commit: 19eaadb66c9b5c5ace815fa0d6016b82ce2f7872 Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com> AuthorDate: Tue Feb 3 09:04:35 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Tue Feb 3 09:04:35 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=19eaadb6
Updated emboss.eclass and removed in-source-building. Amended all build system patches to build out-of-source. --- eclass/emboss.eclass | 20 ++++---- ...bassy-cbstools-1.0.0.650_fix-build-system.patch | 7 +++ .../embassy-emnu-1.05.650_fix-build-system.patch | 7 +++ .../embassy-esim4-1.0.0.650_fix-build-system.patch | 8 +++- ...mbassy-iprscan-4.3.1.650_fix-build-system.patch | 7 +++ .../embassy-mse-3.0.0.650_fix-build-system.patch | 20 +++++++- ...bassy-phylipnew-3.69.650_fix-build-system.patch | 9 +++- .../embassy-topo-2.0.650_fix-build-system.patch | 7 +++ ...embassy-vienna-1.7.2.650_fix-build-system.patch | 2 +- .../files/emboss-6.6.0_fix-build-system.patch | 54 +++++++++++++++++++--- 10 files changed, 121 insertions(+), 20 deletions(-) diff --git a/eclass/emboss.eclass b/eclass/emboss.eclass index e06e430..3ba65bb 100644 --- a/eclass/emboss.eclass +++ b/eclass/emboss.eclass @@ -1,20 +1,22 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/eclass/emboss.eclass,v 1.3 2012/09/27 16:35:41 axs Exp $ +# $Header: $ # @ECLASS: emboss.eclass # @MAINTAINER: # [email protected] # [email protected] +# [email protected] # @AUTHOR: # Original author: Author Olivier Fisette <[email protected]> # Next gen author: Justin Lecher <[email protected]> +# Next gen author: Ted Tanberry <[email protected]> # @BLURB: Use this to easy install EMBOSS and EMBASSY programs (EMBOSS add-ons). # @DESCRIPTION: -# The inheriting ebuild must set EAPI=4 and provide EBO_DESCRIPTION before the inherit line. +# The inheriting ebuild must set at least EAPI=4 and provide EBO_DESCRIPTION before the inherit line. # KEYWORDS should be set. Additionally "(R|P)DEPEND"encies and other standard # ebuild variables can be extended (FOO+=" bar"). -# Default installation of following DOCS="AUTHORS ChangeLog NEWS README" +# Default installation of following DOCS=() # # Example: # @@ -46,7 +48,6 @@ esac if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then AUTOTOOLS_AUTORECONF=1 - AUTOTOOLS_IN_SOURCE_BUILD=1 fi inherit autotools-utils eutils flag-o-matic @@ -85,14 +86,15 @@ if [[ ${PN} == embassy-* ]]; then fi DOCS=() -#DOCS="AUTHORS ChangeLog NEWS README" # @FUNCTION: emboss_src_prepare # @DESCRIPTION: -# Does following things +# Does the following things # -# 1. Patches with "${FILESDIR}"/${PF}.patch, if present -# 2. Runs eautoreconf, unless EBO_EAUTORECONF is set to no +# 1. Patches with "${FILESDIR}"/${P}_fix-build-system.patch, if present, +# and eventually runs eautoreconf in autotools-utils +# 2. Patches with "${WORKDIR}"/${P}-upstream-r1.patch, if ${EBO_PATCH} is set +# 3. Patches with "${FILESDIR}"/${PF}.patch, if present # emboss_src_prepare() { @@ -101,7 +103,7 @@ emboss_src_prepare() { epatch "${FILESDIR}"/${P}_fix-build-system.patch fi - [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch + [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream-r1.patch [[ -f ${FILESDIR}/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch autotools-utils_src_prepare diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch index 811e416..63c67a1 100644 --- a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch @@ -88,3 +88,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif +--- CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am ++++ CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch index a2e80ad..e73eb7b 100644 --- a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch +++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch @@ -118,3 +118,10 @@ - -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB) + -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB) endif +--- EMNU-1.05.650/emboss_acd/Makefile.am ++++ EMNU-1.05.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch index 1e70061..8279071 100644 --- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch @@ -88,4 +88,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif - +--- ESIM4-1.0.0.650/emboss_acd/Makefile.am ++++ ESIM4-1.0.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch index a3a7cb8..955005d 100644 --- a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch +++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch @@ -88,3 +88,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif +--- IPRSCAN-4.3.1.650/emboss_acd/Makefile.am ++++ IPRSCAN-4.3.1.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch index f9dc2b9..8b2f057 100644 --- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch @@ -102,7 +102,7 @@ -AM_CPPFLAGS = -I../h -I${embprefix}/include \ - -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ - $(NLINCLUDES) -+AM_CPPFLAGS = -I../h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) ++AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) endif if ISSHARED @@ -113,3 +113,21 @@ - -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) endif +--- MSE-3.0.0.650/ckit/Makefile.am ++++ MSE-3.0.0.650/ckit/Makefile.am +@@ -2,7 +2,7 @@ + + lib_LTLIBRARIES = libckit.la + +-AM_CPPFLAGS = -I../h ++AM_CPPFLAGS = -I$(top_srcdir)/h + + CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ + seqspec.c ttyinterface.c nextseqentry.c \ +--- MSE-3.0.0.650/emboss_acd/Makefile.am ++++ MSE-3.0.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch index c4b2ffd..e0efb74 100644 --- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch @@ -78,7 +78,7 @@ - -I${embprefix}/include/eplplot \ - $(NLINCLUDES) \ - -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I../include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) ++AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) endif if ISSHARED @@ -89,3 +89,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif +--- PHYLIPNEW-3.69.650/emboss_acd/Makefile.am ++++ PHYLIPNEW-3.69.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch index 03da2af..7ddda05 100644 --- a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch +++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch @@ -88,3 +88,10 @@ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lajax $(NLADD) $(XLIB) endif +--- TOPO-2.0.650/emboss_acd/Makefile.am ++++ TOPO-2.0.650/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch index 7107188..c9ece69 100644 --- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch @@ -77,7 +77,7 @@ -AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \ - $(NLINCLUDES) \ - -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I../H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) ++AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) endif if ISSHARED diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch index 39e3cec..c831c3b 100644 --- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch +++ b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch @@ -1,12 +1,13 @@ --- EMBOSS-6.6.0/ajax/acd/Makefile.am +++ EMBOSS-6.6.0/ajax/acd/Makefile.am -@@ -3,16 +3,19 @@ +@@ -3,16 +3,20 @@ lib_LTLIBRARIES = libacd.la libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) +libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb ++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics -libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre @@ -24,7 +25,7 @@ libacd_la_LDFLAGS = -version-info 6:5:0 --- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am +++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am -@@ -3,14 +3,15 @@ +@@ -3,14 +3,16 @@ lib_LTLIBRARIES = libajaxdb.la libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) @@ -32,6 +33,7 @@ libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl -libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre ++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core if !ESYSTEMLIBS +libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat @@ -94,7 +96,7 @@ +libensembl_la_LIBADD = ../core/libajax.la -libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libensembl_la_CPPFLAGS = ++libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core if !ESYSTEMLIBS +libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat @@ -114,7 +116,7 @@ +libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS) -libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libajaxg_la_CPPFLAGS = ++libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core if !ESYSTEMLIBS +libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat @@ -246,8 +248,11 @@ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL --- EMBOSS-6.6.0/emboss/Makefile.am +++ EMBOSS-6.6.0/emboss/Makefile.am -@@ -30,13 +30,15 @@ +@@ -28,15 +28,18 @@ + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb ++AM_CPPFLAGS += -I$(top_srcdir)/ajax/core AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics -AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre @@ -264,7 +269,7 @@ AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) AM_CPPFLAGS += $(JAVA_CPPFLAGS) -@@ -49,9 +51,11 @@ +@@ -49,9 +52,11 @@ if !ESYSTEMLIBS LDADD += ../ajax/zlib/libezlib.la LDADD += ../ajax/expat/libeexpat.la @@ -277,6 +282,41 @@ LDADD += $(XLIB) #if PURIFY +--- EMBOSS-6.6.0/jemboss/lib/Makefile.am ++++ EMBOSS-6.6.0/jemboss/lib/Makefile.am +@@ -12,7 +12,7 @@ + jalviewApplet.jar \ + jemboss.jar + +-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java ++jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java + if JAVA_BUILD + $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; + endif +--- EMBOSS-6.6.0/m4/idxdbs.m4 ++++ EMBOSS-6.6.0/m4/idxdbs.m4 +@@ -1,17 +1,8 @@ + AC_DEFUN([CHECK_IDXDBS], + [ +-AC_MSG_CHECKING(for EMBOSS pre-indexed databases) ++AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) + +- +-if test -f ./emboss/index/edam.xac; then +-AC_MSG_RESULT(yes) +-else +-AC_MSG_RESULT(no) +-echo "" +-echo "Pre-indexed edam, taxon + drcat databases not found." +-echo "Please download them from within this directory using:" +-echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." +-echo "and then repeat the configure step." +-exit 1 +-fi ++AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], ++ [], ++ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) + ]) --- EMBOSS-6.6.0/Makefile.am +++ EMBOSS-6.6.0/Makefile.am @@ -12,8 +12,11 @@ @@ -315,7 +355,7 @@ -libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot -libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre -+libnucleus_la_CPPFLAGS = ++libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core if !ESYSTEMLIBS +libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot +libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
