Attachment #48575 for bug #74331

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#

PORTNAME=	hmmer
PORTVERSION=	2.3.2
PORTREVISION=	1
CATEGORIES=	biology
MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${PORTVERSION}/
DISTNAME=	${PORTNAME}-${VERSIONSTRING}

MAINTAINER=	fernan@iib.unsam.edu.ar
COMMENT=	Profile hidden Markov models for biological sequence analysis

GNU_CONFIGURE=	yes
USE_PERL5=	yes
CONFIGURE_ARGS+=--enable-threads --enable-lfs

DOCFILES=	00README COPYRIGHT INSTALL LICENSE NOTES Userguide.pdf
EXAMPLES=	7LES_DROME amino.null globins50.msf nucleic.pri rrm.sto \
		Artemia.fa amino.pri globins630.fa pkinase.sto RU1A_HUMAN \
		fn3.sto nucleic.null rrm.hmm
MAN1=		hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 \
		hmmer.1 hmmfetch.1 hmmindex.1 hmmpfam.1 hmmsearch.1 

.if defined(WITH_PVM)
CONFIGURE_ENV+=		PVM_ROOT="${LOCALBASE}/lib/pvm" PVM_ARCH="FREEBSD"
CONFIGURE_ARGS+=	--with-pvm
BUILD_DEPENDS+=		pvm:${PORTSDIR}/net/pvm
.endif

post-install:
.if !defined(NOPORTDOCS)

	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
.endfor
.endif
	@ ${MKDIR} ${EXAMPLESDIR}
.for example in ${EXAMPLES}
	@ ${INSTALL_DATA} ${WRKSRC}/tutorial/${example} ${EXAMPLESDIR}
.endfor
.if !defined(BATCH)
	@ ${CAT} ${PKGMESSAGE}
.endif

Lines 1-2 Link Here

(-)hmmer/distinfo (-2 / +2 lines)
1	MD5 (hmmer-2.2g.tar.gz) = d7def2007a0aaf2eafb9a96a07986b8c	1	MD5 (hmmer-2.3.2.tar.gz) = 5f073340c0cf761288f961a73821228a
2	SIZE (hmmer-2.2g.tar.gz) = 931569	2	SIZE (hmmer-2.3.2.tar.gz) = 1024933




--- Makefile.in.orig	Mon Aug  6 01:55:36 2001
+++ Makefile.in	Wed Aug 22 14:52:30 2001
@@ -34,7 +34,7 @@
 # how to install the man pages; 
 # cp is generally fine, unless you preformat your pages.
 #
-INSTMAN   = cp
+INSTMAN   = $(BSD_INSTALL_MAN)
 MANSUFFIX = 1
 
 # your compiler and compiler flags
@@ -144,12 +144,12 @@
 #          installs man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
 install: 
 	for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\
-	   cp binaries/$$file $(BINDIR)/;\
+	   $(BSD_INSTALL_PROGRAM) binaries/$$file $(BINDIR)/;\
 	done
-	for file in hmmer $(PROGS) $(SQUIDPROGS); do\
+	for file in hmmer $(PROGS); do\
 	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
 	done
-	for file in $(SQUIDPROGS); do\
+	for file in afetch alistat seqstat sfetch shuffle sreformat; do\
 	   $(INSTMAN) squid/Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
 	done
 




--- configure.orig	Mon Aug  6 01:55:52 2001
+++ configure	Thu Jul 11 12:38:47 2002
@@ -1094,6 +1094,9 @@
 
         acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags"
         ;;
+        *freebsd5*)
+	acx_pthread_flags="-lc_r -kthread lthread -pthread"
+        ;;
 esac
 
 if test x"$acx_pthread_ok" = xno; then
@@ -1418,6 +1421,9 @@
         # we'll just look for -pthreads and -lpthread first:
 
         acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags"
+        ;;
+        *freebsd5*)
+	acx_pthread_flags="-lc_r -kthread lthread -pthread"
         ;;
 esac
 




bin/afetch
bin/alistat
bin/hmmalign
bin/hmmbuild
bin/hmmcalibrate

bin/hmmindex
bin/hmmpfam
bin/hmmsearch
%%PORTDOCS%%DOCSDIR%%/00README
%%PORTDOCS%%DOCSDIR%%/COPYRIGHT
%%PORTDOCS%%DOCSDIR%%/INSTALL
%%PORTDOCS%%DOCSDIR%%/LICENSE
%%PORTDOCS%%DOCSDIR%%/NOTES
%%PORTDOCS%%DOCSDIR%%/Userguide.pdf
%%EXAMPLESDIR%%/7LES_DROME
%%EXAMPLESDIR%%/amino.null
%%EXAMPLESDIR%%/globins50.msf
%%EXAMPLESDIR%%/nucleic.pri
%%EXAMPLESDIR%%/rrm.sto
%%EXAMPLESDIR%%/Artemia.fa
%%EXAMPLESDIR%%/amino.pri
%%EXAMPLESDIR%%/globins630.fa
%%EXAMPLESDIR%%/pkinase.sto
%%EXAMPLESDIR%%/RU1A_HUMAN
%%EXAMPLESDIR%%/fn3.sto
%%EXAMPLESDIR%%/nucleic.null
%%EXAMPLESDIR%%/rrm.hmm
%%PORTDOCS%%@dirrm %%DOCSDIR%%
@dirrm %%EXAMPLESDIR%%

Return to bug 74331

Lines 6-29 Link Here

(-)hmmer/Makefile (-11 / +20 lines)
6	#	6	#
7		7
8	PORTNAME= hmmer	8	PORTNAME= hmmer
9	PORTVERSION= 2.2.g	9	PORTVERSION= 2.3.2
10	PORTREVISION= 1
11	CATEGORIES= biology	10	CATEGORIES= biology
12	MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${VERSIONSTRING}/	11	MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${PORTVERSION}/
13	DISTNAME= ${PORTNAME}-${VERSIONSTRING}
14		12
15	MAINTAINER= ports@FreeBSD.org	13	MAINTAINER= fernan@iib.unsam.edu.ar
16	COMMENT= Profile hidden Markov models for biological sequence analysis	14	COMMENT= Profile hidden Markov models for biological sequence analysis
17		15
18	GNU_CONFIGURE= yes	16	GNU_CONFIGURE= yes
19	USE_PERL5= yes	17	USE_PERL5= yes
20	VERSIONSTRING= ${PORTVERSION:C\|\.([^.]*)$\|\1\|}	18	CONFIGURE_ARGS+=--enable-threads --enable-lfs
21		19
22	DOCFILES= 00README COPYRIGHT NOTES Userguide.pdf	20	DOCFILES= 00README COPYRIGHT INSTALL LICENSE NOTES Userguide.pdf
23	MAN1= afetch.1 alistat.1 hmmalign.1 hmmbuild.1 hmmcalibrate.1 \	21	EXAMPLES= 7LES_DROME amino.null globins50.msf nucleic.pri rrm.sto \
24	hmmconvert.1 hmmemit.1 hmmer.1 hmmfetch.1 hmmindex.1 \	22	Artemia.fa amino.pri globins630.fa pkinase.sto RU1A_HUMAN \
25	hmmpfam.1 hmmsearch.1 seqstat.1 sfetch.1 shuffle.1 \	23	fn3.sto nucleic.null rrm.hmm
26	sreformat.1	24	MAN1= hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 \
		25	hmmer.1 hmmfetch.1 hmmindex.1 hmmpfam.1 hmmsearch.1
		26
		27	.if defined(WITH_PVM)
		28	CONFIGURE_ENV+= PVM_ROOT="${LOCALBASE}/lib/pvm" PVM_ARCH="FREEBSD"
		29	CONFIGURE_ARGS+= --with-pvm
		30	BUILD_DEPENDS+= pvm:${PORTSDIR}/net/pvm
		31	.endif
27		32
28	post-install:	33	post-install:
29	.if !defined(NOPORTDOCS)	34	.if !defined(NOPORTDOCS)
Lines 32-37 Link Here
32	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}	37	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
33	.endfor	38	.endfor
34	.endif	39	.endif
		40	@ ${MKDIR} ${EXAMPLESDIR}
		41	.for example in ${EXAMPLES}
		42	@ ${INSTALL_DATA} ${WRKSRC}/tutorial/${example} ${EXAMPLESDIR}
		43	.endfor
35	.if !defined(BATCH)	44	.if !defined(BATCH)
36	@ ${CAT} ${PKGMESSAGE}	45	@ ${CAT} ${PKGMESSAGE}
37	.endif	46	.endif

Lines 1-27 Link Here

(-)hmmer/files/patch-Makefile.in (-27 lines)
1	--- Makefile.in.orig Mon Aug 6 01:55:36 2001
2	+++ Makefile.in Wed Aug 22 14:52:30 2001
3	@@ -34,7 +34,7 @@
4	# how to install the man pages;
5	# cp is generally fine, unless you preformat your pages.
6	#
7	-INSTMAN = cp
8	+INSTMAN = $(BSD_INSTALL_MAN)
9	MANSUFFIX = 1
10
11	# your compiler and compiler flags
12	@@ -144,12 +144,12 @@
13	# installs man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1)
14	install:
15	for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\
16	- cp binaries/$$file $(BINDIR)/;\
17	+ $(BSD_INSTALL_PROGRAM) binaries/$$file $(BINDIR)/;\
18	done
19	- for file in hmmer $(PROGS) $(SQUIDPROGS); do\
20	+ for file in hmmer $(PROGS); do\
21	$(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
22	done
23	- for file in $(SQUIDPROGS); do\
24	+ for file in afetch alistat seqstat sfetch shuffle sreformat; do\
25	$(INSTMAN) squid/Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
26	done
27

Lines 1-22 Link Here

(-)hmmer/files/patch-configure (-22 lines)
1	--- configure.orig Mon Aug 6 01:55:52 2001
2	+++ configure Thu Jul 11 12:38:47 2002
3	@@ -1094,6 +1094,9 @@
4
5	acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags"
6	;;
7	+ freebsd5)
8	+ acx_pthread_flags="-lc_r -kthread lthread -pthread"
9	+ ;;
10	esac
11
12	if test x"$acx_pthread_ok" = xno; then
13	@@ -1418,6 +1421,9 @@
14	# we'll just look for -pthreads and -lpthread first:
15
16	acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags"
17	+ ;;
18	+ freebsd5)
19	+ acx_pthread_flags="-lc_r -kthread lthread -pthread"
20	;;
21	esac
22

Lines 1-5 Link Here

(-)hmmer/pkg-plist (-11 / +20 lines)
1	bin/afetch
2	bin/alistat
3	bin/hmmalign	1	bin/hmmalign
4	bin/hmmbuild	2	bin/hmmbuild
5	bin/hmmcalibrate	3	bin/hmmcalibrate
Lines 9-21 Link Here
9	bin/hmmindex	7	bin/hmmindex
10	bin/hmmpfam	8	bin/hmmpfam
11	bin/hmmsearch	9	bin/hmmsearch
12	bin/seqstat	10	%%PORTDOCS%%DOCSDIR%%/00README
13	bin/sfetch	11	%%PORTDOCS%%DOCSDIR%%/COPYRIGHT
14	bin/shuffle	12	%%PORTDOCS%%DOCSDIR%%/INSTALL
15	bin/sindex	13	%%PORTDOCS%%DOCSDIR%%/LICENSE
16	bin/sreformat	14	%%PORTDOCS%%DOCSDIR%%/NOTES
17	%%PORTDOCS%%%%DOCSDIR%%/00README	15	%%PORTDOCS%%DOCSDIR%%/Userguide.pdf
18	%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT	16	%%EXAMPLESDIR%%/7LES_DROME
19	%%PORTDOCS%%%%DOCSDIR%%/NOTES	17	%%EXAMPLESDIR%%/amino.null
20	%%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf	18	%%EXAMPLESDIR%%/globins50.msf
		19	%%EXAMPLESDIR%%/nucleic.pri
		20	%%EXAMPLESDIR%%/rrm.sto
		21	%%EXAMPLESDIR%%/Artemia.fa
		22	%%EXAMPLESDIR%%/amino.pri
		23	%%EXAMPLESDIR%%/globins630.fa
		24	%%EXAMPLESDIR%%/pkinase.sto
		25	%%EXAMPLESDIR%%/RU1A_HUMAN
		26	%%EXAMPLESDIR%%/fn3.sto
		27	%%EXAMPLESDIR%%/nucleic.null
		28	%%EXAMPLESDIR%%/rrm.hmm
21	%%PORTDOCS%%@dirrm %%DOCSDIR%%	29	%%PORTDOCS%%@dirrm %%DOCSDIR%%
		30	@dirrm %%EXAMPLESDIR%%