From: Justin Lecher Date: Thu, 7 May 2015 10:17:55 +0000 (+0000) Subject: Correct Licenses, bug #548810; make build with newer plplot, bug #548806; add missing... X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=63dbb6e2d3909d2b28e1e0ad6cdb9c59cb5e3e10;p=gentoo.git Correct Licenses, bug #548810; make build with newer plplot, bug #548806; add missing dep, bug #544516 Package-Manager: portage-2.2.18/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 679413e0ad15..090de49e4e0c 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-biology/emboss # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.73 2015/03/28 18:03:23 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.74 2015/05/07 10:17:54 jlec Exp $ + + 07 May 2015; Justin Lecher emboss-6.6.0.ebuild, + files/emboss-6.6.0_fix-build-system.patch: + Correct Licenses, bug #548810; make build with newer plplot, bug #548806; add + missing dep, bug #544516 28 Mar 2015; Justin Lecher -emboss-6.1.0-r1.ebuild, -emboss-6.3.1_p4.ebuild: diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index 7b459a97d399..35bc13d1cbd7 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -8,7 +8,7 @@ AUX README.gentoo 1522 SHA256 3cbb20ef948613f07698ab17c2b432e3aeab0ade6499a965c5 AUX emboss-5.0.0-as-needed.patch 1751 SHA256 e57a60d911e32f1aea16c079e2fd0910a5f7ed43752ea71094d3f3b7575617d3 SHA512 a2d978ce86fc3a63dc691059c4da598ccfb958d51097bc6070204ad6062f257b3ac496b852bb2772041bda087d0732cf03c4a4868462781700705da4faff8b59 WHIRLPOOL 101b8c89052dbc24211363e4fbe45e1407a30f8046013269d360b983a677ad5e62be796baf1d1097ae30dc392dc8db789d784dad51384e9c9b8df526b475a1d6 AUX emboss-6.3.1_p4-r1_plcol.patch 3638 SHA256 dfaf85cf5c53a42047a75b1544ca44b450f2d4219c458c243bab53166f917b64 SHA512 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/var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.6.0.ebuild,v 1.2 2015/05/07 10:17:54 jlec Exp $ EAPI=5 @@ -12,12 +12,14 @@ SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE+=" minimal" +LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" RDEPEND+=" !sys-devel/cons" PDEPEND+=" !minimal? ( sci-biology/aaindex sci-biology/cutg + sci-biology/primer3 sci-biology/prints sci-biology/prosite sci-biology/rebase 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 c831c3ba7e28..266bddd95a37 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 @@ -1,5 +1,60 @@ ---- EMBOSS-6.6.0/ajax/acd/Makefile.am -+++ EMBOSS-6.6.0/ajax/acd/Makefile.am + Makefile.am | 9 +++--- + ajax/Makefile.am | 4 +-- + ajax/acd/Makefile.am | 8 +++-- + ajax/ajaxdb/Makefile.am | 6 ++-- + ajax/core/Makefile.am | 6 ++-- + ajax/core/ajreg.h | 7 ++-- + ajax/ensembl/Makefile.am | 6 ++-- + ajax/graphics/Makefile.am | 8 +++-- + configure.ac | 82 ++++++++++++++++++++++++++--------------------- + emboss/Makefile.am | 13 +++++--- + jemboss/lib/Makefile.am | 2 +- + m4/idxdbs.m4 | 17 +++------- + nucleus/Makefile.am | 8 +++-- + 13 files changed, 100 insertions(+), 76 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 177dec5..18dd99a 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -12,8 +12,11 @@ LICENSE \ + ONEWS \ + PROBLEMS + +-SUBDIRS = \ +-plplot \ ++SUBDIRS = ++if !ESYSTEMLIBS ++SUBDIRS += plplot ++endif ++SUBDIRS += \ + ajax \ + nucleus \ + emboss \ +@@ -33,5 +36,3 @@ dist-hook: + tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) + tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) + +-install-exec-hook: +- $(bindir)/embossupdate +diff --git a/ajax/Makefile.am b/ajax/Makefile.am +index f27472c..de34e17 100644 +--- a/ajax/Makefile.am ++++ b/ajax/Makefile.am +@@ -1,7 +1,7 @@ + ## Process this file with automake to produce Makefile.in + +-SUBDIRS = pcre ++SUBDIRS = + if !ESYSTEMLIBS +-SUBDIRS += expat zlib ++SUBDIRS += pcre expat zlib + endif + SUBDIRS += core graphics ensembl ajaxdb acd +diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am +index 9f0f700..3295a1d 100644 +--- a/ajax/acd/Makefile.am ++++ b/ajax/acd/Makefile.am @@ -3,16 +3,20 @@ lib_LTLIBRARIES = libacd.la @@ -23,8 +78,10 @@ libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) libacd_la_LDFLAGS = -version-info 6:5:0 ---- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am -+++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am +diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am +index c2b0c00..9de14fe 100644 +--- a/ajax/ajaxdb/Makefile.am ++++ b/ajax/ajaxdb/Makefile.am @@ -3,14 +3,16 @@ lib_LTLIBRARIES = libajaxdb.la @@ -44,8 +101,32 @@ libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS) ---- EMBOSS-6.6.0/ajax/core/ajreg.h -+++ EMBOSS-6.6.0/ajax/core/ajreg.h +diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am +index 2906837..3189c34 100644 +--- a/ajax/core/Makefile.am ++++ b/ajax/core/Makefile.am +@@ -3,13 +3,15 @@ + lib_LTLIBRARIES = libajax.la + + libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) + +-libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libajax_la_CPPFLAGS = + if !ESYSTEMLIBS ++libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif + libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot ++endif + libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) + libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS) + libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS) +diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h +index 1623c82..5d928cf 100644 +--- a/ajax/core/ajreg.h ++++ b/ajax/core/ajreg.h @@ -39,9 +39,8 @@ #include "ajdefine.h" #include "ajstr.h" @@ -58,7 +139,7 @@ AJ_BEGIN_DECLS -@@ -84,7 +83,7 @@ +@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS typedef struct AjSRegexp { @@ -67,28 +148,10 @@ pcre_extra *extra; int *ovector; const char* orig; ---- EMBOSS-6.6.0/ajax/core/Makefile.am -+++ EMBOSS-6.6.0/ajax/core/Makefile.am -@@ -3,13 +3,15 @@ - lib_LTLIBRARIES = libajax.la - - libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) - --libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libajax_la_CPPFLAGS = - if !ESYSTEMLIBS -+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) - libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS) - libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS) ---- EMBOSS-6.6.0/ajax/ensembl/Makefile.am -+++ EMBOSS-6.6.0/ajax/ensembl/Makefile.am +diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am +index 0d1250b..5484c02 100644 +--- a/ajax/ensembl/Makefile.am ++++ b/ajax/ensembl/Makefile.am @@ -3,13 +3,15 @@ lib_LTLIBRARIES = libensembl.la @@ -107,8 +170,10 @@ libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) libensembl_la_LDFLAGS = -version-info 6:5:0 ---- EMBOSS-6.6.0/ajax/graphics/Makefile.am -+++ EMBOSS-6.6.0/ajax/graphics/Makefile.am +diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am +index a4f202b..1114c2c 100644 +--- a/ajax/graphics/Makefile.am ++++ b/ajax/graphics/Makefile.am @@ -3,12 +3,16 @@ lib_LTLIBRARIES = libajaxg.la @@ -128,21 +193,11 @@ libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) libajaxg_la_LDFLAGS = -version-info 6:5:0 ---- EMBOSS-6.6.0/ajax/Makefile.am -+++ EMBOSS-6.6.0/ajax/Makefile.am -@@ -1,7 +1,7 @@ - ## Process this file with automake to produce Makefile.in - --SUBDIRS = pcre -+SUBDIRS = - if !ESYSTEMLIBS --SUBDIRS += expat zlib -+SUBDIRS += pcre expat zlib - endif - SUBDIRS += core graphics ensembl ajaxdb acd ---- EMBOSS-6.6.0/configure.ac -+++ EMBOSS-6.6.0/configure.ac -@@ -629,32 +629,6 @@ +diff --git a/configure.ac b/configure.ac +index a7bd9c6..9ba3121 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -629,32 +629,6 @@ AS_CASE([${host_os}], @@ -175,7 +230,7 @@ dnl Define where the EMBOSS package is located AC_SUBST([AJAX_FIXED_ROOT]) AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" -@@ -743,17 +717,7 @@ +@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL @@ -193,24 +248,25 @@ -@@ -849,7 +813,51 @@ +@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs], AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) -- +AS_IF([test "x${enable_systemlibs}" = "xyes"], +[ +dnl using system libraries + PKG_CHECK_MODULES([PCRE], [libpcre]) + PKG_CHECK_MODULES([EXPAT], [expat]) + PKG_CHECK_MODULES([ZLIB], [zlib]) -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) +], +[ +dnl using bundled libraries + dnl PCRE library definitions - see the MAJOR and MINOR values + dnl to see which version's configure.ac these lines come from -+ + + dnl Provide the current PCRE version information. Do not use numbers + dnl with leading zeros for the minor version, as they end up in a C + dnl macro, and may be treated as octal constants. Stick to single @@ -246,30 +302,33 @@ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- EMBOSS-6.6.0/emboss/Makefile.am -+++ EMBOSS-6.6.0/emboss/Makefile.am -@@ -28,15 +28,18 @@ +diff --git a/emboss/Makefile.am b/emboss/Makefile.am +index 89ada78..f987d40 100644 +--- a/emboss/Makefile.am ++++ b/emboss/Makefile.am +@@ -28,15 +28,18 @@ endif 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 - if !ESYSTEMLIBS -+AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre ++if !ESYSTEMLIBS + AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre +-if !ESYSTEMLIBS AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib -+AM_CPPFLAGS += -I$(top_srcdir)/plplot +-endif +-AM_CPPFLAGS += -I$(top_srcdir)/nucleus + AM_CPPFLAGS += -I$(top_srcdir)/plplot +else +AM_CFLAGS += $(PLPLOT_CFLAGS) - endif - AM_CPPFLAGS += -I$(top_srcdir)/nucleus --AM_CPPFLAGS += -I$(top_srcdir)/plplot ++endif ++AM_CPPFLAGS += -I$(top_srcdir)/nucleus AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) AM_CPPFLAGS += $(JAVA_CPPFLAGS) -@@ -49,9 +52,11 @@ +@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la if !ESYSTEMLIBS LDADD += ../ajax/zlib/libezlib.la LDADD += ../ajax/expat/libeexpat.la @@ -282,9 +341,11 @@ LDADD += $(XLIB) #if PURIFY ---- EMBOSS-6.6.0/jemboss/lib/Makefile.am -+++ EMBOSS-6.6.0/jemboss/lib/Makefile.am -@@ -12,7 +12,7 @@ +diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am +index 5f7e21e..8b45ce2 100644 +--- a/jemboss/lib/Makefile.am ++++ b/jemboss/lib/Makefile.am +@@ -12,7 +12,7 @@ mail.jar \ jalviewApplet.jar \ jemboss.jar @@ -293,8 +354,10 @@ 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 +diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4 +index 0ca7ea9..9b54f2a 100644 +--- a/m4/idxdbs.m4 ++++ b/m4/idxdbs.m4 @@ -1,17 +1,8 @@ AC_DEFUN([CHECK_IDXDBS], [ @@ -317,30 +380,10 @@ + [], + [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 @@ - ONEWS \ - PROBLEMS - --SUBDIRS = \ --plplot \ -+SUBDIRS = -+if !ESYSTEMLIBS -+SUBDIRS += plplot -+endif -+SUBDIRS += \ - ajax \ - nucleus \ - emboss \ -@@ -33,5 +36,3 @@ - tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) - tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) - --install-exec-hook: -- $(bindir)/embossupdate ---- EMBOSS-6.6.0/nucleus/Makefile.am -+++ EMBOSS-6.6.0/nucleus/Makefile.am +diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am +index 37b8543..5819c89 100644 +--- a/nucleus/Makefile.am ++++ b/nucleus/Makefile.am @@ -3,6 +3,7 @@ lib_LTLIBRARIES = libnucleus.la @@ -349,7 +392,7 @@ if ISSHARED if ISAIXIA64 -@@ -10,11 +11,14 @@ +@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm endif endif