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Tue, 22 Mar 2022 00:07:14 GMT (envelope-from git) Date: Tue, 22 Mar 2022 00:07:14 GMT Message-Id: <202203220007.22M07E48078922@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 929ed699367f - main - biology/dsr-pdb: Remove -pg (mcount instrumentation) flag 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: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 929ed699367f119574a299b211b395ac2b2d74c9 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; 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mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=929ed699367f119574a299b211b395ac2b2d74c9 commit 929ed699367f119574a299b211b395ac2b2d74c9 Author: Yuri Victorovich AuthorDate: 2022-03-22 00:06:18 +0000 Commit: Yuri Victorovich CommitDate: 2022-03-22 00:07:11 +0000 biology/dsr-pdb: Remove -pg (mcount instrumentation) flag This causes failure on aarch64: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=262709 --- biology/dsr-pdb/Makefile | 5 +++-- biology/dsr-pdb/files/patch-lib_Makefile.in | 13 +++++++++++++ 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/biology/dsr-pdb/Makefile b/biology/dsr-pdb/Makefile index c73b661acd4f..b17e471da589 100644 --- a/biology/dsr-pdb/Makefile +++ b/biology/dsr-pdb/Makefile @@ -1,6 +1,6 @@ PORTNAME= dsr-pdb DISTVERSION= 1.0.3 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= biology MASTER_SITES= https://graphics.stanford.edu/~drussel/ DISTNAME= ${PORTNAME} @@ -17,9 +17,10 @@ BROKEN_aarch64= ld: error: undefined symbol: .mcount (see bug#262709) LIB_DEPENDS= libboost_program_options.so:devel/boost-libs USES= compiler:c++11-lang gmake libtool localbase:ldflags tar:tgz -GNU_CONFIGURE= yes USE_LDCONFIG= yes +GNU_CONFIGURE= yes + WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} CXXFLAGS+= -fPIC --std=c++11 # libboost_program_options.so isn't found without --std=c++11 diff --git a/biology/dsr-pdb/files/patch-lib_Makefile.in b/biology/dsr-pdb/files/patch-lib_Makefile.in new file mode 100644 index 000000000000..58a5ed2003b5 --- /dev/null +++ b/biology/dsr-pdb/files/patch-lib_Makefile.in @@ -0,0 +1,13 @@ +- workaround for https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=262709 + +--- lib/Makefile.in.orig 2022-03-22 00:02:00 UTC ++++ lib/Makefile.in +@@ -180,7 +180,7 @@ sysconfdir = @sysconfdir@ + target_alias = @target_alias@ + lib_LTLIBRARIES = libdsrpdb.la + noinst_HEADERS = pdb_utils.h Residue_data.h +-AM_CPPFLAGS = -I../include -pg ++AM_CPPFLAGS = -I../include + libdsrpdb_la_SOURCES = Residue.cc Protein.cc Residue_data.cc Protein_pdb.cc pdb_utils.cc Model.cc PDB.cc align.cc distance.cc Error_logger.cc + libdsrpdb_la_LDFLAGS = -static + all: all-am