git: 299862ff2afc - main - biology/ugene: update Unipro UGENE to version 40.0.

[Alexey Dokuchaev]

The branch main has been updated by danfe:

URL: https://cgit.FreeBSD.org/ports/commit/?id=299862ff2afc17f5a415843ba9fc87ee6074fa87

commit 299862ff2afc17f5a415843ba9fc87ee6074fa87
Author:     Alexey Dokuchaev <danfe at FreeBSD.org>
AuthorDate: 2021-09-16 09:48:26 +0000
Commit:     Alexey Dokuchaev <danfe at FreeBSD.org>
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 <h2+fbsdports at fsfe.org>
 
 PORTNAME=	ugene
-PORTVERSION=	39.0
+PORTVERSION=	40.0
 CATEGORIES=	biology science
 
 MAINTAINER=	h2+fbsdports at 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 <X11/extensions/XTest.h>
-@@ -32,7 +32,7 @@
+ #    include <X11/keysym.h>
+ #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