svn commit: r495214 - in head/science/massxpert: . files
Yuri Victorovich
yuri at FreeBSD.org
Sat Mar 9 23:23:35 UTC 2019
Author: yuri
Date: Sat Mar 9 23:23:33 2019
New Revision: 495214
URL: https://svnweb.freebsd.org/changeset/ports/495214
Log:
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
Deleted:
head/science/massxpert/files/patch-lib_cleaveSpec.cpp
head/science/massxpert/files/patch-lib_propListHolder.cpp
head/science/massxpert/files/patch-plugins-src_seqToolsPlugin_seqToolsPluginDlg.cpp
Modified:
head/science/massxpert/Makefile
head/science/massxpert/distinfo
head/science/massxpert/files/patch-CMakeLists.txt
head/science/massxpert/pkg-descr
head/science/massxpert/pkg-plist
Modified: head/science/massxpert/Makefile
==============================================================================
--- head/science/massxpert/Makefile Sat Mar 9 22:53:28 2019 (r495213)
+++ head/science/massxpert/Makefile Sat Mar 9 23:23:33 2019 (r495214)
@@ -2,19 +2,15 @@
# $FreeBSD$
PORTNAME= massxpert
-PORTVERSION= 3.4.0
-PORTREVISION= 12
+DISTVERSION= 3.6.1
CATEGORIES= science
-MASTER_SITES= http://download.tuxfamily.org/massxpert/source/
MAINTAINER= ports at FreeBSD.org
COMMENT= massXpert software for (bio)chemists
LICENSE= GPLv3
+LICENSE_FILE= ${WRKSRC}/COPYING
-DEPRECATED= Qt4 has been EOL since december 2015
-EXPIRATION_DATE= 2019-03-15
-
BUILD_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/pthread-stubs.pc:devel/libpthread-stubs
LIB_DEPENDS= libpcre.so:devel/pcre \
libpng.so:graphics/png \
@@ -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>
Modified: head/science/massxpert/distinfo
==============================================================================
--- head/science/massxpert/distinfo Sat Mar 9 22:53:28 2019 (r495213)
+++ head/science/massxpert/distinfo Sat Mar 9 23:23:33 2019 (r495214)
@@ -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
Modified: head/science/massxpert/files/patch-CMakeLists.txt
==============================================================================
--- head/science/massxpert/files/patch-CMakeLists.txt Sat Mar 9 22:53:28 2019 (r495213)
+++ head/science/massxpert/files/patch-CMakeLists.txt Sat Mar 9 23:23:33 2019 (r495214)
@@ -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)
-
-
Modified: head/science/massxpert/pkg-descr
==============================================================================
--- head/science/massxpert/pkg-descr Sat Mar 9 22:53:28 2019 (r495213)
+++ head/science/massxpert/pkg-descr Sat Mar 9 23:23:33 2019 (r495214)
@@ -17,4 +17,4 @@ to another (using a dictionary, like between the 1-let
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
Modified: head/science/massxpert/pkg-plist
==============================================================================
--- head/science/massxpert/pkg-plist Sat Mar 9 22:53:28 2019 (r495213)
+++ head/science/massxpert/pkg-plist Sat Mar 9 23:23:33 2019 (r495214)
@@ -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
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