On Mon, Nov 04 2019, Edd Barrett <e...@theunixzoo.co.uk> wrote:
> On Mon, Nov 04, 2019 at 05:03:14PM +0000, Stuart Henderson wrote:
>> Besides texlive, biology/emboss also conflicts with aguri, pscan, yank.
>> With nearly 200 fairly generic files in bin/, it's probably best to move
>> the whole lot into a different directory, and add a MESSAGE suggesting
>> that users add it to their PATH if wanted.
>
> Sounds sensible to me.
Regarding texlive-2019: works for me, ok jca@
Here's a diff to move emboss programs to libexec/emboss and remove the
conflict marker. ok?
Index: biology/emboss/Makefile
===================================================================
RCS file: /cvs/ports/biology/emboss/Makefile,v
retrieving revision 1.14
diff -u -p -r1.14 Makefile
--- biology/emboss/Makefile 12 Jul 2019 20:43:43 -0000 1.14
+++ biology/emboss/Makefile 11 Nov 2019 15:24:49 -0000
@@ -5,7 +5,7 @@ PORTROACH= ignore:1
COMMENT= European Molecular Biology Open Software Suite
DISTNAME= EMBOSS-6.0.1
-REVISION= 4
+REVISION= 5
SHARED_LIBS += eplplot 0.0 # .5.7
SHARED_LIBS += ajax 1.0 # .6.0
SHARED_LIBS += ajaxg 1.0 # .6.0
@@ -24,7 +24,8 @@ WANTLIB += X11 c m xcb
CONFIGURE_STYLE=gnu
CONFIGURE_ARGS+= --without-java \
- --without-pngdriver
+ --without-pngdriver \
+ --bindir="${PREFIX}/libexec/emboss"
CONFIGURE_ENV= CPPFLAGS="-I${LOCALBASE}/include" \
LDFLAGS="-L${LOCALBASE}/lib"
Index: biology/emboss/pkg/MESSAGE
===================================================================
RCS file: biology/emboss/pkg/MESSAGE
diff -N biology/emboss/pkg/MESSAGE
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ biology/emboss/pkg/MESSAGE 11 Nov 2019 15:24:49 -0000
@@ -0,0 +1,2 @@
+The EMBOSS programs can be found in ${PREFIX}/libexec/emboss/.
+You might want to add that directory to your PATH.
Index: biology/emboss/pkg/PLIST
===================================================================
RCS file: /cvs/ports/biology/emboss/pkg/PLIST,v
retrieving revision 1.5
diff -u -p -r1.5 PLIST
--- biology/emboss/pkg/PLIST 16 Mar 2015 18:07:37 -0000 1.5
+++ biology/emboss/pkg/PLIST 11 Nov 2019 15:24:49 -0000
@@ -1,196 +1,4 @@
@comment $OpenBSD: PLIST,v 1.5 2015/03/16 18:07:37 naddy Exp $
-@conflict aguri-*
-@conflict pscan-*
-@bin bin/aaindexextract
-@bin bin/abiview
-@bin bin/acdc
-@bin bin/acdpretty
-@bin bin/acdtable
-@bin bin/acdtrace
-@bin bin/acdvalid
-@bin bin/aligncopy
-@bin bin/aligncopypair
-@bin bin/antigenic
-@bin bin/backtranambig
-@bin bin/backtranseq
-@bin bin/banana
-@bin bin/biosed
-@bin bin/btwisted
-@bin bin/cai
-@bin bin/chaos
-@bin bin/charge
-@bin bin/checktrans
-@bin bin/chips
-@bin bin/cirdna
-@bin bin/codcmp
-@bin bin/codcopy
-@bin bin/coderet
-@bin bin/compseq
-@bin bin/cons
-@bin bin/consambig
-@bin bin/cpgplot
-@bin bin/cpgreport
-@bin bin/cusp
-@bin bin/cutgextract
-@bin bin/cutseq
-@bin bin/dan
-@bin bin/dbiblast
-@bin bin/dbifasta
-@bin bin/dbiflat
-@bin bin/dbigcg
-@bin bin/dbxfasta
-@bin bin/dbxflat
-@bin bin/dbxgcg
-@bin bin/degapseq
-@bin bin/density
-@bin bin/descseq
-@bin bin/diffseq
-@bin bin/digest
-@bin bin/distmat
-@bin bin/dotmatcher
-@bin bin/dotpath
-@bin bin/dottup
-@bin bin/dreg
-@bin bin/edialign
-@bin bin/einverted
-@bin bin/embossdata
-@bin bin/embossversion
-@bin bin/emma
-@bin bin/emowse
-@bin bin/entret
-@bin bin/epestfind
-@bin bin/eprimer3
-@bin bin/equicktandem
-@bin bin/est2genome
-@bin bin/etandem
-@bin bin/extractalign
-@bin bin/extractfeat
-@bin bin/extractseq
-@bin bin/featcopy
-@bin bin/featreport
-@bin bin/findkm
-@bin bin/freak
-@bin bin/fuzznuc
-@bin bin/fuzzpro
-@bin bin/fuzztran
-@bin bin/garnier
-@bin bin/geecee
-@bin bin/getorf
-@bin bin/helixturnhelix
-@bin bin/hmoment
-@bin bin/iep
-@bin bin/infoalign
-@bin bin/infobase
-@bin bin/inforesidue
-@bin bin/infoseq
-@bin bin/isochore
-@bin bin/jaspextract
-@bin bin/jaspscan
-@bin bin/jembossctl
-@bin bin/lindna
-@bin bin/listor
-@bin bin/makenucseq
-@bin bin/makeprotseq
-@bin bin/marscan
-@bin bin/maskambignuc
-@bin bin/maskambigprot
-@bin bin/maskfeat
-@bin bin/maskseq
-@bin bin/matcher
-@bin bin/megamerger
-@bin bin/merger
-@bin bin/msbar
-@bin bin/mwcontam
-@bin bin/mwfilter
-@bin bin/needle
-@bin bin/newcpgreport
-@bin bin/newcpgseek
-@bin bin/newseq
-@bin bin/nohtml
-@bin bin/noreturn
-@bin bin/nospace
-@bin bin/notab
-@bin bin/notseq
-@bin bin/nthseq
-@bin bin/octanol
-@bin bin/oddcomp
-@bin bin/palindrome
-@bin bin/pasteseq
-@bin bin/patmatdb
-@bin bin/patmatmotifs
-@bin bin/pepcoil
-@bin bin/pepinfo
-@bin bin/pepnet
-@bin bin/pepstats
-@bin bin/pepwheel
-@bin bin/pepwindow
-@bin bin/pepwindowall
-@bin bin/plotcon
-@bin bin/plotorf
-@bin bin/polydot
-@bin bin/preg
-@bin bin/prettyplot
-@bin bin/prettyseq
-@bin bin/primersearch
-@bin bin/printsextract
-@bin bin/profit
-@bin bin/prophecy
-@bin bin/prophet
-@bin bin/prosextract
-@bin bin/pscan
-@bin bin/psiphi
-@bin bin/rebaseextract
-@bin bin/recoder
-@bin bin/redata
-@bin bin/remap
-@bin bin/restover
-@bin bin/restrict
-@bin bin/revseq
-bin/runJemboss.csh
-@bin bin/seealso
-@bin bin/seqmatchall
-@bin bin/seqret
-@bin bin/seqretsplit
-@bin bin/showalign
-@bin bin/showdb
-@bin bin/showfeat
-@bin bin/showorf
-@bin bin/showseq
-@bin bin/shuffleseq
-@bin bin/sigcleave
-@bin bin/silent
-@bin bin/sirna
-@bin bin/sixpack
-@bin bin/sizeseq
-@bin bin/skipredundant
-@bin bin/skipseq
-@bin bin/splitter
-@bin bin/stretcher
-@bin bin/stssearch
-@bin bin/supermatcher
-@bin bin/syco
-@bin bin/tcode
-@bin bin/textsearch
-@bin bin/tfextract
-@bin bin/tfm
-@bin bin/tfscan
-@bin bin/tmap
-@bin bin/tranalign
-@bin bin/transeq
-@bin bin/trimest
-@bin bin/trimseq
-@bin bin/trimspace
-@bin bin/twofeat
-@bin bin/union
-@bin bin/vectorstrip
-@bin bin/water
-@bin bin/whichdb
-@bin bin/wobble
-@bin bin/wordcount
-@bin bin/wordfinder
-@bin bin/wordmatch
-@bin bin/wossname
-@bin bin/yank
include/ajacd.h
include/ajalign.h
include/ajarch.h
@@ -293,18 +101,209 @@ include/eplplot/plstrm.h
include/eplplot/plunicode-type1.h
include/eplplot/plxwd.h
include/eplplot/ps.h
-lib/libajax.a
+@static-lib lib/libajax.a
lib/libajax.la
@lib lib/libajax.so.${LIBajax_VERSION}
-lib/libajaxg.a
+@static-lib lib/libajaxg.a
lib/libajaxg.la
@lib lib/libajaxg.so.${LIBajaxg_VERSION}
-lib/libeplplot.a
+@static-lib lib/libeplplot.a
lib/libeplplot.la
@lib lib/libeplplot.so.${LIBeplplot_VERSION}
-lib/libnucleus.a
+@static-lib lib/libnucleus.a
lib/libnucleus.la
@lib lib/libnucleus.so.${LIBnucleus_VERSION}
+libexec/emboss/
+@bin libexec/emboss/aaindexextract
+@bin libexec/emboss/abiview
+@bin libexec/emboss/acdc
+@bin libexec/emboss/acdpretty
+@bin libexec/emboss/acdtable
+@bin libexec/emboss/acdtrace
+@bin libexec/emboss/acdvalid
+@bin libexec/emboss/aligncopy
+@bin libexec/emboss/aligncopypair
+@bin libexec/emboss/antigenic
+@bin libexec/emboss/backtranambig
+@bin libexec/emboss/backtranseq
+@bin libexec/emboss/banana
+@bin libexec/emboss/biosed
+@bin libexec/emboss/btwisted
+@bin libexec/emboss/cai
+@bin libexec/emboss/chaos
+@bin libexec/emboss/charge
+@bin libexec/emboss/checktrans
+@bin libexec/emboss/chips
+@bin libexec/emboss/cirdna
+@bin libexec/emboss/codcmp
+@bin libexec/emboss/codcopy
+@bin libexec/emboss/coderet
+@bin libexec/emboss/compseq
+@bin libexec/emboss/cons
+@bin libexec/emboss/consambig
+@bin libexec/emboss/cpgplot
+@bin libexec/emboss/cpgreport
+@bin libexec/emboss/cusp
+@bin libexec/emboss/cutgextract
+@bin libexec/emboss/cutseq
+@bin libexec/emboss/dan
+@bin libexec/emboss/dbiblast
+@bin libexec/emboss/dbifasta
+@bin libexec/emboss/dbiflat
+@bin libexec/emboss/dbigcg
+@bin libexec/emboss/dbxfasta
+@bin libexec/emboss/dbxflat
+@bin libexec/emboss/dbxgcg
+@bin libexec/emboss/degapseq
+@bin libexec/emboss/density
+@bin libexec/emboss/descseq
+@bin libexec/emboss/diffseq
+@bin libexec/emboss/digest
+@bin libexec/emboss/distmat
+@bin libexec/emboss/dotmatcher
+@bin libexec/emboss/dotpath
+@bin libexec/emboss/dottup
+@bin libexec/emboss/dreg
+@bin libexec/emboss/edialign
+@bin libexec/emboss/einverted
+@bin libexec/emboss/embossdata
+@bin libexec/emboss/embossversion
+@bin libexec/emboss/emma
+@bin libexec/emboss/emowse
+@bin libexec/emboss/entret
+@bin libexec/emboss/epestfind
+@bin libexec/emboss/eprimer3
+@bin libexec/emboss/equicktandem
+@bin libexec/emboss/est2genome
+@bin libexec/emboss/etandem
+@bin libexec/emboss/extractalign
+@bin libexec/emboss/extractfeat
+@bin libexec/emboss/extractseq
+@bin libexec/emboss/featcopy
+@bin libexec/emboss/featreport
+@bin libexec/emboss/findkm
+@bin libexec/emboss/freak
+@bin libexec/emboss/fuzznuc
+@bin libexec/emboss/fuzzpro
+@bin libexec/emboss/fuzztran
+@bin libexec/emboss/garnier
+@bin libexec/emboss/geecee
+@bin libexec/emboss/getorf
+@bin libexec/emboss/helixturnhelix
+@bin libexec/emboss/hmoment
+@bin libexec/emboss/iep
+@bin libexec/emboss/infoalign
+@bin libexec/emboss/infobase
+@bin libexec/emboss/inforesidue
+@bin libexec/emboss/infoseq
+@bin libexec/emboss/isochore
+@bin libexec/emboss/jaspextract
+@bin libexec/emboss/jaspscan
+@bin libexec/emboss/jembossctl
+@bin libexec/emboss/lindna
+@bin libexec/emboss/listor
+@bin libexec/emboss/makenucseq
+@bin libexec/emboss/makeprotseq
+@bin libexec/emboss/marscan
+@bin libexec/emboss/maskambignuc
+@bin libexec/emboss/maskambigprot
+@bin libexec/emboss/maskfeat
+@bin libexec/emboss/maskseq
+@bin libexec/emboss/matcher
+@bin libexec/emboss/megamerger
+@bin libexec/emboss/merger
+@bin libexec/emboss/msbar
+@bin libexec/emboss/mwcontam
+@bin libexec/emboss/mwfilter
+@bin libexec/emboss/needle
+@bin libexec/emboss/newcpgreport
+@bin libexec/emboss/newcpgseek
+@bin libexec/emboss/newseq
+@bin libexec/emboss/nohtml
+@bin libexec/emboss/noreturn
+@bin libexec/emboss/nospace
+@bin libexec/emboss/notab
+@bin libexec/emboss/notseq
+@bin libexec/emboss/nthseq
+@bin libexec/emboss/octanol
+@bin libexec/emboss/oddcomp
+@bin libexec/emboss/palindrome
+@bin libexec/emboss/pasteseq
+@bin libexec/emboss/patmatdb
+@bin libexec/emboss/patmatmotifs
+@bin libexec/emboss/pepcoil
+@bin libexec/emboss/pepinfo
+@bin libexec/emboss/pepnet
+@bin libexec/emboss/pepstats
+@bin libexec/emboss/pepwheel
+@bin libexec/emboss/pepwindow
+@bin libexec/emboss/pepwindowall
+@bin libexec/emboss/plotcon
+@bin libexec/emboss/plotorf
+@bin libexec/emboss/polydot
+@bin libexec/emboss/preg
+@bin libexec/emboss/prettyplot
+@bin libexec/emboss/prettyseq
+@bin libexec/emboss/primersearch
+@bin libexec/emboss/printsextract
+@bin libexec/emboss/profit
+@bin libexec/emboss/prophecy
+@bin libexec/emboss/prophet
+@bin libexec/emboss/prosextract
+@bin libexec/emboss/pscan
+@bin libexec/emboss/psiphi
+@bin libexec/emboss/rebaseextract
+@bin libexec/emboss/recoder
+@bin libexec/emboss/redata
+@bin libexec/emboss/remap
+@bin libexec/emboss/restover
+@bin libexec/emboss/restrict
+@bin libexec/emboss/revseq
+libexec/emboss/runJemboss.csh
+@bin libexec/emboss/seealso
+@bin libexec/emboss/seqmatchall
+@bin libexec/emboss/seqret
+@bin libexec/emboss/seqretsplit
+@bin libexec/emboss/showalign
+@bin libexec/emboss/showdb
+@bin libexec/emboss/showfeat
+@bin libexec/emboss/showorf
+@bin libexec/emboss/showseq
+@bin libexec/emboss/shuffleseq
+@bin libexec/emboss/sigcleave
+@bin libexec/emboss/silent
+@bin libexec/emboss/sirna
+@bin libexec/emboss/sixpack
+@bin libexec/emboss/sizeseq
+@bin libexec/emboss/skipredundant
+@bin libexec/emboss/skipseq
+@bin libexec/emboss/splitter
+@bin libexec/emboss/stretcher
+@bin libexec/emboss/stssearch
+@bin libexec/emboss/supermatcher
+@bin libexec/emboss/syco
+@bin libexec/emboss/tcode
+@bin libexec/emboss/textsearch
+@bin libexec/emboss/tfextract
+@bin libexec/emboss/tfm
+@bin libexec/emboss/tfscan
+@bin libexec/emboss/tmap
+@bin libexec/emboss/tranalign
+@bin libexec/emboss/transeq
+@bin libexec/emboss/trimest
+@bin libexec/emboss/trimseq
+@bin libexec/emboss/trimspace
+@bin libexec/emboss/twofeat
+@bin libexec/emboss/union
+@bin libexec/emboss/vectorstrip
+@bin libexec/emboss/water
+@bin libexec/emboss/whichdb
+@bin libexec/emboss/wobble
+@bin libexec/emboss/wordcount
+@bin libexec/emboss/wordfinder
+@bin libexec/emboss/wordmatch
+@bin libexec/emboss/wossname
+@bin libexec/emboss/yank
share/EMBOSS/
share/EMBOSS/acd/
share/EMBOSS/acd/aaindexextract.acd
Index: devel/pscan/Makefile
===================================================================
RCS file: /cvs/ports/devel/pscan/Makefile,v
retrieving revision 1.8
diff -u -p -r1.8 Makefile
--- devel/pscan/Makefile 12 Jul 2019 20:45:16 -0000 1.8
+++ devel/pscan/Makefile 11 Nov 2019 15:24:49 -0000
@@ -3,6 +3,7 @@
COMMENT= limited problem scanner for C source files
V= 1.3
+REVISION= 0
PKGNAME= pscan-$V
DISTNAME= pscan
Index: devel/pscan/pkg/PLIST
===================================================================
RCS file: /cvs/ports/devel/pscan/pkg/PLIST,v
retrieving revision 1.3
diff -u -p -r1.3 PLIST
--- devel/pscan/pkg/PLIST 15 Apr 2017 22:05:29 -0000 1.3
+++ devel/pscan/pkg/PLIST 11 Nov 2019 15:24:49 -0000
@@ -1,5 +1,4 @@
@comment $OpenBSD: PLIST,v 1.3 2017/04/15 22:05:29 sthen Exp $
-@conflict emboss-*
bin/find_formats.sh
bin/pscan
share/examples/pscan/
--
jca | PGP : 0x1524E7EE / 5135 92C1 AD36 5293 2BDF DDCC 0DFA 74AE 1524 E7EE
