Date: Mon, 29 Jan 2001 16:34:29 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/24717: Port update/fix: biology/emboss (MAINTAINER) Message-ID: <E14NFO1-0006v8-00@fling.sanbi.ac.za>
next in thread | raw e-mail | index | archive | help
>Number: 24717
>Category: ports
>Synopsis: Port update/fix: biology/emboss (MAINTAINER)
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Mon Jan 29 06:40:01 PST 2001
>Closed-Date:
>Last-Modified:
>Originator: Johann Visagie
>Release: FreeBSD 5.0-CURRENT i386
>Organization:
Electric Genetics
>Environment:
>Description:
- Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1
- Update the EMBASSY package EMNU from 1.0.2 to 1.0.3
- Merged the four pkg-plist* files into one
- EMBOSS now looks for its databases in sensible default locations - this is
a bigger deal than it may sound! :-)
- Fixed a broken patch - EMBOSS now correctly looks for its configuration
file in ${PREFIX}/etc
- Added some sensible defaults to the sample configuration file which is
installed to ${PREFIX}/etc
- Files added:
- files/patch-configure
- files/patch-emboss-acd-emboss.default
- Files deleted:
- pkg-plist.EMNU
- pkg-plist.MSE
- pkg-plist.PHYLIP
- pkg-plist.TOPO
- Only tested on -CURRENT; I know there are still issues with ncurses on
3-STABLE
>How-To-Repeat:
>Fix:
diff -ruN emboss.bak/Makefile emboss/Makefile
--- emboss.bak/Makefile Mon Jan 29 16:27:10 2001
+++ emboss/Makefile Fri Jan 26 11:17:12 2001
@@ -6,10 +6,11 @@
#
PORTNAME= emboss
-PORTVERSION= 1.9.0
+PORTVERSION= 1.9.1
CATEGORIES= biology
MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
ftp://ftp.no.embnet.org/pub/EMBOSS/ \
+ ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
DIST_SUBDIR= ${PORTNAME}
@@ -24,7 +25,6 @@
USE_LIBTOOL= yes
USE_XLIB= yes
USE_MOTIF= yes
-PLIST= ${WRKDIR}/pkg-plist
PKGMESSAGE= ${WRKDIR}/pkg-message
.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
@@ -33,29 +33,30 @@
CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include/gd" \
LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib"
-
SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \
- MKDIR="${MKDIR}" \
- RM="${RM}"
+ MKDIR="${MKDIR}" RM="${RM}"
WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY
-EMNU_VERSION= 1.0.2
+EMNU_VERSION= 1.0.3
MSE_VERSION= 0.0.4
TOPO_VERSION= 0.1
PHYLIP_VERSION= 3.573c
+DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
+
.for app in EMNU MSE PHYLIP TOPO
SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}"
.if defined(WITH_${app})
APPLIST+= ${app}
-PLISTS+= ${PKGDIR}/pkg-plist.${app}
${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION}
${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX}
DISTFILES+= ${${app}_DISTFILE}
+PLIST_${app}= ""
+.else
+PLIST_${app}= "@comment "
.endif
+PLIST_SUB+= PLIST_${app}=${PLIST_${app}}
.endfor
-PLISTS+= ${PKGDIR}/pkg-plist
-DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
pre-fetch:
@ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME}
@@ -74,7 +75,7 @@
post-patch:
.for DIR in ${DOC_DIRS}
@ ${PERL} -pi.orig -e \
- "s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \
+ 's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \
${WRKSRC}/${DIR}/Makefile.in
.endfor
@@ -96,9 +97,6 @@
${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
${MAKE_ARGS})
.endfor
-
-pre-install:
- @ ${CAT} ${PLISTS} > ${PLIST}
post-install:
.for app in ${APPLIST}
diff -ruN emboss.bak/distinfo emboss/distinfo
--- emboss.bak/distinfo Mon Jan 29 16:27:10 2001
+++ emboss/distinfo Fri Jan 26 10:25:48 2001
@@ -1,5 +1,5 @@
-MD5 (emboss/EMBOSS-1.9.0.tar.gz) = f2b0ea093986df4f67428b2614583a7c
-MD5 (emboss/EMNU-1.0.2.tar.gz) = 86a8ad78d25de4b56e251a266a64f46b
-MD5 (emboss/MSE-0.0.4.tar.gz) = 28652ee772f31ced0e62415d8770311f
-MD5 (emboss/PHYLIP-3.573c.tar.gz) = a868fbf7bbee8d97b566be6794f51eb3
-MD5 (emboss/TOPO-0.1.tar.gz) = 83c76fddd2cb64d90eed4e7bb4ac0d29
+MD5 (emboss/EMBOSS-1.9.1.tar.gz) = 569ff1f9f2df08928b2dfb8ae1a331b9
+MD5 (emboss/EMNU-1.0.3.tar.gz) = 829dedc516e72144563d3a1a77793678
+MD5 (emboss/MSE-0.0.4.tar.gz) = 83b989776fbd59e346a2f90e7dc7f266
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = bb1d9da41c6bfdb47828a7a9e0e40b2f
+MD5 (emboss/TOPO-0.1.tar.gz) = 039b26ed333a3ba6bed20d1caf707834
diff -ruN emboss.bak/files/patch-aa emboss/files/patch-aa
--- emboss.bak/files/patch-aa Mon Jan 29 16:27:10 2001
+++ emboss/files/patch-aa Thu Jan 25 16:08:08 2001
@@ -17,7 +17,7 @@
+ if (!prefixRootFile)
+ {
+ ajFmtPrintS (&namRootStr, "%s/etc/%s.default",
-+ namInstallRoot, prefixCap, prefix);
++ namInstallRoot, prefix);
+ prefixRootFile = fopen (ajStrStr(namRootStr), "r");
+ }
+
diff -ruN emboss.bak/files/patch-configure emboss/files/patch-configure
--- emboss.bak/files/patch-configure Thu Jan 1 02:00:00 1970
+++ emboss/files/patch-configure Thu Jan 25 19:08:09 2001
@@ -0,0 +1,11 @@
+--- configure.orig Mon Jan 22 23:28:17 2001
++++ configure Thu Jan 25 19:07:33 2001
+@@ -1473,7 +1473,7 @@
+
+
+
+-AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
++AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\""
+
+ #AC_PROG_CXX
+ for ac_prog in mawk gawk nawk awk
diff -ruN emboss.bak/files/patch-emboss-acd-emboss.default emboss/files/patch-emboss-acd-emboss.default
--- emboss.bak/files/patch-emboss-acd-emboss.default Thu Jan 1 02:00:00 1970
+++ emboss/files/patch-emboss-acd-emboss.default Mon Jan 29 16:24:53 2001
@@ -0,0 +1,32 @@
+--- emboss/acd/emboss.default.orig Mon Jan 22 23:26:54 2001
++++ emboss/acd/emboss.default Mon Jan 29 16:23:15 2001
+@@ -1,9 +1,26 @@
+-SET emboss_tempdata /nfs/WWW/data/EMBOSS/test
++#####################################################
++### Configuration options for FreeBSD EMBOSS port ###
++#####################################################
+
+-# Logfile - set this to a file that any user can append to
+-# and EMBOSS applications will automatically write log information
++# This is the compiled-in default. Change only if
++# you know what you're doing!
++#
++#SET emboss_data /usr/local/share/EMBOSS/data
+
++# This is where your local databases reside
++# (this will differ from site to site):
++#
++SET emboss_tempdata /var/db/bio
++
++# Logfile - set this to a file that any user can append to and EMBOSS
++# applications will automatically write log information
++#
+ #SET emboss_logfile /packages/emboss/emboss/log
++
++
++###########################################
++### Configuration options for databases ###
++###########################################
+
+ # swissprot (Puffer fish entries)
+ # =========
diff -ruN emboss.bak/pkg-plist emboss/pkg-plist
--- emboss.bak/pkg-plist Mon Jan 29 16:27:10 2001
+++ emboss/pkg-plist Fri Jan 26 10:37:26 2001
@@ -1,3 +1,61 @@
+%%PLIST_EMNU%%bin/emnu
+%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
+%%PLIST_MSE%%bin/mse
+%%PLIST_MSE%%lib/libckit.a
+%%PLIST_MSE%%lib/libckit.la
+%%PLIST_MSE%%lib/libckit.so
+%%PLIST_MSE%%lib/libckit.so.1
+%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
+%%PLIST_PHYLIP%%bin/eclique
+%%PLIST_PHYLIP%%bin/econsense
+%%PLIST_PHYLIP%%bin/econtml
+%%PLIST_PHYLIP%%bin/econtrast
+%%PLIST_PHYLIP%%bin/ednacomp
+%%PLIST_PHYLIP%%bin/ednadist
+%%PLIST_PHYLIP%%bin/ednainvar
+%%PLIST_PHYLIP%%bin/ednaml
+%%PLIST_PHYLIP%%bin/ednamlk
+%%PLIST_PHYLIP%%bin/ednapars
+%%PLIST_PHYLIP%%bin/ednapenny
+%%PLIST_PHYLIP%%bin/edollop
+%%PLIST_PHYLIP%%bin/edolpenny
+%%PLIST_PHYLIP%%bin/efactor
+%%PLIST_PHYLIP%%bin/efitch
+%%PLIST_PHYLIP%%bin/egendist
+%%PLIST_PHYLIP%%bin/ekitsch
+%%PLIST_PHYLIP%%bin/emix
+%%PLIST_PHYLIP%%bin/eneighbor
+%%PLIST_PHYLIP%%bin/epenny
+%%PLIST_PHYLIP%%bin/eprotdist
+%%PLIST_PHYLIP%%bin/eprotpars
+%%PLIST_PHYLIP%%bin/erestml
+%%PLIST_PHYLIP%%bin/eseqboot
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd
+%%PLIST_TOPO%%bin/topo
+%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
bin/abiview
bin/acdc
bin/antigenic
diff -ruN emboss.bak/pkg-plist.EMNU emboss/pkg-plist.EMNU
--- emboss.bak/pkg-plist.EMNU Mon Jan 29 16:27:10 2001
+++ emboss/pkg-plist.EMNU Thu Jan 1 02:00:00 1970
@@ -1,2 +0,0 @@
-bin/emnu
-share/EMBOSS/acd/emnu.acd
diff -ruN emboss.bak/pkg-plist.MSE emboss/pkg-plist.MSE
--- emboss.bak/pkg-plist.MSE Mon Jan 29 16:27:10 2001
+++ emboss/pkg-plist.MSE Thu Jan 1 02:00:00 1970
@@ -1,6 +0,0 @@
-bin/mse
-lib/libckit.a
-lib/libckit.la
-lib/libckit.so
-lib/libckit.so.1
-share/EMBOSS/acd/mse.acd
diff -ruN emboss.bak/pkg-plist.PHYLIP emboss/pkg-plist.PHYLIP
--- emboss.bak/pkg-plist.PHYLIP Mon Jan 29 16:27:10 2001
+++ emboss/pkg-plist.PHYLIP Thu Jan 1 02:00:00 1970
@@ -1,48 +0,0 @@
-bin/eclique
-bin/econsense
-bin/econtml
-bin/econtrast
-bin/ednacomp
-bin/ednadist
-bin/ednainvar
-bin/ednaml
-bin/ednamlk
-bin/ednapars
-bin/ednapenny
-bin/edollop
-bin/edolpenny
-bin/efactor
-bin/efitch
-bin/egendist
-bin/ekitsch
-bin/emix
-bin/eneighbor
-bin/epenny
-bin/eprotdist
-bin/eprotpars
-bin/erestml
-bin/eseqboot
-share/EMBOSS/acd/eclique.acd
-share/EMBOSS/acd/econsense.acd
-share/EMBOSS/acd/econtml.acd
-share/EMBOSS/acd/econtrast.acd
-share/EMBOSS/acd/ednacomp.acd
-share/EMBOSS/acd/ednadist.acd
-share/EMBOSS/acd/ednainvar.acd
-share/EMBOSS/acd/ednaml.acd
-share/EMBOSS/acd/ednamlk.acd
-share/EMBOSS/acd/ednapars.acd
-share/EMBOSS/acd/ednapenny.acd
-share/EMBOSS/acd/edollop.acd
-share/EMBOSS/acd/edolpenny.acd
-share/EMBOSS/acd/efactor.acd
-share/EMBOSS/acd/efitch.acd
-share/EMBOSS/acd/egendist.acd
-share/EMBOSS/acd/ekitsch.acd
-share/EMBOSS/acd/emix.acd
-share/EMBOSS/acd/eneighbor.acd
-share/EMBOSS/acd/epenny.acd
-share/EMBOSS/acd/eprotdist.acd
-share/EMBOSS/acd/eprotpars.acd
-share/EMBOSS/acd/erestml.acd
-share/EMBOSS/acd/eseqboot.acd
diff -ruN emboss.bak/pkg-plist.TOPO emboss/pkg-plist.TOPO
--- emboss.bak/pkg-plist.TOPO Mon Jan 29 16:27:10 2001
+++ emboss/pkg-plist.TOPO Thu Jan 1 02:00:00 1970
@@ -1,2 +0,0 @@
-bin/topo
-share/EMBOSS/acd/topo.acd
>Release-Note:
>Audit-Trail:
>Unformatted:
To Unsubscribe: send mail to majordomo@FreeBSD.org
with "unsubscribe freebsd-ports" in the body of the message
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?E14NFO1-0006v8-00>