From owner-dev-commits-ports-main@freebsd.org Thu Sep 16 09:49:52 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 7EE31678211; Thu, 16 Sep 2021 09:49:52 +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 4H9C402bmMz4dPN; Thu, 16 Sep 2021 09:49:52 +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 3A9C81F2AC; Thu, 16 Sep 2021 09:49:52 +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 18G9nqGu097071; Thu, 16 Sep 2021 09:49:52 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 18G9nq57097070; Thu, 16 Sep 2021 09:49:52 GMT (envelope-from git) Date: Thu, 16 Sep 2021 09:49:52 GMT Message-Id: <202109160949.18G9nq57097070@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Alexey Dokuchaev Subject: git: 299862ff2afc - main - biology/ugene: update Unipro UGENE to version 40.0. MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: danfe X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 299862ff2afc17f5a415843ba9fc87ee6074fa87 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 16 Sep 2021 09:49:52 -0000 The branch main has been updated by danfe: URL: https://cgit.FreeBSD.org/ports/commit/?id=299862ff2afc17f5a415843ba9fc87ee6074fa87 commit 299862ff2afc17f5a415843ba9fc87ee6074fa87 Author: Alexey Dokuchaev AuthorDate: 2021-09-16 09:48:26 +0000 Commit: Alexey Dokuchaev CommitDate: 2021-09-16 09:48:26 +0000 biology/ugene: update Unipro UGENE to version 40.0. --- biology/ugene/Makefile | 13 ++++--------- biology/ugene/distinfo | 6 +++--- ...bs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp | 13 ++++++------- biology/ugene/pkg-plist | 2 ++ 4 files changed, 15 insertions(+), 19 deletions(-) diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 0737101475c8..52036dcf0c70 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -1,7 +1,7 @@ # Created by: Hannes Hauswedell PORTNAME= ugene -PORTVERSION= 39.0 +PORTVERSION= 40.0 CATEGORIES= biology science MAINTAINER= h2+fbsdports@fsfe.org @@ -47,7 +47,7 @@ post-patch: # yes, bash is required, stuff will not execute with sh @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \ ${WRKSRC}/src/gen_bin_script.cmd \ - ${WRKSRC}/installer/_common_data/ugene + ${WRKSRC}/etc/shared/ugene ${WRKSRC}/etc/shared/ugened @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \ ${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp @${REINPLACE_CMD} 's, -lbreakpad$$$$D,,' \ @@ -55,13 +55,8 @@ post-patch: ${WRKSRC}/src/plugins_checker/plugins_checker.pri \ ${WRKSRC}/src/ugenecl/ugenecl.pri \ ${WRKSRC}/src/ugeneui/ugeneui.pri - @${REINPLACE_CMD} -e '218,220s|NULL)|false)|' \ - ${WRKSRC}/src/plugins/GUITestBase/src/GTUtilsMdi.cpp - @${REINPLACE_CMD} -e '/--no-pie/s,unix:!macx,linux-g++,' \ - ${WRKSRC}/src/plugins_checker/plugins_checker.pri \ - ${WRKSRC}/src/ugenecl/ugenecl.pri \ - ${WRKSRC}/src/ugenem/ugenem.pro \ - ${WRKSRC}/src/ugeneui/ugeneui.pri + @${REINPLACE_CMD} -e '/ugene\.desktop/s,share,&d,' \ + ${WRKSRC}/ugene.pri post-stage: @cd ${STAGEDIR}${PREFIX} && ${RM} bin/ecp.* lib/ugene/ecp.* diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo index de58bef3c1a8..645944ea4647 100644 --- a/biology/ugene/distinfo +++ b/biology/ugene/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1623340087 -SHA256 (ugeneunipro-ugene-39.0_GH0.tar.gz) = 1e5141c097b22735497d91d59a47356a6fc132f8355c0a0bc97e26097c43570a -SIZE (ugeneunipro-ugene-39.0_GH0.tar.gz) = 24940304 +TIMESTAMP = 1631110733 +SHA256 (ugeneunipro-ugene-40.0_GH0.tar.gz) = 7a2f06141d571f45ce61e68af0a2456a3b3892b2d97104ec7ddfd1113b447c0f +SIZE (ugeneunipro-ugene-40.0_GH0.tar.gz) = 28789225 diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp index 469dbb04e207..c6956606c3ed 100644 --- a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp +++ b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp @@ -1,22 +1,21 @@ Use the Linux driver for FreeBSD as well. Fixes crash on startup. ---- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2018-09-02 00:22:54 UTC +--- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2021-09-08 14:18:53 UTC +++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp -@@ -23,7 +23,7 @@ +@@ -21,14 +21,14 @@ #include "GTKeyboardDriver.h" -#if defined __linux__ +#if defined(__linux__) || defined(__FreeBSD__) - # define XK_LATIN1 // for latin symbol - # define XK_MISCELLANY // for action keys # include -@@ -32,7 +32,7 @@ + # include + #endif namespace HI { -#if defined __linux__ +#if defined(__linux__) || defined(__FreeBSD__) - # define GT_CLASS_NAME "GTKeyboardDriverLinux" - + bool GTKeyboardDriver::keyPress(char key, Qt::KeyboardModifiers modifiers) { + DRIVER_CHECK(key != 0, "key = 0"); diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist index 1787b082f22b..1e72bae02143 100644 --- a/biology/ugene/pkg-plist +++ b/biology/ugene/pkg-plist @@ -228,6 +228,7 @@ share/pixmaps/ugene.xpm %%DATADIR%%/cmdline/hmm2-build.uwl %%DATADIR%%/cmdline/hmm2-search.uwl %%DATADIR%%/cmdline/hmm3-build-and-search.uwl +%%DATADIR%%/cmdline/hmm3-search.uwl %%DATADIR%%/cmdline/join-quality.uwl %%DATADIR%%/cmdline/local-blast+.uwl %%DATADIR%%/cmdline/pfm-build.uwl @@ -1033,6 +1034,7 @@ share/pixmaps/ugene.xpm %%DATADIR%%/samples/PDB/3INS.PDB %%DATADIR%%/samples/Raw/raw.seq %%DATADIR%%/samples/SCF/90-JRI-07.scf +%%DATADIR%%/samples/Sanger/alignment.ugenedb %%DATADIR%%/samples/Stockholm/CBS.sto %%DATADIR%%/samples/Stockholm/UPSK.sto %%DATADIR%%/samples/Swiss-Prot/D0VTW9.txt