ports/181883: biology/fasta3: Update to version 36.3.6c
KATO Tsuguru
tkato432 at yahoo.com
Fri Sep 6 18:10:03 UTC 2013
>Number: 181883
>Category: ports
>Synopsis: biology/fasta3: Update to version 36.3.6c
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Fri Sep 06 18:10:03 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator: KATO Tsuguru
>Release: FreeBSD 8.4-RELEASE-p3 i386
>Organization:
>Environment:
>Description:
- Update to version 36.3.6c
>How-To-Repeat:
>Fix:
diff -urN /usr/ports/biology/fasta3/Makefile biology/fasta3/Makefile
--- /usr/ports/biology/fasta3/Makefile 2013-09-05 01:47:14.000000000 +0900
+++ biology/fasta3/Makefile 2013-09-07 00:00:00.000000000 +0900
@@ -2,7 +2,7 @@
# $FreeBSD: head/biology/fasta3/Makefile 323293 2013-07-19 14:08:02Z wen $
PORTNAME= fasta3
-PORTVERSION= 36.3.6
+PORTVERSION= 36.3.6c
CATEGORIES= biology
MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta36/
DISTNAME= fasta-${PORTVERSION}
@@ -10,18 +10,31 @@
MAINTAINER= ports at FreeBSD.org
COMMENT= Collection of programs for searching DNA and protein databases
+OPTIONS_DEFINE= DOCS EXAMPLES
+
NO_CDROM= May not be sold or incorporated into a commercial product
+
WRKSRC= ${WRKDIR}/${DISTNAME}
BUILD_WRKSRC= ${WRKSRC}/src
INSTALL_WRKSRC= ${BUILD_WRKSRC}
-SUB_FILES= pkg-message
+
MAKEFILE= Makefile.freebsd
+MAKE_ENV= THR_LIBS="-pthread" XDIR="${PREFIX}/bin" \
+ FASTA_HOST="$$(${UNAME} -n)"
-XDIR= ${PREFIX}/bin
-FASTA_HOST!= /usr/bin/uname -n
+SUB_FILES= pkg-message
+
+PLIST_SUB= VER="${PORTVERSION:R:R}"
-MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \
- FASTA_HOST='"${FASTA_HOST}"'
+MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 \
+ fasta36.1 tfastx35.1 fasta36.1 fasty35.1 \
+ fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \
+ fasta36.1 fastf35.1 fasta36.1 fasts35.1 \
+ fasta36.1 tfasts35.1 fasta36.1 fastm35.1 \
+ fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \
+ fasta36.1 lalign35.1 fasta36.1 prss35.1 \
+ fasta36.1 prfx35.1
+MAN1= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
FASTA3_DOCS= README.versions \
fasta_func.doc readme.* fasta.defaults \
@@ -29,39 +42,36 @@
DATA= data/*.mat
EXAMPLES= seq/*.aa seq/*.lc seq/*.seq seq/*.lib
-MAN1= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
-MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \
- fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \
- fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \
- fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \
- fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1
-PLIST_SUB= VER=${PORTVERSION:R:R}
+.include <bsd.port.options.mk>
post-patch:
- @ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/
+ @${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}
+
post-install:
- ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin/
- ${INSTALL_DATA} ${WRKSRC}/conf/fastlibs ${PREFIX}/etc/fastlibs.sample
- @ ${MKDIR} ${DATADIR}
+ (cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${PREFIX}/bin)
+ (cd ${WRKSRC}/conf && ${INSTALL_DATA} fastlibs ${PREFIX}/etc/fastlibs.sample)
+ @${MKDIR} ${DATADIR}
.for data in ${DATA}
- ${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
-.endfor
- @ ${MKDIR} ${EXAMPLESDIR}
-.for ex in ${EXAMPLES}
- ${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
+ (cd ${WRKSRC} && ${INSTALL_DATA} ${data} ${DATADIR})
.endfor
.for manpage in ${MAN1}
- ${INSTALL_MAN} ${WRKSRC}/doc/${manpage} ${MAN1PREFIX}/man/man1/
+ (cd ${WRKSRC}/doc && ${INSTALL_MAN} ${manpage} ${MAN1PREFIX}/man/man1)
+.endfor
+.if ${PORT_OPTIONS:MDOCS}
+ @${MKDIR} ${DOCSDIR}
+.for i in COPYRIGHT FASTA_LIST README
+ (cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${DOCSDIR})
.endfor
-.if !defined(NOPORTDOCS)
- @ ${MKDIR} ${DOCSDIR}
- ${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
- ${INSTALL_DATA} ${WRKSRC}/COPYRIGHT ${DOCSDIR}
- ${INSTALL_DATA} ${WRKSRC}/FASTA_LIST ${DOCSDIR}
.for docfile in ${FASTA3_DOCS}
- @ ${INSTALL_DATA} ${WRKSRC}/doc/${docfile} ${DOCSDIR}
+ (cd ${WRKSRC}/doc && ${INSTALL_DATA} ${docfile} ${DOCSDIR})
+.endfor
+.endif
+.if ${PORT_OPTIONS:MEXAMPLES}
+ @${MKDIR} ${EXAMPLESDIR}
+.for ex in ${EXAMPLES}
+ (cd ${WRKSRC} && ${INSTALL_DATA} ${ex} ${EXAMPLESDIR})
.endfor
.endif
- @ ${CAT} ${PKGMESSAGE}
+ @${CAT} ${PKGMESSAGE}
.include <bsd.port.mk>
diff -urN /usr/ports/biology/fasta3/distinfo biology/fasta3/distinfo
--- /usr/ports/biology/fasta3/distinfo 2013-09-05 01:47:14.000000000 +0900
+++ biology/fasta3/distinfo 2013-09-07 00:00:00.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (fasta-36.3.6.tar.gz) = d6c526c307941fe8c98a16406cb01df6bb5712d3c2b7f4a90e126ceba682db6f
-SIZE (fasta-36.3.6.tar.gz) = 995298
+SHA256 (fasta-36.3.6c.tar.gz) = a6abe630a061ddf9d52064aedf5466896b410fccf7adc8802bce8363e7c9e8dd
+SIZE (fasta-36.3.6c.tar.gz) = 996137
diff -urN /usr/ports/biology/fasta3/pkg-plist biology/fasta3/pkg-plist
--- /usr/ports/biology/fasta3/pkg-plist 2013-09-05 01:47:14.000000000 +0900
+++ biology/fasta3/pkg-plist 2013-09-07 00:00:00.000000000 +0900
@@ -17,11 +17,17 @@
bin/tfastx%%VER%%
bin/tfasty%%VER%%
etc/fastlibs.sample
-%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
%%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
+%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/README.versions
+%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
+%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
+%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
+%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
+%%PORTDOCS%%%%DOCSDIR%%/fasta.options
%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
+%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
%%PORTDOCS%%%%DOCSDIR%%/readme.v30
%%PORTDOCS%%%%DOCSDIR%%/readme.v30t6
%%PORTDOCS%%%%DOCSDIR%%/readme.v30t7
@@ -33,57 +39,51 @@
%%PORTDOCS%%%%DOCSDIR%%/readme.v35
%%PORTDOCS%%%%DOCSDIR%%/readme.v36
%%PORTDOCS%%%%DOCSDIR%%/readme.w32
-%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
-%%PORTDOCS%%%%DOCSDIR%%/fasta.options
-%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
-%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
-%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
-%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
-%%EXAMPLESDIR%%/dyr_human.aa
-%%EXAMPLESDIR%%/egmsmg.aa
-%%EXAMPLESDIR%%/gstt1_drome.aa
-%%EXAMPLESDIR%%/gtm1_human.aa
-%%EXAMPLESDIR%%/gtt1_drome.aa
-%%EXAMPLESDIR%%/h10_human.aa
-%%EXAMPLESDIR%%/hahu.aa
-%%EXAMPLESDIR%%/lcbo.aa
-%%EXAMPLESDIR%%/m1r.aa
-%%EXAMPLESDIR%%/m2.aa
-%%EXAMPLESDIR%%/mchu.aa
-%%EXAMPLESDIR%%/mgstm1.aa
-%%EXAMPLESDIR%%/ms1.aa
-%%EXAMPLESDIR%%/musplfm.aa
-%%EXAMPLESDIR%%/mwkw.aa
-%%EXAMPLESDIR%%/mwrtc1.aa
-%%EXAMPLESDIR%%/myosin_bp.aa
-%%EXAMPLESDIR%%/n0.aa
-%%EXAMPLESDIR%%/n1.aa
-%%EXAMPLESDIR%%/n2.aa
-%%EXAMPLESDIR%%/n2s.aa
-%%EXAMPLESDIR%%/n2t.aa
-%%EXAMPLESDIR%%/ngt.aa
-%%EXAMPLESDIR%%/ngts.aa
-%%EXAMPLESDIR%%/oohu.aa
-%%EXAMPLESDIR%%/prio_atepa.aa
-%%EXAMPLESDIR%%/qrhuld.aa
-%%EXAMPLESDIR%%/titin_hum.aa
-%%EXAMPLESDIR%%/xurt8c.aa
-%%EXAMPLESDIR%%/xurtg.aa
-%%EXAMPLESDIR%%/mgstm1.lc
-%%EXAMPLESDIR%%/xurt8c.lc
-%%EXAMPLESDIR%%/bovgh.seq
-%%EXAMPLESDIR%%/bovprl.seq
-%%EXAMPLESDIR%%/gst.seq
-%%EXAMPLESDIR%%/hsgstm1b.seq
-%%EXAMPLESDIR%%/humgstd.seq
-%%EXAMPLESDIR%%/mgstm1.seq
-%%EXAMPLESDIR%%/mgstm1_genclone.seq
-%%EXAMPLESDIR%%/mgtt2_x.seq
-%%EXAMPLESDIR%%/titin_hum.seq
-%%EXAMPLESDIR%%/mu.lib
-%%EXAMPLESDIR%%/n2_fs.lib
-%%EXAMPLESDIR%%/n_fs.lib
-%%EXAMPLESDIR%%/prot_test.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovgh.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovprl.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dyr_human.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/egmsmg.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gst.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gstt1_drome.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtm1_human.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtt1_drome.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h10_human.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hahu.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hsgstm1b.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/humgstd.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lcbo.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m1r.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m2.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mchu.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.lc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1_genclone.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgtt2_x.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ms1.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mu.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/musplfm.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwkw.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwrtc1.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myosin_bp.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n0.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n1.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2_fs.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2s.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2t.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n_fs.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngt.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngts.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/oohu.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prio_atepa.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prot_test.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/qrhuld.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.lc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurtg.aa
%%DATADIR%%/blosum45.mat
%%DATADIR%%/blosum50.mat
%%DATADIR%%/blosum62.mat
@@ -97,6 +97,6 @@
%%DATADIR%%/pam250.mat
%%DATADIR%%/rna.mat
%%DATADIR%%/vtml160.mat
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
- at dirrm %%EXAMPLESDIR%%
@dirrm %%DATADIR%%
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
>Release-Note:
>Audit-Trail:
>Unformatted:
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