ports/93050: unbreak and update biology/t_coffee

[Fernan Aguero]

>Number:         93050
>Category:       ports
>Synopsis:       unbreak and update biology/t_coffee
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Wed Feb 08 19:10:06 GMT 2006
>Closed-Date:
>Last-Modified:
>Originator:     Fernan Aguero
>Release:        FreeBSD 6.0-RELEASE-p4 i386
>Organization:
IIB-UNSAM
>Environment:

System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan at omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386

	
>Description:
	
	
	
	i. build fails on gcc-3.4 (base gcc in FreeBSD-6.0) but not on
	gcc-3.3 (USE_GCC=3.3, FreeBSD-6.0) or on gcc-2.95 (base gcc in
	FreeBSD-4.11).  The problem is an internal compiler error, the
	software author has been notified and while we wait for a
	resolution, the proposed fix is to just USE_GCC=3.3 For this we
	have to also patch the t_coffee Makefile, as it is hardcoding
	cc.
	
	ii. I also take the opportunity to update the port to the latest
	version. The issue reported in (i) occurs in both the old (3.18)
	and the new (3.27) t_coffe, as well as in a development version
	provided by the author.

>How-To-Repeat:
	
	
>Fix:

	



--- t_coffee.diff begins here ---
diff -ruN /usr/ports/biology/t_coffee/Makefile t_coffee/Makefile
--- /usr/ports/biology/t_coffee/Makefile	Mon Jan  2 14:10:12 2006
+++ t_coffee/Makefile	Tue Feb  7 15:30:08 2006
@@ -7,7 +7,7 @@
 #
 
 PORTNAME=	t_coffee
-PORTVERSION=	3.18
+PORTVERSION=	3.27
 CATEGORIES=	biology
 MASTER_SITES=	http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
 DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}
@@ -15,6 +15,7 @@
 MAINTAINER=	fernan at iib.unsam.edu.ar
 COMMENT=	A multiple DNA or protein sequence alignment package
 
+USE_GCC=	3.3
 BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
@@ -25,25 +26,19 @@
 MAKEFILE=	makefile
 
 do-install:
-	@ ${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
 
 post-install:
 .if !defined(NOPORTDOCS)
 	@ ${MKDIR} ${DOCSDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
 	@ ${MKDIR} ${EXAMPLESDIR}
 	@ cd ${WRKSRC}/example && ${FIND} * \
 	  | ${CPIO} --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
 	@ ${MKDIR} ${DATADIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/license.txt ${DATADIR}
+	${INSTALL_DATA} ${WRKSRC}/license.txt ${DATADIR}
 	@ ${MKDIR} ${DATADIR}/html
-	@ ${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}/html
+	${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}/html
 .endif
 
-.include <bsd.port.pre.mk>
-
-.if ${OSVERSION} >= 600000
-BROKEN=		"Does not build on FreeBSD >= 6.x"
-.endif
-
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff -ruN /usr/ports/biology/t_coffee/files/patch-Makefile t_coffee/files/patch-Makefile
--- /usr/ports/biology/t_coffee/files/patch-Makefile	Wed Dec 31 21:00:00 1969
+++ t_coffee/files/patch-Makefile	Tue Feb  7 15:11:23 2006
@@ -0,0 +1,8 @@
+--- t_coffee_source/makefile.orig	Tue Feb  7 15:11:00 2006
++++ t_coffee_source/makefile	Tue Feb  7 15:10:36 2006
+@@ -1,4 +1,4 @@
+-CC=cc
++#CC=cc
+ t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o t_coffee.o 
+ 	$(CC)  -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o t_coffee.o  -lm
+ 	mv  t_coffee  ../bin
--- t_coffee.diff ends here ---

>Release-Note:
>Audit-Trail:
>Unformatted: