diff -ur seqanBAK/Makefile seqan/Makefile --- seqanBAK/Makefile 2015-03-21 12:53:27.000000000 +0100 +++ seqan/Makefile 2016-01-14 19:11:20.895712874 +0100 @@ -3,32 +3,28 @@ PORTNAME= seqan PORTVERSION= 1.3.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= biology MASTER_SITES= http://ftp.seqan.de/releases/ MAINTAINER= h2+fbsdports@fsfe.org COMMENT= C++ Sequence Analysis Library -LICENSE= BSD3CLAUSE GPLv3 -LICENSE_COMB= multi - +LICENSE= BSD3CLAUSE LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE -LICENSE_FILE_GPLv3=${WRKSRC}/apps/LICENSE -USES= cmake:outsource python:build zip -CMAKE_SOURCE_PATH=${WRKSRC}/cmake -MAKE_JOB_SAFE= yes - -SUB_FILES= pkg-message -PKG_MESSAGE= ${WRKDIR}/pkg-message - -USE_GCC= 4.8 - -# unsafe workaround because FreeBSD lacks logl and expl -# see "BUGS" in `man 3 math` -post-patch: - @${REINPLACE_CMD} -e 's|expl|exp|g' ${WRKSRC}/apps/snp_store/snp_store.h - @${REINPLACE_CMD} -e 's|logl|log|g' ${WRKSRC}/apps/snp_store/snp_store.h +USES= zip +NO_BUILD= yes + +CONFLICTS= seqan[2-9]* + +do-install: + ${MKDIR} ${STAGEDIR}/${PREFIX}/include/${PORTNAME} + cd ${WRKSRC} && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include + cd ${WRKSRC} && ${INSTALL_DATA} ./${PORTNAME}.h ${STAGEDIR}/${PREFIX}/include + +post-install: + ${MKDIR} ${STAGEDIR}${DOCSDIR} + cd ${WRKSRC}/docs && ${COPYTREE_SHARE} ./ ${STAGEDIR}${DOCSDIR} .include Only in seqanBAK: files diff -ur seqanBAK/pkg-descr seqan/pkg-descr --- seqanBAK/pkg-descr 2014-01-22 16:44:51.000000000 +0100 +++ seqan/pkg-descr 2016-01-14 18:59:24.560762970 +0100 @@ -1,6 +1,10 @@ SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the -focus on biological data. The library is licensed under the -3-clause BSD license except the applications which are GPL. +focus on biological data. + +This port includes only the library, the apps have been +moved to biology/seqan-apps. This is the last release of +the version 1 API, it is highly recommended to upgrade to +biology/seqan2. WWW: http://www.seqan.de/ diff -ur seqanBAK/pkg-plist seqan/pkg-plist --- seqanBAK/pkg-plist 2014-10-20 09:10:48.000000000 +0200 +++ seqan/pkg-plist 2016-01-14 18:54:12.946784896 +0100 @@ -1,21 +1,5 @@ -bin/dfi -bin/insegt -bin/mason -bin/micro_razers -bin/pair_align -bin/param_chooser -bin/rabema -bin/razers -bin/razers2 -bin/rep_sep -bin/sak -bin/seqan_tcoffee -bin/seqcons -bin/snp_store -bin/splazers -bin/stellar -bin/tree_recon include/seqan.h +include/seqan/LICENSE include/seqan/align.h include/seqan/align/align_algorithms.h include/seqan/align/align_base.h @@ -521,1591 +505,1479 @@ include/seqan/system/system_sema.h include/seqan/system/system_thread.h include/seqan/version.h -%%DATADIR%%/docs/ADAPTION.char+array.html -%%DATADIR%%/docs/ADAPTION.std_3a_3a_F_I_L_E+_2a.html -%%DATADIR%%/docs/ADAPTION.std_3a_3abasic__string.html -%%DATADIR%%/docs/ADAPTION.std_3a_3aiostream.html -%%DATADIR%%/docs/ADAPTION.std_3a_3alist.html -%%DATADIR%%/docs/ADAPTION.std_3a_3avector.html 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