Attachment 14456 Details for Bug 27179 – file.diff

[patch] file.diff

file.diff (text/plain), 12.32 KB, created by johann on 2001-05-07 11:50:01 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: johann

Created: 2001-05-07 11:50:01 UTC

Size: 12.32 KB

patch

obsolete

>diff -ruN emboss.bak/Makefile emboss/Makefile
>--- emboss.bak/Makefile	Mon May  7 12:36:56 2001
>+++ emboss/Makefile	Wed Apr 18 11:07:07 2001
>@@ -6,7 +6,7 @@
> #
> 
> PORTNAME=	emboss
>-PORTVERSION=	1.11.0
>+PORTVERSION=	1.12.0
> CATEGORIES=	biology
> MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
> 		ftp://ftp.no.embnet.org/pub/EMBOSS/ \
>diff -ruN emboss.bak/distinfo emboss/distinfo
>--- emboss.bak/distinfo	Mon May  7 12:36:56 2001
>+++ emboss/distinfo	Fri May  4 13:14:42 2001
>@@ -1,5 +1,5 @@
>-MD5 (emboss/EMBOSS-1.11.0.tar.gz) = b7376e98ea7d86eb4b5411013bd98dd3
>+MD5 (emboss/EMBOSS-1.12.0.tar.gz) = 7d2d770dcc037624e5ee52c143c8923b
> MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8
>-MD5 (emboss/MSE-0.0.4.tar.gz) = 96f87f4f321e6c6d65793391971504a1
>-MD5 (emboss/PHYLIP-3.573c.tar.gz) = d6062201d6492676c82f2b7b8e9d8c95
>-MD5 (emboss/TOPO-0.1.tar.gz) = ab3ff940e689d044476528b47e983184
>+MD5 (emboss/MSE-0.0.4.tar.gz) = f490638c4f0b789d0c1117513406d76a
>+MD5 (emboss/PHYLIP-3.573c.tar.gz) = 4a4fff45f4a51a430731a46f3f37f37f
>+MD5 (emboss/TOPO-0.1.tar.gz) = fa1a85bfde1054136af5aa9587c2433f
>diff -ruN emboss.bak/pkg-plist emboss/pkg-plist
>--- emboss.bak/pkg-plist	Mon May  7 12:36:56 2001
>+++ emboss/pkg-plist	Mon May  7 11:15:51 2001
>@@ -62,6 +62,7 @@
> bin/backtranseq
> bin/banana
> bin/btwisted
>+bin/cai
> bin/chaos
> bin/charge
> bin/checktrans
>@@ -84,6 +85,7 @@
> bin/descseq
> bin/diffseq
> bin/digest
>+bin/distmat
> bin/domainer
> bin/dotmatcher
> bin/dotpath
>@@ -161,6 +163,7 @@
> bin/restover
> bin/restrict
> bin/revseq
>+bin/scopalign
> bin/scope
> bin/seealso
> bin/seqmatchall
>@@ -215,6 +218,7 @@
> share/EMBOSS/acd/backtranseq.acd
> share/EMBOSS/acd/banana.acd
> share/EMBOSS/acd/btwisted.acd
>+share/EMBOSS/acd/cai.acd
> share/EMBOSS/acd/chaos.acd
> share/EMBOSS/acd/charge.acd
> share/EMBOSS/acd/checktrans.acd
>@@ -738,134 +742,27 @@
> share/EMBOSS/test/wormpep/division.lkp
> share/EMBOSS/test/wormpep/entrynam.idx
> share/EMBOSS/test/wormpep/wormpep
>+share/doc/EMBOSS/manuals/EMBOSS-FreeBSD-HOWTO.txt
>+share/doc/EMBOSS/manuals/admin.aux
>+share/doc/EMBOSS/manuals/admin.dvi
>+share/doc/EMBOSS/manuals/admin.log
>+share/doc/EMBOSS/manuals/admin.pdf
>+share/doc/EMBOSS/manuals/admin.ps
> share/doc/EMBOSS/manuals/admin.sty
> share/doc/EMBOSS/manuals/admin.tex
>+share/doc/EMBOSS/manuals/admin.toc
>+share/doc/EMBOSS/manuals/adminguide.tar.gz
>+share/doc/EMBOSS/manuals/emboss_qg.pdf
>+share/doc/EMBOSS/manuals/emboss_qg.ps
> share/doc/EMBOSS/manuals/program.ps.gz
>-share/doc/EMBOSS/programs/html/SITE-DIRECTED.html
>-share/doc/EMBOSS/programs/html/abi_trace_files_group.html
>-share/doc/EMBOSS/programs/html/abiview.html
> share/doc/EMBOSS/programs/html/abiview0.gif
>-share/doc/EMBOSS/programs/html/alignment_global_group.html
>-share/doc/EMBOSS/programs/html/alignment_group.html
>-share/doc/EMBOSS/programs/html/alignment_local_group.html
>-share/doc/EMBOSS/programs/html/alignment_multiple_group.html
>-share/doc/EMBOSS/programs/html/antigenic.html
>-share/doc/EMBOSS/programs/html/assorted_group.html
>-share/doc/EMBOSS/programs/html/backtranseq.html
>-share/doc/EMBOSS/programs/html/banana.html
> share/doc/EMBOSS/programs/html/banana0.gif
>-share/doc/EMBOSS/programs/html/btwisted.html
>-share/doc/EMBOSS/programs/html/chaos.html
> share/doc/EMBOSS/programs/html/chaos0.gif
>-share/doc/EMBOSS/programs/html/checktrans.html
>-share/doc/EMBOSS/programs/html/chips.html
>-share/doc/EMBOSS/programs/html/cirdna.html
>-share/doc/EMBOSS/programs/html/clique.html
>-share/doc/EMBOSS/programs/html/codcmp.html
>-share/doc/EMBOSS/programs/html/coderet.html
>-share/doc/EMBOSS/programs/html/coding_regions_group.html
>-share/doc/EMBOSS/programs/html/comparison_group.html
>-share/doc/EMBOSS/programs/html/compseq.html
>-share/doc/EMBOSS/programs/html/cons.html
>-share/doc/EMBOSS/programs/html/consense.html
>-share/doc/EMBOSS/programs/html/contml.html
>-share/doc/EMBOSS/programs/html/contrast.html
>-share/doc/EMBOSS/programs/html/cpg_islands_group.html
>-share/doc/EMBOSS/programs/html/cpgplot.html
> share/doc/EMBOSS/programs/html/cpgplot0.gif
>-share/doc/EMBOSS/programs/html/cpgreport.html
>-share/doc/EMBOSS/programs/html/cusp.html
>-share/doc/EMBOSS/programs/html/cutseq.html
>-share/doc/EMBOSS/programs/html/dan.html
>-share/doc/EMBOSS/programs/html/database_entry_extraction_group.html
>-share/doc/EMBOSS/programs/html/database_indexing_group.html
>-share/doc/EMBOSS/programs/html/database_information_group.html
>-share/doc/EMBOSS/programs/html/dbiblast.html
>-share/doc/EMBOSS/programs/html/dbifasta.html
>-share/doc/EMBOSS/programs/html/dbiflat.html
>-share/doc/EMBOSS/programs/html/dbigcg.html
>-share/doc/EMBOSS/programs/html/degapseq.html
>-share/doc/EMBOSS/programs/html/descseq.html
>-share/doc/EMBOSS/programs/html/diffseq.html
>-share/doc/EMBOSS/programs/html/digest.html
>-share/doc/EMBOSS/programs/html/display_alignment_multiple_group.html
>-share/doc/EMBOSS/programs/html/dna_sequence_composition_group.html
>-share/doc/EMBOSS/programs/html/dna_sequence_features_group.html
>-share/doc/EMBOSS/programs/html/dna_sequence_properties_group.html
>-share/doc/EMBOSS/programs/html/dnacomp.html
>-share/doc/EMBOSS/programs/html/dnadist.html
>-share/doc/EMBOSS/programs/html/dnainvar.html
>-share/doc/EMBOSS/programs/html/dnaml.html
>-share/doc/EMBOSS/programs/html/dnamlk.html
>-share/doc/EMBOSS/programs/html/dnapars.html
>-share/doc/EMBOSS/programs/html/dnapenny.html
>-share/doc/EMBOSS/programs/html/dollop.html
>-share/doc/EMBOSS/programs/html/dolpenny.html
>-share/doc/EMBOSS/programs/html/domainer.html
>-share/doc/EMBOSS/programs/html/dotmatcher.html
> share/doc/EMBOSS/programs/html/dotmatcher0.gif
>-share/doc/EMBOSS/programs/html/dotpath.html
>-share/doc/EMBOSS/programs/html/dottup.html
> share/doc/EMBOSS/programs/html/dottup0.gif
>-share/doc/EMBOSS/programs/html/dreg.html
>-share/doc/EMBOSS/programs/html/eclique.html
>-share/doc/EMBOSS/programs/html/econsense.html
>-share/doc/EMBOSS/programs/html/econtml.html
>-share/doc/EMBOSS/programs/html/econtrast.html
>-share/doc/EMBOSS/programs/html/ednacomp.html
>-share/doc/EMBOSS/programs/html/ednadist.html
>-share/doc/EMBOSS/programs/html/ednainvar.html
>-share/doc/EMBOSS/programs/html/ednaml.html
>-share/doc/EMBOSS/programs/html/ednamlk.html
>-share/doc/EMBOSS/programs/html/ednapars.html
>-share/doc/EMBOSS/programs/html/ednapenny.html
>-share/doc/EMBOSS/programs/html/edollop.html
>-share/doc/EMBOSS/programs/html/edolpenny.html
>-share/doc/EMBOSS/programs/html/efactor.html
>-share/doc/EMBOSS/programs/html/efitch.html
>-share/doc/EMBOSS/programs/html/egendist.html
>-share/doc/EMBOSS/programs/html/einverted.html
>-share/doc/EMBOSS/programs/html/ekitsch.html
> share/doc/EMBOSS/programs/html/emboss_icon.gif
>-share/doc/EMBOSS/programs/html/embossdata.html
>-share/doc/EMBOSS/programs/html/emix.html
>-share/doc/EMBOSS/programs/html/emma.html
>-share/doc/EMBOSS/programs/html/emnu.html
>-share/doc/EMBOSS/programs/html/emowse.html
>-share/doc/EMBOSS/programs/html/eneighbor.html
>-share/doc/EMBOSS/programs/html/entret.html
>-share/doc/EMBOSS/programs/html/enzyme_kinetics_group.html
>-share/doc/EMBOSS/programs/html/epenny.html
>-share/doc/EMBOSS/programs/html/eprotdist.html
>-share/doc/EMBOSS/programs/html/eprotpars.html
>-share/doc/EMBOSS/programs/html/equicktandem.html
>-share/doc/EMBOSS/programs/html/erestml.html
>-share/doc/EMBOSS/programs/html/eseqboot.html
>-share/doc/EMBOSS/programs/html/est2genome.html
>-share/doc/EMBOSS/programs/html/etandem.html
>-share/doc/EMBOSS/programs/html/extractseq.html
>-share/doc/EMBOSS/programs/html/factor.html
>-share/doc/EMBOSS/programs/html/findkm.html
> share/doc/EMBOSS/programs/html/findkm0.gif
>-share/doc/EMBOSS/programs/html/fitch.html
>-share/doc/EMBOSS/programs/html/freak.html
>-share/doc/EMBOSS/programs/html/fuzznuc.html
>-share/doc/EMBOSS/programs/html/fuzzpro.html
>-share/doc/EMBOSS/programs/html/fuzztran.html
>-share/doc/EMBOSS/programs/html/garnier.html
>-share/doc/EMBOSS/programs/html/geecee.html
>-share/doc/EMBOSS/programs/html/gendist.html
>-share/doc/EMBOSS/programs/html/gene_finding_group.html
>-share/doc/EMBOSS/programs/html/getorf.html
>-share/doc/EMBOSS/programs/html/groups.html
>-share/doc/EMBOSS/programs/html/helixturnhelix.html
>-share/doc/EMBOSS/programs/html/hydropathy_group.html
>-share/doc/EMBOSS/programs/html/iep.html
>-share/doc/EMBOSS/programs/html/index.html
>-share/doc/EMBOSS/programs/html/infoseq.html
>-share/doc/EMBOSS/programs/html/isochore.html
>-share/doc/EMBOSS/programs/html/isochore0.gif
>-share/doc/EMBOSS/programs/html/kitsch.html
> share/doc/EMBOSS/programs/html/lindna.html
> share/doc/EMBOSS/programs/html/marscan.html
> share/doc/EMBOSS/programs/html/maskfeat.html
>@@ -890,7 +787,6 @@
> share/doc/EMBOSS/programs/html/nrscope.html
> share/doc/EMBOSS/programs/html/nthseq.html
> share/doc/EMBOSS/programs/html/octanol.html
>-share/doc/EMBOSS/programs/html/octanol0.gif
> share/doc/EMBOSS/programs/html/oddcomp.html
> share/doc/EMBOSS/programs/html/palindrome.html
> share/doc/EMBOSS/programs/html/pasteseq.html
>@@ -900,26 +796,17 @@
> share/doc/EMBOSS/programs/html/penny.html
> share/doc/EMBOSS/programs/html/pepcoil.html
> share/doc/EMBOSS/programs/html/pepinfo.html
>-share/doc/EMBOSS/programs/html/pepinfo1.gif
>-share/doc/EMBOSS/programs/html/pepinfo2.gif
> share/doc/EMBOSS/programs/html/pepnet.html
>-share/doc/EMBOSS/programs/html/pepnet0.gif
> share/doc/EMBOSS/programs/html/pepstats.html
> share/doc/EMBOSS/programs/html/pepwheel.html
>-share/doc/EMBOSS/programs/html/pepwheel0.gif
> share/doc/EMBOSS/programs/html/pepwindow.html
>-share/doc/EMBOSS/programs/html/pepwindow0.gif
> share/doc/EMBOSS/programs/html/pepwindowall.html
>-share/doc/EMBOSS/programs/html/pepwindowall0.gif
>+share/doc/EMBOSS/programs/html/phylogeny_group.html
> share/doc/EMBOSS/programs/html/plotcon.html
> share/doc/EMBOSS/programs/html/plotorf.html
>-share/doc/EMBOSS/programs/html/plotorf0.gif
> share/doc/EMBOSS/programs/html/polydot.html
>-share/doc/EMBOSS/programs/html/polydot0.gif
> share/doc/EMBOSS/programs/html/preg.html
> share/doc/EMBOSS/programs/html/prettyplot.html
>-share/doc/EMBOSS/programs/html/prettyplot3.gif
>-share/doc/EMBOSS/programs/html/prettyplot4.gif
> share/doc/EMBOSS/programs/html/prettyseq.html
> share/doc/EMBOSS/programs/html/prima.html
> share/doc/EMBOSS/programs/html/primers_group.html
>@@ -976,16 +863,12 @@
> share/doc/EMBOSS/programs/html/stssearch.html
> share/doc/EMBOSS/programs/html/supermatcher.html
> share/doc/EMBOSS/programs/html/syco.html
>-share/doc/EMBOSS/programs/html/syco0.gif
>-share/doc/EMBOSS/programs/html/syco1.gif
> share/doc/EMBOSS/programs/html/text_search_group.html
> share/doc/EMBOSS/programs/html/textsearch.html
> share/doc/EMBOSS/programs/html/tfextract.html
> share/doc/EMBOSS/programs/html/tfm.html
> share/doc/EMBOSS/programs/html/tfscan.html
> share/doc/EMBOSS/programs/html/tmap.html
>-share/doc/EMBOSS/programs/html/tmap0.gif
>-share/doc/EMBOSS/programs/html/topo.gif
> share/doc/EMBOSS/programs/html/topo.html
> share/doc/EMBOSS/programs/html/transcription_group.html
> share/doc/EMBOSS/programs/html/transeq.html
>@@ -997,7 +880,6 @@
> share/doc/EMBOSS/programs/html/vectorstrip.html
> share/doc/EMBOSS/programs/html/water.html
> share/doc/EMBOSS/programs/html/wobble.html
>-share/doc/EMBOSS/programs/html/wobble0.gif
> share/doc/EMBOSS/programs/html/wordcount.html
> share/doc/EMBOSS/programs/html/wordmatch.html
> share/doc/EMBOSS/programs/html/wossname.html
>@@ -1007,7 +889,9 @@
> share/doc/EMBOSS/programs/text/backtranseq.txt
> share/doc/EMBOSS/programs/text/banana.txt
> share/doc/EMBOSS/programs/text/btwisted.txt
>+share/doc/EMBOSS/programs/text/cai.txt
> share/doc/EMBOSS/programs/text/chaos.txt
>+share/doc/EMBOSS/programs/text/charge.txt
> share/doc/EMBOSS/programs/text/checktrans.txt
> share/doc/EMBOSS/programs/text/chips.txt
> share/doc/EMBOSS/programs/text/cirdna.txt
>@@ -1033,6 +917,7 @@
> share/doc/EMBOSS/programs/text/descseq.txt
> share/doc/EMBOSS/programs/text/diffseq.txt
> share/doc/EMBOSS/programs/text/digest.txt
>+share/doc/EMBOSS/programs/text/distmat.txt
> share/doc/EMBOSS/programs/text/dnacomp.txt
> share/doc/EMBOSS/programs/text/dnadist.txt
> share/doc/EMBOSS/programs/text/dnainvar.txt
>@@ -1093,6 +978,7 @@
> share/doc/EMBOSS/programs/text/gendist.txt
> share/doc/EMBOSS/programs/text/getorf.txt
> share/doc/EMBOSS/programs/text/helixturnhelix.txt
>+share/doc/EMBOSS/programs/text/hmoment.txt
> share/doc/EMBOSS/programs/text/iep.txt
> share/doc/EMBOSS/programs/text/infoseq.txt
> share/doc/EMBOSS/programs/text/isochore.txt
>@@ -1189,6 +1075,7 @@
> share/doc/EMBOSS/programs/text/wossname.txt
> share/doc/EMBOSS/tutorials/biblio.bib
> share/doc/EMBOSS/tutorials/dottup.ps.gz
>+share/doc/EMBOSS/tutorials/emboss-talk.ppt
> share/doc/EMBOSS/tutorials/emboss_tutorial.tex
> share/doc/EMBOSS/tutorials/pepinfo1.ps.gz
> share/doc/EMBOSS/tutorials/pepinfo2.ps.gz

Actions: View | Diff

Attachments on bug 27179: 14456