Date: Wed, 8 Feb 2006 16:02:04 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/93050: unbreak and update biology/t_coffee Message-ID: <200602081902.k18J24rw037559@omega.iib.unsam.edu.ar> Resent-Message-ID: <200602081910.k18JA7v0010077@freefall.freebsd.org>
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>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@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_${PORTVERSION} @@ -15,6 +15,7 @@ MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= A multiple DNA or protein sequence alignment package +USE_GCC= 3.3 BUILD_DEPENDS= clustalw:${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:
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