[gentoo-commits] proj/sci:master commit in: sci-biology/embassy-mse/files/, sci-biology/embassy-vienna/files/, ...

[Justin Lecher]

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:
 # sci-biology@g.o
 # jlec@g.o
+# ted.tanberry@×××××.com
 # @AUTHOR:
 # Original author: Author Olivier Fisette <ofisette@×××××.com>
 # Next gen author: Justin Lecher <jlec@g.o>
+# Next gen author: Ted Tanberry <ted.tanberry@×××××.com>
 # @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