From owner-svn-ports-all@freebsd.org Wed May 16 15:13:44 2018 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 24653EE7E69; Wed, 16 May 2018 15:13:44 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id CABF36CFCF; Wed, 16 May 2018 15:13:43 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id ABC5D1BDE1; Wed, 16 May 2018 15:13:43 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w4GFDhix046615; Wed, 16 May 2018 15:13:43 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w4GFDhIr046613; Wed, 16 May 2018 15:13:43 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <201805161513.w4GFDhIr046613@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Wed, 16 May 2018 15:13:43 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r470124 - in head/biology/fastx-toolkit: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/fastx-toolkit: . files X-SVN-Commit-Revision: 470124 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.26 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 16 May 2018 15:13:44 -0000 Author: jwb Date: Wed May 16 15:13:43 2018 New Revision: 470124 URL: https://svnweb.freebsd.org/changeset/ports/470124 Log: biology/fastx-toolkit: Fix build on FreeBSD 12 Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15451 Added: head/biology/fastx-toolkit/files/ head/biology/fastx-toolkit/files/patch-src_libfastx_fastx.h (contents, props changed) Modified: head/biology/fastx-toolkit/Makefile Modified: head/biology/fastx-toolkit/Makefile ============================================================================== --- head/biology/fastx-toolkit/Makefile Wed May 16 14:16:09 2018 (r470123) +++ head/biology/fastx-toolkit/Makefile Wed May 16 15:13:43 2018 (r470124) @@ -15,10 +15,8 @@ LIB_DEPENDS= libgtextutils.so:biology/libgtextutils USES= autoreconf libtool perl5 pkgconfig shebangfix USE_PERL5= run SHEBANG_FILES= scripts/*.pl - USE_GITHUB= yes GH_ACCOUNT= agordon - GNU_CONFIGURE= yes .include Added: head/biology/fastx-toolkit/files/patch-src_libfastx_fastx.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fastx-toolkit/files/patch-src_libfastx_fastx.h Wed May 16 15:13:43 2018 (r470124) @@ -0,0 +1,19 @@ +--- src/libfastx/fastx.h.orig 2018-05-16 14:50:08 UTC ++++ src/libfastx/fastx.h +@@ -58,7 +58,7 @@ typedef enum { + OUTPUT_SAME_AS_INPUT=3 + } OUTPUT_FILE_TYPE; + +-#pragma pack(1) ++#pragma pack(push,1) + typedef struct + { + /* Record data - common for FASTA/FASTQ */ +@@ -115,6 +115,7 @@ typedef struct + FILE* input; + FILE* output; + } FASTX ; ++#pragma pack(pop) + + + void fastx_init_reader(FASTX *pFASTX, const char* filename,