My first DM upload: emboss 5.0.0-4
Dear all,
I am about to make my first uplad as a DM !
This minor revision contains a bug fix from upstream, as well as a patch
of mine that makes the `tfm' ("the fine manual") application use
/usr/bin/pager instead of /usr/bin/more as a default. Other changes in
this debdiff are disabled by commenting parts of debian/rules and
debian/emboss.install, because we do not yet have agreement from Applied
Biosystems to use application/vnd.appliedbiosystems.* MIME types (I do
not know if it is mandatory, but it would be better). While it makes the
debdiff (attached) heavier, I think that it is better than reverting
changes in the SVN and re-applying then, isn't it ?
Have a nice day,
--
Charles Plessy
http://charles.plessy.org
Wakō, Saitama, Japan
diff -u emboss-5.0.0/debian/emboss.install emboss-5.0.0/debian/emboss.install
--- emboss-5.0.0/debian/emboss.install
+++ emboss-5.0.0/debian/emboss.install
@@ -2,0 +3 @@
+#debian/abiview.desktop usr/share/applications
diff -u emboss-5.0.0/debian/patches/series emboss-5.0.0/debian/patches/series
--- emboss-5.0.0/debian/patches/series
+++ emboss-5.0.0/debian/patches/series
@@ -1,2 +1,4 @@
+embindex-fix-2008-01-19.patch
+using-pager-in-tfm.patch
psiphi-fix-2007-07-27.patch
ajindex-fix-2008-01-09.patch
diff -u emboss-5.0.0/debian/changelog emboss-5.0.0/debian/changelog
--- emboss-5.0.0/debian/changelog
+++ emboss-5.0.0/debian/changelog
@@ -1,3 +1,15 @@
+emboss (5.0.0-4) unstable; urgency=low
+
+ * debian/patches:
+ - using-pager-in-tfm.patch:
+ Patching tfm so that it uses the alternatives system `/usr/bin/pager' if
+ the `PAGER' environment variable is not defined.
+ - embindex-fix-2008-01-19.patch:
+ Official fix 3. EMBOSS-5.0.0/nucleus/embindex.c 18 Jan 2008.
+ Order and fill fixes to sort out potential problems with kw/de/tx indexes.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org> Mon, 21 Jan 2008 08:40:14 +0900
+
emboss (5.0.0-3) unstable; urgency=low
[ Nelson A. de Oliveira ]
diff -u emboss-5.0.0/debian/rules emboss-5.0.0/debian/rules
--- emboss-5.0.0/debian/rules
+++ emboss-5.0.0/debian/rules
@@ -126,6 +126,8 @@
dh_installchangelogs ChangeLog
dh_installdocs
# dh_installmenu
+# dh_desktop
+# dh_installmime
dh_install
# Install the manpages and provide a symlink for the renamed binaries.
diff -u emboss-5.0.0/debian/emboss.dirs emboss-5.0.0/debian/emboss.dirs
--- emboss-5.0.0/debian/emboss.dirs
+++ emboss-5.0.0/debian/emboss.dirs
@@ -1,4 +1,5 @@
usr/bin
+#usr/share/applications
usr/lib
etc/emboss/embossrc.d
usr/share/man/man1
only in patch2:
unchanged:
--- emboss-5.0.0.orig/debian/emboss.sharedmimeinfo
+++ emboss-5.0.0/debian/emboss.sharedmimeinfo
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
+ <mime-type type="application/x-dna">
+ <alias type="application/abi1"/>
+ <sub-class-of type="application/octet-stream"/>
+ <comment>ABIF Applied Biosystems Inc. chromatogram</comment>
+ <comment xml:lang="fr">Chromatogramme au format ABIF Applied Biosystems Inc.</comment>
+ <!-- Format spec available at http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf -->
+ <!-- offset 4 and 5 stand for the version number -->
+ <magic priority="50">
+ <match type="string" offset="0"
+ value="ABIF??tdir"
+ mask="0xffffffff0000ffffffff"/>
+ </magic>
+ <glob pattern="*.ab1"/>
+ </mime-type>
+</mime-info>
only in patch2:
unchanged:
--- emboss-5.0.0.orig/debian/emboss.mime
+++ emboss-5.0.0/debian/emboss.mime
@@ -0,0 +1,2 @@
+application/x-dna; abiview -outseq /dev/null -graph x11 '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1
+application/abi1; abiview -outseq /dev/null -graph x11 '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1
only in patch2:
unchanged:
--- emboss-5.0.0.orig/debian/patches/embindex-fix-2008-01-19.patch
+++ emboss-5.0.0/debian/patches/embindex-fix-2008-01-19.patch
@@ -0,0 +1,56 @@
+Fix 3. EMBOSS-5.0.0/nucleus/embindex.c
+
+18 Jan 2008: Order and fill fixes to sort out potential problems
+ with kw/de/tx indexes.
+Index: EMBOSS-5.0.0/nucleus/embindex.c
+===================================================================
+--- EMBOSS-5.0.0.orig/nucleus/embindex.c
++++ EMBOSS-5.0.0/nucleus/embindex.c
+@@ -1196,13 +1196,13 @@
+ entry->txorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
+ entry->txfill = (entry->pagesize - 16) / (entry->txlen + 28);
+
+- entry->kwsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
+- entry->desecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
+- entry->txsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
+-
+- entry->kwsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
+- entry->desecfill = (entry->pagesize - 16) / (entry->idlen + 4);
+- entry->txsecfill = (entry->pagesize - 16) / (entry->idlen + 4);
++ entry->kwsecorder = (entry->pagesize - 60) / ((entry->kwlen + 1) + 12);
++ entry->desecorder = (entry->pagesize - 60) / ((entry->delen + 1) + 12);
++ entry->txsecorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
++
++ entry->kwsecfill = (entry->pagesize - 16) / (entry->kwlen + 4);
++ entry->desecfill = (entry->pagesize - 16) / (entry->delen + 4);
++ entry->txsecfill = (entry->pagesize - 16) / (entry->txlen + 4);
+
+ entry->idsecorder = (entry->pagesize - 60) / 24;
+ entry->idsecfill = (entry->pagesize - 60) / 20;
+@@ -1251,7 +1251,7 @@
+ entry->cachesize,
+ entry->idsecorder, slevel,
+ entry->idsecfill, count,
+- entry->kwlen);
++ entry->idlen);
+ if(!entry->idcache)
+ ajFatal("Cannot open ID index");
+
+@@ -1267,7 +1267,7 @@
+ entry->cachesize,
+ entry->acsecorder, slevel,
+ entry->acsecfill, count,
+- entry->kwlen);
++ entry->aclen);
+ if(!entry->accache)
+ ajFatal("Cannot open ACC index");
+
+@@ -1282,7 +1282,7 @@
+ entry->cachesize,
+ entry->svsecorder, slevel,
+ entry->svsecfill, count,
+- entry->kwlen);
++ entry->svlen);
+ if(!entry->svcache)
+ ajFatal("Cannot open SV index");
+
only in patch2:
unchanged:
--- emboss-5.0.0.orig/debian/patches/using-pager-in-tfm.patch
+++ emboss-5.0.0/debian/patches/using-pager-in-tfm.patch
@@ -0,0 +1,13 @@
+By default, use /usr/bin/pager, which always exist in Debian and is managed
+through the alternatives system.
+--- a/emboss/tfm.c
++++ b/emboss/tfm.c
+@@ -87,7 +87,7 @@
+ if(shellpager)
+ ajStrAssignC(&pager,shellpager);
+ if(!ajStrGetLen(pager))
+- ajStrAssignC(&pager,"more");
++ ajStrAssignC(&pager,"pager");
+ }
+ ajFmtPrintS(&cmd,"%S %S",pager,path);
+ system(ajStrGetPtr(cmd));
only in patch2:
unchanged:
--- emboss-5.0.0.orig/debian/abiview.desktop
+++ emboss-5.0.0/debian/abiview.desktop
@@ -0,0 +1,16 @@
+[Desktop Entry]
+Version=1.0
+Terminal=false
+#Icon=abiview
+Exec=abiview -outseq /dev/null -graph x11 %f
+Name=abiview
+GenericName=Chromatogram viewer
+GenericName[en]=Chromatogram viewer
+GenericName[fr]=Visualisateur de chromatogrammes
+Comment=Displays ABIF Applied Biosystems Inc. chromatograms.
+Comment[en]=Displays ABIF Applied Biosystems Inc. chromatograms.
+Comment[fr]=Affiche les chromatogrammes au format ABIF (Applied Biosystems Inc.).
+Type=Application
+Categories=Biology;Science;Education;
+MimeType=application/x-dna;
+NoDisplay=true
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