science/massxpert: Update 3.4.0 -> 3.6.1

This software seems to be abandoned by its upstream, and rescued by the Debian team.
I've set its source to Debian's GitLab server, where they source it from now.

Port changes:
* 3.6.1 is Qt5-based: remove the DEPRECATED lines
* USE_GCC seems to be needed due to clang error messages
* MAKE_JOBS_UNSAFE isn't needed

8 files changed, 52 insertions, 93 deletions

diff --git a/science/massxpert/Makefile b/science/massxpert/Makefile
index 6ce98a6f6fd6..2800386124b9 100644
--- a/science/massxpert/Makefile
+++ b/science/massxpert/Makefile
@@ -2,18 +2,14 @@
 # $FreeBSD$
 
 PORTNAME=	massxpert
-PORTVERSION=	3.4.0
-PORTREVISION=	12
+DISTVERSION=	3.6.1
 CATEGORIES=	science
-MASTER_SITES=	http://download.tuxfamily.org/massxpert/source/
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	massXpert software for (bio)chemists
 
 LICENSE=	GPLv3
-
-DEPRECATED=		Qt4 has been EOL since december 2015
-EXPIRATION_DATE=	2019-03-15
+LICENSE_FILE=	${WRKSRC}/COPYING
 
 BUILD_DEPENDS=	${LOCALBASE}/libdata/pkgconfig/pthread-stubs.pc:devel/libpthread-stubs
 LIB_DEPENDS=	libpcre.so:devel/pcre \
@@ -22,13 +18,15 @@ LIB_DEPENDS=	libpcre.so:devel/pcre \
 		libexpat.so:textproc/expat2 \
 		libfontconfig.so:x11-fonts/fontconfig
 
-USE_GCC=	any
-USES=		cmake gettext qt:4 tar:bzip2
+USES=		cmake gettext gnome qt:5 tar:bzip2
+USE_GITLAB=	yes
+GL_SITE=	https://salsa.debian.org/
+GL_ACCOUNT=	debichem-team
+GL_COMMIT=	c229f4a1abde3c20b83a90e50f9c5d79104dfa5f
+USE_GCC=	any # build breaks in clang
 USE_XORG=	ice sm x11 xau xcb xdmcp xext xrender
 USE_GNOME=	glib20
-USE_QT=		corelib gui xml rcc_build qmake_build uic_build moc_build \
-		svg
+USE_QT=		core gui svg xml widgets buildtools_build qmake_build
 USE_LDCONFIG=	yes
-MAKE_JOBS_UNSAFE=	yes
 
 .include <bsd.port.mk>
diff --git a/science/massxpert/distinfo b/science/massxpert/distinfo
index 4089e4a89aa7..6ac8bd9df020 100644
--- a/science/massxpert/distinfo
+++ b/science/massxpert/distinfo
@@ -1,2 +1,3 @@
-SHA256 (massxpert-3.4.0.tar.bz2) = b06314722b4cbdf68dc76e55933a79487848c655fc65341a8dbc707ed89cc9e8
-SIZE (massxpert-3.4.0.tar.bz2) = 16544044
+TIMESTAMP = 1552172511
+SHA256 (debichem-team-massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f_GL0.tar.gz) = 28bdfb73a12c3f198450f1cf2aac57b647168006ea82d5eee7af0caaf0a2841e
+SIZE (debichem-team-massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f_GL0.tar.gz) = 17469770
diff --git a/science/massxpert/files/patch-CMakeLists.txt b/science/massxpert/files/patch-CMakeLists.txt
index e1b2d600d479..dd14622c2dc3 100644
--- a/science/massxpert/files/patch-CMakeLists.txt
+++ b/science/massxpert/files/patch-CMakeLists.txt
@@ -1,29 +1,31 @@
---- CMakeLists.txt.orig	2010-05-11 01:23:01.000000000 +0800
-+++ CMakeLists.txt	2010-05-21 20:17:36.000000000 +0800
-@@ -153,7 +153,7 @@
-   # The manual page
-   IF (UNIX AND NOT APPLE)
-     INSTALL (FILES massxpert.1
--      DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1)
-+      DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1)
-   ENDIF (UNIX AND NOT APPLE)
+--- CMakeLists.txt.orig	2019-03-09 23:08:57 UTC
++++ CMakeLists.txt
+@@ -130,8 +130,8 @@ CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/CMake
+ # install stuff
  
-   ###############
-@@ -188,7 +188,7 @@
-   # The manual pages (data)
-   IF (UNIX AND NOT APPLE)
-     INSTALL (FILES massxpert-data.7
+ # The license file
+-INSTALL(FILES COPYING
+-  DESTINATION ${MASSXPERT_DOC_DIR})
++#INSTALL(FILES COPYING
++#  DESTINATION ${MASSXPERT_DOC_DIR})
+ 
+ # The desktop file
+ IF(UNIX AND NOT APPLE)
+@@ -142,7 +142,7 @@ ENDIF(UNIX AND NOT APPLE)
+ # The manual page
+ IF(UNIX AND NOT APPLE)
+   INSTALL(FILES massxpert.1
+-    DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1)
++    DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1)
+ ENDIF(UNIX AND NOT APPLE)
+ 
+ 
+@@ -169,7 +169,7 @@ IF(${BUILD_DATA})
+   # The manual pages(data)
+   IF(UNIX AND NOT APPLE)
+     INSTALL(FILES massxpert-data.7
 -      DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man7)
 +      DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man7)
-   ENDIF (UNIX AND NOT APPLE)
+   ENDIF(UNIX AND NOT APPLE)
    
    #################
-@@ -222,7 +222,7 @@
-   # The manual pages (user manual)
-   IF (UNIX AND NOT APPLE)
-     INSTALL (FILES massxpert-doc.7
--      DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man7)
-+      DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man7)
-   ENDIF (UNIX AND NOT APPLE)
-   
-   
diff --git a/science/massxpert/files/patch-lib_cleaveSpec.cpp b/science/massxpert/files/patch-lib_cleaveSpec.cpp
deleted file mode 100644
index 904af6ac2aca..000000000000
--- a/science/massxpert/files/patch-lib_cleaveSpec.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- lib/cleaveSpec.cpp.orig	2012-12-25 21:02:43 UTC
-+++ lib/cleaveSpec.cpp
-@@ -427,7 +427,7 @@ namespace massXpert
-       return false;
- 
-   
--    if (parse() == -1)
-+    if (parse() == false)
-       return false;
-   
-     // If there are rules, we have to check them all.
diff --git a/science/massxpert/files/patch-lib_propListHolder.cpp b/science/massxpert/files/patch-lib_propListHolder.cpp
deleted file mode 100644
index b6f037a8009c..000000000000
--- a/science/massxpert/files/patch-lib_propListHolder.cpp
+++ /dev/null
@@ -1,19 +0,0 @@
-Fixes the build with GCC 6 (in addition to fixing an actual bug).
-
-/wrkdirs/usr/ports/science/massxpert/work/massxpert-3.4.0/lib/propListHolder.cpp: In member function 'bool massXpert::PropListHolder::removeProp(const QString&)':
-/wrkdirs/usr/ports/science/massxpert/work/massxpert-3.4.0/lib/propListHolder.cpp:216:2: error: this 'if' clause does not guard... [-Werror=misleading-indentation]
-  if(m_propList.at(iter)->name() == name);
-  ^~
-/wrkdirs/usr/ports/science/massxpert/work/massxpert-3.4.0/lib/propListHolder.cpp:217:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
-  {
---- lib/propListHolder.cpp.orig	2017-07-26 17:06:18 UTC
-+++ lib/propListHolder.cpp
-@@ -213,7 +213,7 @@ namespace massXpert
-   {
-     for (int iter = 0; iter < m_propList.size(); ++iter)
-       {
--	if(m_propList.at(iter)->name() == name);
-+	if(m_propList.at(iter)->name() == name)
- 	{
- 	  m_propList.removeAt(iter);
- 	  
diff --git a/science/massxpert/files/patch-plugins-src_seqToolsPlugin_seqToolsPluginDlg.cpp b/science/massxpert/files/patch-plugins-src_seqToolsPlugin_seqToolsPluginDlg.cpp
deleted file mode 100644
index 46c261227c5f..000000000000
--- a/science/massxpert/files/patch-plugins-src_seqToolsPlugin_seqToolsPluginDlg.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- plugins-src/seqToolsPlugin/seqToolsPluginDlg.cpp.orig	2012-12-25 21:02:43 UTC
-+++ plugins-src/seqToolsPlugin/seqToolsPluginDlg.cpp
-@@ -215,7 +215,7 @@ SeqToolsPluginDlg::loadDictionary ()
- 
-       QStringList stringList = line.split (">", QString::SkipEmptyParts);
-       
--      if (!stringList.size () == 2)
-+      if (stringList.size () != 2)
- 	{
- 	  QMessageBox::warning (this,
- 				tr ("Sequence Manipulation Tools Plugin"),
diff --git a/science/massxpert/pkg-descr b/science/massxpert/pkg-descr
index 6a571361839a..6ad116f435a0 100644
--- a/science/massxpert/pkg-descr
+++ b/science/massxpert/pkg-descr
@@ -17,4 +17,4 @@ to another (using a dictionary, like between the 1-letter code and the 3-letter
 code of proteins) 2) conversion of number format according to any localized
 number format 3) sort mass lists.
 
-WWW: http://massxpert.tuxfamily.org/
+WWW: https://salsa.debian.org/debichem-team/massxpert
diff --git a/science/massxpert/pkg-plist b/science/massxpert/pkg-plist
index 1a360a985ed4..e4002e2c2c02 100644
--- a/science/massxpert/pkg-plist
+++ b/science/massxpert/pkg-plist
@@ -1,11 +1,13 @@
 bin/massxpert
-lib/massxpert/plugins/libmassListSorterPlugin.so
-lib/massxpert/plugins/libseqToolsPlugin.so
-lib/massxpert/plugins/libnumeralsLocaleConverterPlugin.so
 man/man1/massxpert.1.gz
 man/man7/massxpert-data.7.gz
-%%DOCSDIR%%/COPYING
 share/applications/massxpert.desktop
+%%DATADIR%%/chem_pad.conf
+%%DATADIR%%/dictionaries/codon-to-protein-1.dic
+%%DATADIR%%/dictionaries/codon-to-protein-3.dic
+%%DATADIR%%/dictionaries/pdb-protein-to-mxp.dic
+%%DATADIR%%/dictionaries/protein-1-to-3.dic
+%%DATADIR%%/dictionaries/protein-3-to-1.dic
 %%DATADIR%%/locales/massxpert_fr.qm
 %%DATADIR%%/pol-chem-defs/dna/adenine.svg
 %%DATADIR%%/pol-chem-defs/dna/biotlink.svg
@@ -49,8 +51,8 @@ share/applications/massxpert.desktop
 %%DATADIR%%/pol-chem-defs/nucac/oxidation.svg
 %%DATADIR%%/pol-chem-defs/nucac/phospho.svg
 %%DATADIR%%/pol-chem-defs/nucac/ps-dadenine.svg
-%%DATADIR%%/pol-chem-defs/nucac/ps-dguanine.svg
 %%DATADIR%%/pol-chem-defs/nucac/ps-dcytosine.svg
+%%DATADIR%%/pol-chem-defs/nucac/ps-dguanine.svg
 %%DATADIR%%/pol-chem-defs/nucac/ps-dthymine.svg
 %%DATADIR%%/pol-chem-defs/nucac/ps-radenine.svg
 %%DATADIR%%/pol-chem-defs/nucac/ps-rcytosine.svg
@@ -76,7 +78,9 @@ share/applications/massxpert.desktop
 %%DATADIR%%/pol-chem-defs/protein-1-letter/disulfidebond-cross-link.svg
 %%DATADIR%%/pol-chem-defs/protein-1-letter/glutamate.svg
 %%DATADIR%%/pol-chem-defs/protein-1-letter/glutamine.svg
+%%DATADIR%%/pol-chem-defs/protein-1-letter/glutamylation.svg
 %%DATADIR%%/pol-chem-defs/protein-1-letter/glycine.svg
+%%DATADIR%%/pol-chem-defs/protein-1-letter/glycylation.svg
 %%DATADIR%%/pol-chem-defs/protein-1-letter/histidine.svg
 %%DATADIR%%/pol-chem-defs/protein-1-letter/hydroxylation.svg
 %%DATADIR%%/pol-chem-defs/protein-1-letter/isoleucine.svg
@@ -119,12 +123,12 @@ share/applications/massxpert.desktop
 %%DATADIR%%/pol-chem-defs/protein-3-letters/leucine.svg
 %%DATADIR%%/pol-chem-defs/protein-3-letters/lysine.svg
 %%DATADIR%%/pol-chem-defs/protein-3-letters/methionine.svg
-%%DATADIR%%/pol-chem-defs/protein-3-letters/phospho.svg
 %%DATADIR%%/pol-chem-defs/protein-3-letters/modification_dictionary
 %%DATADIR%%/pol-chem-defs/protein-3-letters/monomer_dictionary
 %%DATADIR%%/pol-chem-defs/protein-3-letters/oxidation.svg
 %%DATADIR%%/pol-chem-defs/protein-3-letters/pdb-code-conversion.dic
 %%DATADIR%%/pol-chem-defs/protein-3-letters/phenylalanine.svg
+%%DATADIR%%/pol-chem-defs/protein-3-letters/phospho.svg
 %%DATADIR%%/pol-chem-defs/protein-3-letters/proline.svg
 %%DATADIR%%/pol-chem-defs/protein-3-letters/protein-3-letters.xml
 %%DATADIR%%/pol-chem-defs/protein-3-letters/protonloss.svg
@@ -188,6 +192,7 @@ share/applications/massxpert.desktop
 %%DATADIR%%/pol-chem-defs/saccharide/xylulose-text.svg
 %%DATADIR%%/pol-chem-defs/saccharide/xylulose.svg
 %%DATADIR%%/pol-seqs/17-mer-ps-po-dna-chimera.mxp
+%%DATADIR%%/pol-seqs/beta-2-tubulin.mxp
 %%DATADIR%%/pol-seqs/centrin-2-human.mxp
 %%DATADIR%%/pol-seqs/cerulean-histag.mxp
 %%DATADIR%%/pol-seqs/chicken-telokin.mxp
@@ -195,17 +200,11 @@ share/applications/massxpert.desktop
 %%DATADIR%%/pol-seqs/cyan-fluorescent-protein-h148d-histag.mxp
 %%DATADIR%%/pol-seqs/cyan-fluorescent-protein.mxp
 %%DATADIR%%/pol-seqs/horse-myoglobin.mxp
+%%DATADIR%%/pol-seqs/insulin-a-ox.mxp
+%%DATADIR%%/pol-seqs/insulin-b-ox.mxp
 %%DATADIR%%/pol-seqs/kunitz-inhibitor-human.mxp
 %%DATADIR%%/pol-seqs/leu-enkephalin.mxp
 %%DATADIR%%/pol-seqs/protein-1-letter.mxp
 %%DATADIR%%/pol-seqs/protein-3-letters.mxp
 %%DATADIR%%/pol-seqs/tev-protease-his-tag.mxp
 %%DATADIR%%/pol-seqs/yellow-fluorescent-protein.mxp
-%%DATADIR%%/pol-seqs/insulin-a-ox.mxp
-%%DATADIR%%/pol-seqs/insulin-b-ox.mxp
-%%DATADIR%%/dictionaries/codon-to-protein-1.dic
-%%DATADIR%%/dictionaries/codon-to-protein-3.dic
-%%DATADIR%%/dictionaries/pdb-protein-to-mxp.dic
-%%DATADIR%%/dictionaries/protein-1-to-3.dic
-%%DATADIR%%/dictionaries/protein-3-to-1.dic
-%%DATADIR%%/chem_pad.conf