diff options
Diffstat (limited to 'science/massxpert')
| -rw-r--r-- | science/massxpert/Makefile | 20 | ||||
| -rw-r--r-- | science/massxpert/distinfo | 5 | ||||
| -rw-r--r-- | science/massxpert/files/patch-CMakeLists.txt | 50 | ||||
| -rw-r--r-- | science/massxpert/files/patch-lib_cleaveSpec.cpp | 11 | ||||
| -rw-r--r-- | science/massxpert/files/patch-lib_propListHolder.cpp | 19 | ||||
| -rw-r--r-- | science/massxpert/files/patch-plugins-src_seqToolsPlugin_seqToolsPluginDlg.cpp | 11 | ||||
| -rw-r--r-- | science/massxpert/pkg-descr | 2 | ||||
| -rw-r--r-- | science/massxpert/pkg-plist | 27 |
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 |