From nobody Wed Oct 20 16:37:54 2021 X-Original-To: dev-commits-ports-main@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 C0DDF17F60EC; Wed, 20 Oct 2021 16:37:54 +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 4HZGW654nyz4m38; Wed, 20 Oct 2021 16:37:54 +0000 (UTC) (envelope-from git@FreeBSD.org) 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 8AEA5302A; Wed, 20 Oct 2021 16:37:54 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 19KGbsQC013588; Wed, 20 Oct 2021 16:37:54 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 19KGbsqD013587; Wed, 20 Oct 2021 16:37:54 GMT (envelope-from git) Date: Wed, 20 Oct 2021 16:37:54 GMT Message-Id: <202110201637.19KGbsqD013587@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: f6c6c5a37954 - main - biology/fastp: Update to 0.23.1 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@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: f6c6c5a37954173f208f39515fdf79d1dc6e2689 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=f6c6c5a37954173f208f39515fdf79d1dc6e2689 commit f6c6c5a37954173f208f39515fdf79d1dc6e2689 Author: Jason W. Bacon AuthorDate: 2021-10-20 16:35:11 +0000 Commit: Jason W. Bacon CommitDate: 2021-10-20 16:37:39 +0000 biology/fastp: Update to 0.23.1 Performance improvements, more reproducible output Fix seg fault when running with no args --- biology/fastp/Makefile | 7 +++-- biology/fastp/distinfo | 6 ++--- biology/fastp/files/patch-Makefile | 47 ++++++++++++++++++++++------------ biology/fastp/files/patch-src_main.cpp | 17 ++++++++++++ 4 files changed, 56 insertions(+), 21 deletions(-) diff --git a/biology/fastp/Makefile b/biology/fastp/Makefile index 2b8ec0278e58..904ebb18ad56 100644 --- a/biology/fastp/Makefile +++ b/biology/fastp/Makefile @@ -1,6 +1,6 @@ PORTNAME= fastp DISTVERSIONPREFIX= v -DISTVERSION= 0.22.0 +DISTVERSION= 0.23.1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -9,7 +9,10 @@ COMMENT= Ultra-fast all-in-one FASTQ preprocessor LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -USES= compiler:c++11-lang gmake +LIB_DEPENDS= libdeflate.so:archivers/libdeflate \ + libisal.so:devel/isa-l + +USES= compiler:c++11-lang gmake localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= OpenGene diff --git a/biology/fastp/distinfo b/biology/fastp/distinfo index 3ecec1406b78..a6994823ad4b 100644 --- a/biology/fastp/distinfo +++ b/biology/fastp/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1630006835 -SHA256 (OpenGene-fastp-v0.22.0_GH0.tar.gz) = a7ef81cc39daed7ac6bfc254697345c448095539e1b5b45f3a8ab286098be456 -SIZE (OpenGene-fastp-v0.22.0_GH0.tar.gz) = 141257 +TIMESTAMP = 1634739193 +SHA256 (OpenGene-fastp-v0.23.1_GH0.tar.gz) = 32cb16ea1199a5f722d3c5caa24d1aaace4b24f6efa0fd774f227d8a80ebb8f3 +SIZE (OpenGene-fastp-v0.23.1_GH0.tar.gz) = 163190 diff --git a/biology/fastp/files/patch-Makefile b/biology/fastp/files/patch-Makefile index 595fdc96c6e6..da927edbe011 100644 --- a/biology/fastp/files/patch-Makefile +++ b/biology/fastp/files/patch-Makefile @@ -1,42 +1,57 @@ ---- Makefile.orig 2020-04-08 07:26:52 UTC +--- Makefile.orig 2021-10-19 02:19:29 UTC +++ Makefile -@@ -3,9 +3,11 @@ DIR_SRC := ./src +@@ -2,11 +2,13 @@ DIR_INC := ./inc + DIR_SRC := ./src DIR_OBJ := ./obj - PREFIX ?= /usr/local -+DESTDIR ?= - BINDIR ?= $(PREFIX)/bin - INCLUDE_DIRS ?= - LIBRARY_DIRS ?= -+STRIP_CMD ?= strip +-PREFIX ?= /usr/local +-BINDIR ?= $(PREFIX)/bin +-INCLUDE_DIRS ?= +-LIBRARY_DIRS ?= ++PREFIX ?= /usr/local ++BINDIR ?= $(PREFIX)/bin ++INCLUDE_DIRS ?= ++LIBRARY_DIRS ?= ++STRIP ?= strip ++ SRC := $(wildcard ${DIR_SRC}/*.cpp) OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC})) -@@ -15,13 +17,14 @@ TARGET := fastp + +@@ -15,15 +17,19 @@ TARGET := fastp BIN_TARGET := ${TARGET} CXX ?= g++ --CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} +-CXXFLAGS := -std=c++11 -pthread -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} ++# Optional flags that the user can override by setting CXXFLAGS in the ++# env or make argument +CXXFLAGS ?= -g -O3 ++# Required flags +CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) - LIBS := -lz -lpthread + LIBS := -lisal -ldeflate -lpthread + STATIC_FLAGS := -static -Wl,--no-as-needed -pthread -LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS) ++# Append required flags to standard LDFLAGS from env +LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) + STATIC_LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_FLAGS) $(LIBS) $(STATIC_LD_FLAGS) - +- ${BIN_TARGET}:${OBJ} - $(CXX) $(OBJ) -o $@ $(LD_FLAGS) + $(CXX) $(OBJ) -o $@ $(LDFLAGS) - ${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir - $(CXX) -c $< -o $@ $(CXXFLAGS) -@@ -38,5 +41,8 @@ make_obj_dir: + static:${OBJ} + $(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS) +@@ -49,6 +55,11 @@ make_obj_dir: + mkdir $(DIR_OBJ) ; \ fi ++# Respect DESTDIR for staged installs (used by most package managers) install: - install $(TARGET) $(BINDIR)/$(TARGET) + install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET) @echo "Installed." + ++# Many package managers use install-strip target if debugging is not enabled +install-strip: install -+ $(STRIP_CMD) $(DESTDIR)$(BINDIR)/$(TARGET) ++ $(STRIP) $(DESTDIR)$(BINDIR)/$(TARGET) diff --git a/biology/fastp/files/patch-src_main.cpp b/biology/fastp/files/patch-src_main.cpp new file mode 100644 index 000000000000..28e5bf918991 --- /dev/null +++ b/biology/fastp/files/patch-src_main.cpp @@ -0,0 +1,17 @@ +--- src/main.cpp.orig 2021-10-19 02:19:29 UTC ++++ src/main.cpp +@@ -1,4 +1,5 @@ + #include ++#include + #include "fastqreader.h" + #include "unittest.h" + #include +@@ -18,7 +19,7 @@ int main(int argc, char* argv[]){ + if(argc == 1) { + cerr << "fastp: an ultra-fast all-in-one FASTQ preprocessor" << endl << "version " << FASTP_VER << endl; + //cerr << "fastp --help to see the help"<