FreeBSD Bugzilla – Attachment 165571 Details for
Bug 204127
[MAINTAINER] biology/seqan split apps out into biology/seqan-apps
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[patch]
remove apps from port
seqan1.patch (text/plain), 152.09 KB, created by
Hannes Hauswedell
on 2016-01-14 18:19:33 UTC
(
hide
)
Description:
remove apps from port
Filename:
MIME Type:
Creator:
Hannes Hauswedell
Created:
2016-01-14 18:19:33 UTC
Size:
152.09 KB
patch
obsolete
>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 <bsd.port.mk> >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 >-%%DATADIR%%/docs/CLASS_Align.html >-%%DATADIR%%/docs/CLASS_Align_Cols.html >-%%DATADIR%%/docs/CLASS_Align_Config.html >-%%DATADIR%%/docs/CLASS_Align_Quality_Store_Element.html >-%%DATADIR%%/docs/CLASS_Aligned_Read_Layout.html >-%%DATADIR%%/docs/CLASS_Aligned_Read_Store_Element.html >-%%DATADIR%%/docs/CLASS_Allocator.html >-%%DATADIR%%/docs/CLASS_Async_Request.html >-%%DATADIR%%/docs/CLASS_Auto_Seq_Format.html >-%%DATADIR%%/docs/CLASS_Blast_Hit.html >-%%DATADIR%%/docs/CLASS_Blast_Hsp.html >-%%DATADIR%%/docs/CLASS_Blast_Report.html >-%%DATADIR%%/docs/CLASS_Bundle2.html >-%%DATADIR%%/docs/CLASS_Bundle3.html >-%%DATADIR%%/docs/CLASS_Bundle5.html >-%%DATADIR%%/docs/CLASS_Command_Line_Option.html >-%%DATADIR%%/docs/CLASS_Command_Line_Parser.html >-%%DATADIR%%/docs/CLASS_Concatenator_Many_To_One.html >-%%DATADIR%%/docs/CLASS_Contig_File.html 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