Attachment 62213 Details for Bug 93050 – t_coffee.diff

[patch] t_coffee.diff

t_coffee.diff (text/plain; charset=us-ascii), 4.14 KB, created by Fernan Aguero on 2006-02-09 14:11:52 UTC

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Creator: Fernan Aguero

Created: 2006-02-09 14:11:52 UTC

Size: 4.14 KB

patch

obsolete

>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/distinfo t_coffee/distinfo
>--- /usr/ports/biology/t_coffee/distinfo	Mon Jan  2 14:10:12 2006
>+++ t_coffee/distinfo	Thu Feb  9 09:55:04 2006
>@@ -1,3 +1,3 @@
>-MD5 (T-COFFEE_distribution_Version_3.18.tar.gz) = e671383b9e6b90ded56c615acd2f51c4
>-SHA256 (T-COFFEE_distribution_Version_3.18.tar.gz) = e6769bbfecbcd4a00493564ab8e08aefd0d89c7452e5b30114d0d8aec4d36aee
>-SIZE (T-COFFEE_distribution_Version_3.18.tar.gz) = 1540558
>+MD5 (T-COFFEE_distribution_Version_3.27.tar.gz) = 747d907f4b87e07d7b1e670a2b263e23
>+SHA256 (T-COFFEE_distribution_Version_3.27.tar.gz) = ffb7920919b24a6144492bec71580cda8a3ef4698acf762f76ebadfcae9aa01a
>+SIZE (T-COFFEE_distribution_Version_3.27.tar.gz) = 1295287
>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

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Attachments on bug 93050: 62212 | 62213