Date: Sat, 9 Mar 2019 23:23:33 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r495214 - in head/science/massxpert: . files Message-ID: <201903092323.x29NNX2U066195@repo.freebsd.org>
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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@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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