYYFwghKhiARk1hTxFlyfU2qX1d8GfmV2CDLcx7SD1EfNyw== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4R0lV93z34zWsC; Tue, 11 Jul 2023 15:41:53 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 36BFfra1071229; Tue, 11 Jul 2023 15:41:53 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 36BFfr5k071228; Tue, 11 Jul 2023 15:41:53 GMT (envelope-from git) Date: Tue, 11 Jul 2023 15:41:53 GMT Message-Id: <202307111541.36BFfr5k071228@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: ffa0a812a476 - main - biology/cdbfasta: Update to 2023.07.10 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: ffa0a812a47681edb1b7de3cc38e6cd27c3c1296 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=ffa0a812a47681edb1b7de3cc38e6cd27c3c1296 commit ffa0a812a47681edb1b7de3cc38e6cd27c3c1296 Author: Jason W. Bacon AuthorDate: 2023-07-11 15:40:27 +0000 Commit: Jason W. Bacon CommitDate: 2023-07-11 15:40:27 +0000 biology/cdbfasta: Update to 2023.07.10 Upstreamed patches against 2018.10.05 commit --- biology/cdbfasta/Makefile | 6 +- biology/cdbfasta/distinfo | 6 +- biology/cdbfasta/files/patch-Makefile | 62 ------------------ 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 ---- 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 char* GHash::NextKey() { - } - - template char* GHash::NextKey() { -- register int pos=fCurrentEntry; -+ int pos=fCurrentEntry; - while (pos OBJ* GHash::NextData() { - } - - template OBJ* GHash::NextData() { -- register int pos=fCurrentEntry; -+ int pos=fCurrentEntry; - while (pos OBJ* GHash::NextData(char* & - } - - template OBJ* GHash::NextData(char* &nextkey) { -- register int pos=fCurrentEntry; -+ int pos=fCurrentEntry; - while (pos int GHash::First() const { - - // Get first non-empty entry - template int GHash::First() const { -- register int pos=0; -+ int pos=0; - while(pos int GHash::Last() const { - - // Get last non-empty entry - template int GHash::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 void GHash::Clear(){ - - // Remove all - template void GHash::Clear(){ -- register int i; -+ int i; - for(i=0; i=0){ - if (hash[i].keyalloc) GFREE((hash[i].key)); -@@ -681,7 +681,7 @@ template GHash::~GHash(){ - - // Destroy table - template GHash::~GHash(){ -- register int i; -+ int i; - for(i=0; i=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; istartchars[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; istartchars[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; istartchars[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; istartchars[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;