[gentoo-commits] repo/gentoo:master commit in: sci-biology/embassy-vienna/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/embassy-vienna/files/

[David Seifert]

commit:     711ecbd8f3b6e2adaeee1cea2134b7d817f727a0
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 13 12:05:01 2021 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 13 12:05:01 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=711ecbd8

sci-biology/embassy-vienna: Fix building against clang/LLD

Closes: https://bugs.gentoo.org/731852
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 ...embassy-vienna-1.7.2.650_fix-build-system.patch | 42 ++++++++++++++--------
 1 file changed, 27 insertions(+), 15 deletions(-)

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 5ce365ed549..8bd816b0e67 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
@@ -1,12 +1,6 @@
- configure.ac    | 49 +++++++------------------------------------------
- src/Makefile.am |  7 +++----
- 2 files changed, 10 insertions(+), 46 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index f5a4ecf..bbe0743 100644
 --- a/configure.ac
 +++ b/configure.ac
-@@ -649,33 +649,6 @@ AS_CASE([${host_os}],
+@@ -649,33 +649,6 @@
  
  
  
@@ -40,7 +34,7 @@ index f5a4ecf..bbe0743 100644
  dnl FIXME: This does no longer seem required with Autoconf 2.67?
  dnl Intel MacOSX 10.6 puts X11 in a non-standard place
  dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -751,21 +724,6 @@ AX_LIB_POSTGRESQL
+@@ -751,21 +724,6 @@
  
  
  
@@ -62,7 +56,7 @@ index f5a4ecf..bbe0743 100644
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -888,6 +846,13 @@ AC_ARG_ENABLE([systemlibs],
+@@ -888,6 +846,13 @@
  AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
  
  
@@ -76,11 +70,18 @@ index f5a4ecf..bbe0743 100644
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 1f5b756..e178914 100644
 --- a/src/Makefile.am
 +++ b/src/Makefile.am
-@@ -32,9 +32,7 @@ AM_CPPFLAGS = -I../H -I../../../nucleus -I../../../ajax/pcre \
+@@ -10,7 +10,7 @@
+ -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leplplot -leexpat \
+ -lezlib -lepcre
+ else
+-CYGWIN_LDVIENNA = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl \
++CYGWIN_LDVIENNA = -lnucleus -lacd -lajaxdb -lensembl \
+                 -lajaxg -lajax -leplplot -leexpat -lezlib -lepcre
+ endif
+ endif
+@@ -32,9 +32,7 @@
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -91,7 +92,16 @@ index 1f5b756..e178914 100644
  endif
  
  if ISSHARED
-@@ -87,6 +85,7 @@ LINKFLAGS = $(VERS_INF)
+@@ -49,7 +47,7 @@
+ -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre \
+  $(NLAIXLIBS) -leplplot
+ else
+-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
+ -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre $(NLAIXLIBS) -leplplot
+ endif
+ endif
+@@ -87,6 +85,7 @@
  endif
  
  liboviennarna_la_LDFLAGS = $(LINKFLAGS)
@@ -99,10 +109,12 @@ index 1f5b756..e178914 100644
  
  ovrnaalifold_SOURCES = vrnaalifold.c
  ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c
-@@ -119,5 +118,5 @@ LDADD = liboviennarna.la \
+@@ -118,6 +117,6 @@
+ 	../../../plplot/libeplplot.la \
  	$(XLIB)
  else
- LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
+-LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
 -	-lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++LDADD = liboviennarna.la -lnucleus -lacd -lajaxdb \
 +	-lensembl -lajaxg -lajax $(NLADD) $(XLIB)
  endif