[med-svn] [Git][med-team/arb][master] 8 commits: Add perl-xs-dev to Build-Depends.
Charles Plessy (@plessy)
gitlab at salsa.debian.org
Fri Aug 7 07:50:30 BST 2026
Charles Plessy pushed to branch master at Debian Med / arb
Commits:
56628b56 by Charles Plessy at 2026-08-07T14:11:37+09:00
Add perl-xs-dev to Build-Depends.
Closes: #1102816
- - - - -
ceb1d075 by Charles Plessy at 2026-08-07T14:12:34+09:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
6c477217 by Charles Plessy at 2026-08-07T14:12:35+09:00
debhelper-compat 13 (routine-update)
- - - - -
a79231a8 by Charles Plessy at 2026-08-07T14:14:50+09:00
Changes made by cme
- - - - -
1225f3b7 by Charles Plessy at 2026-08-07T14:14:56+09:00
Drop 'Rules-Requires-Root: no' from d/control (routine-update)
- - - - -
5420aedf by Charles Plessy at 2026-08-07T14:15:28+09:00
Reorder Files paragraphs in debian/copyright by directory depth.
Changes-By: lintian-brush
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
- - - - -
bf2a6de4 by Charles Plessy at 2026-08-07T14:15:41+09:00
Run debconf-updatepo after template changes.
Changes-By: lintian-brush
Fixes: lintian: newer-debconf-templates
See-also: https://lintian.debian.org/tags/newer-debconf-templates.html
- - - - -
cb2c88d8 by Charles Plessy at 2026-08-07T15:49:57+09:00
More fixes but it still fails to build.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/gcc-16+
- debian/patches/series
- debian/po/id.po
- debian/po/templates.pot
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+arb (6.0.6-9) UNRELEASED; urgency=medium
+
+ * Add perl-xs-dev to Build-Depends. Closes: #1102816
+ * Standards-Version: 4.7.4 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Reflow Uploaders field (cme)
+ * Remove Priority field (cme)
+ * Drop 'Rules-Requires-Root: no' from d/control (routine-update)
+ * Reorder Files paragraphs in debian/copyright by directory depth.
+ * Run debconf-updatepo after template changes.
+
+ -- Charles Plessy <plessy at debian.org> Fri, 07 Aug 2026 14:10:47 +0900
+
arb (6.0.6-8) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,58 +1,63 @@
Source: arb
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Elmar Pruesse <elmar at pruesse.net>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
+ Elmar Pruesse <elmar at pruesse.net>,
Section: non-free/science
XS-Autobuild: yes
-Priority: optional
-Build-Depends: chrpath,
- debhelper-compat (= 11),
- freeglut3-dev | libglu-dev,
- libbio-perl-perl,
- libglew-dev,
- libglib2.0-dev,
- libglw1-mesa-dev,
- libglu1-mesa-dev,
- libmotif-dev,
- libpng-dev,
- libtiff-dev,
- libtirpc-dev,
- libxaw7-dev,
- libxml2-utils,
- libxpm-dev,
- lynx,
- time,
- perl-doc,
- xsltproc,
- xutils-dev
-Standards-Version: 4.6.2
+Build-Depends:
+ chrpath,
+ debhelper-compat (= 13),
+ freeglut3-dev | libglu-dev,
+ libbio-perl-perl,
+ libb-lint-perl,
+ libglew-dev,
+ libglib2.0-dev,
+ libglw1-mesa-dev,
+ libglu1-mesa-dev,
+ libmotif-dev,
+ libpng-dev,
+ libtiff-dev,
+ libtirpc-dev,
+ libxaw7-dev,
+ libxml2-utils,
+ libxpm-dev,
+ lynx,
+ time,
+ perl-doc,
+ perl-xs-dev,
+ xsltproc,
+ xutils-dev,
Vcs-Browser: https://salsa.debian.org/med-team/arb
Vcs-Git: https://salsa.debian.org/med-team/arb.git
Homepage: http://www.arb-home.de/
-Rules-Requires-Root: no
Package: arb
Architecture: any
-Depends: arb-common (= ${source:Version}),
- fastdnaml,
- libarb (= ${binary:Version}),
- openssh-client,
- mafft,
- mrbayes,
- phylip,
- phyml,
- raxml,
- readseq,
- fig2dev,
- tree-puzzle,
- xdg-utils,
- ${misc:Depends},
- ${shlibs:Depends}
-Recommends: bioperl,
- xfig
-Suggests: arb-database,
- gnuplot,
- gv
+Depends:
+ arb-common (= ${source:Version}),
+ fastdnaml,
+ libarb (= ${binary:Version}),
+ openssh-client,
+ mafft,
+ mrbayes,
+ phylip,
+ phyml,
+ raxml,
+ readseq,
+ fig2dev,
+ tree-puzzle,
+ xdg-utils,
+ ${misc:Depends},
+ ${shlibs:Depends},
+Recommends:
+ bioperl,
+ xfig,
+Suggests:
+ arb-database,
+ gnuplot,
+ gv,
Description: phylogenetic sequence analysis suite - main program
ARB is a graphical suite of tools for sequence database handling and data
analysis. A central database of processed (aligned) sequences and any
@@ -69,9 +74,11 @@ Description: phylogenetic sequence analysis suite - main program
Package: libarb
Architecture: any
-Depends: ${misc:Depends},
- ${shlibs:Depends}
-Recommends: arb
+Depends:
+ ${misc:Depends},
+ ${shlibs:Depends},
+Recommends:
+ arb,
Description: phylogenetic sequence analysis suite - libraries
ARB is a graphical suite of tools for sequence database handling and data
analysis. A central database of processed (aligned) sequences and any
@@ -91,8 +98,9 @@ Description: phylogenetic sequence analysis suite - libraries
Package: libarb-dev
Architecture: any
Section: non-free/libdevel
-Depends: libarb (= ${binary:Version}),
- ${misc:Depends}
+Depends:
+ libarb (= ${binary:Version}),
+ ${misc:Depends},
Description: phylogenetic sequence analysis suite - development files
ARB is a graphical suite of tools for sequence database handling and data
analysis. A central database of processed (aligned) sequences and any
@@ -112,13 +120,15 @@ Description: phylogenetic sequence analysis suite - development files
Package: arb-common
Architecture: all
-Depends: adduser,
- arb-doc (= ${source:Version}),
- ghostscript | postscript-preview,
- gv | postscript-viewer,
- ${perl:Depends},
- ${misc:Depends}
-Recommends: arb
+Depends:
+ adduser,
+ arb-doc (= ${source:Version}),
+ ghostscript | postscript-preview,
+ gv | postscript-viewer,
+ ${perl:Depends},
+ ${misc:Depends},
+Recommends:
+ arb,
Description: phylogenetic sequence analysis suite - common files
ARB is a graphical suite of tools for sequence database handling and data
analysis. A central database of processed (aligned) sequences and any
@@ -138,10 +148,12 @@ Description: phylogenetic sequence analysis suite - common files
Package: arb-doc
Architecture: all
Section: non-free/doc
-Depends: ghostscript | postscript-preview,
- gv | postscript-viewer,
- ${misc:Depends}
-Suggests: arb
+Depends:
+ ghostscript | postscript-preview,
+ gv | postscript-viewer,
+ ${misc:Depends},
+Suggests:
+ arb,
Description: phylogenetic sequence analysis suite - documentation
ARB is a graphical suite of tools for sequence database handling and data
analysis. A central database of processed (aligned) sequences and any
=====================================
debian/copyright
=====================================
@@ -100,6 +100,31 @@ License: GDE
by the GDE are copyrighted by, and are the property of their respective
authors unless otherwise stated.
+Files: CONVERTALN/*
+Copyright: (C) 1992 Wen-Min Kuan
+License: ARP_permissive
+ The files in this directory do not contain an explicite license
+ statement. It has to be assumed that the license is the same as the
+ general usage and redistribution license for Arb and the authors of
+ Arb got a permission to distribute this code in their product.
+ .
+ This paragraph was just added to the copyright file to mention that
+ there is some copyrighted work which was not mentioned above.
+Comment: convert_aln -- an alignment(or sequence) converter written
+ by Wen-Min Kuan for the Ribsomal Database Project(RDP), April 28, 1992.
+ .
+ Remark from the Debian package maintainer Andreas Tille:
+ I was unable to find a source URL where this program which is
+ claimed as external can be downloaded.
+
+Files: READSEQ/*
+Copyright: 1990-1993 D. Gilbert <gilbertd at bio.indiana.edu>
+License: PD
+ readseq is public domain software
+Comment: This code is not used in the binary package because it is
+ available as official Debian package and has a free license (see this
+ package).
+
Files: GDE/PHYLIP/*
Copyright: (c) Copyright 1986-1993 by Joseph Felsenstein and the University
of Washington.
@@ -121,23 +146,6 @@ Comment: Remark from the Debian package maintainer Andreas Tille
I was unable to find a source URL where this program which is
claimed as external can be downloaded.
-Files: CONVERTALN/*
-Copyright: (C) 1992 Wen-Min Kuan
-License: ARP_permissive
- The files in this directory do not contain an explicite license
- statement. It has to be assumed that the license is the same as the
- general usage and redistribution license for Arb and the authors of
- Arb got a permission to distribute this code in their product.
- .
- This paragraph was just added to the copyright file to mention that
- there is some copyrighted work which was not mentioned above.
-Comment: convert_aln -- an alignment(or sequence) converter written
- by Wen-Min Kuan for the Ribsomal Database Project(RDP), April 28, 1992.
- .
- Remark from the Debian package maintainer Andreas Tille:
- I was unable to find a source URL where this program which is
- claimed as external can be downloaded.
-
Files: GDE/FASTDNAML/*
Copyright: (C) 1998, 1999, 2000 by Gary J. Olsen,
1986 - 1990 by the University of Washington and Joseph Felsenstein.
@@ -205,14 +213,6 @@ License: GPL
Comment: This code is not used in the binary package because it is available
as official Debian package and has a free license (see this package).
-Files: READSEQ/*
-Copyright: 1990-1993 D. Gilbert <gilbertd at bio.indiana.edu>
-License: PD
- readseq is public domain software
-Comment: This code is not used in the binary package because it is
- available as official Debian package and has a free license (see this
- package).
-
Files: debian/*
Copyright: (C) 2008-2013 Andreas Tille <tille at debian.org>
License: GPL
=====================================
debian/patches/gcc-16+
=====================================
@@ -0,0 +1,28 @@
+Index: arb/PROBE/PT_new_design.cxx
+===================================================================
+--- arb.orig/PROBE/PT_new_design.cxx
++++ arb/PROBE/PT_new_design.cxx
+@@ -1235,7 +1235,7 @@ public:
+ };
+
+ struct SCP_Less {
+- bool operator()(const SmartCharPtr& p1, const SmartCharPtr& p2) { return &*p1 < &*p2; } // simply compare addresses
++ bool operator()(const SmartCharPtr& p1, const SmartCharPtr& p2) const { return &*p1 < &*p2; } // simply compare addresses
+ };
+
+ class ProbeCandidates {
+Index: arb/GDE/SUPPORT/CAP2.c
+===================================================================
+--- arb.orig/GDE/SUPPORT/CAP2.c
++++ arb/GDE/SUPPORT/CAP2.c
+@@ -284,8 +284,8 @@ char *argv[];
+ char *sequence; /* Storing all segments */
+ char *reverse; /* Storing all reverse segments */
+ int symbol, prev; /* The next character */
+- FILE *Ap, *ckopen(); /* For the sequence file */
+- char *my_calloc(int); /* space-allocating function */
++ FILE *Ap, *ckopen(char *name, char *mode); /* For the sequence file */
++ char *my_calloc(int size); /* space-allocating function */
+ register int i, j, k; /* index variables */
+ /* Mod by S.S. */
+ int jj;
=====================================
debian/patches/series
=====================================
@@ -10,3 +10,4 @@
100_use_tirpc.patch
110_narrowing.patch
111_fgets.patch
+gcc-16+
=====================================
debian/po/id.po
=====================================
@@ -7,16 +7,16 @@ msgid ""
msgstr ""
"Project-Id-Version: arb\n"
"Report-Msgid-Bugs-To: arb at packages.debian.org\n"
-"POT-Creation-Date: 2017-05-18 22:09+0700\n"
+"POT-Creation-Date: 2026-08-07 14:15+0900\n"
"PO-Revision-Date: 2017-05-18 22:20+0700\n"
"Last-Translator: Kukuh Syafaat <syafaatkukuh at gmail.com>\n"
-"Language-Team: Debian Indonesia Translator <debian-l10n-indonesian at lists."
-"debian.org>\n"
+"Language-Team: Debian Indonesia Translator <debian-l10n-"
+"indonesian at lists.debian.org>\n"
+"Language: id\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"X-Generator: Poedit 1.8.11\n"
-"Language: id\n"
#. Type: multiselect
#. Description
@@ -29,13 +29,13 @@ msgstr " Administrator ARB PT-server:"
#: ../arb-common.templates:2001
msgid ""
"The default configuration of PT-server slots in /etc/arb/arb_tcp.dat gives "
-"ARB three global slots accessible by all users (connecting to localhost:"
-"${PORT}), as well as three slots to give private per-user access (connecting "
+"ARB three global slots accessible by all users (connecting to localhost:$"
+"{PORT}), as well as three slots to give private per-user access (connecting "
"to ~/.arb_pts/${USER}${NUMBER}.socket)."
msgstr ""
"Konfigurasi bawaan slot PT-server di /etc/arb/arb_tcp.dat memberi ARB tiga "
-"slot global yang dapat diakses oleh semua pengguna (terhubung ke localhost:"
-"${PORT}), serta tiga slot untuk memberikan akses per pengguna pribadi "
+"slot global yang dapat diakses oleh semua pengguna (terhubung ke localhost:$"
+"{PORT}), serta tiga slot untuk memberikan akses per pengguna pribadi "
"(menghubungkan ke ~/.arb_pts/${USER}${NUMBER}.socket)."
#. Type: multiselect
=====================================
debian/po/templates.pot
=====================================
@@ -1,6 +1,6 @@
# SOME DESCRIPTIVE TITLE.
# Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER
-# This file is distributed under the same license as the PACKAGE package.
+# This file is distributed under the same license as the arb package.
# FIRST AUTHOR <EMAIL at ADDRESS>, YEAR.
#
#, fuzzy
@@ -8,7 +8,7 @@ msgid ""
msgstr ""
"Project-Id-Version: arb\n"
"Report-Msgid-Bugs-To: arb at packages.debian.org\n"
-"POT-Creation-Date: 2014-10-11 07:42+0200\n"
+"POT-Creation-Date: 2026-08-07 14:15+0900\n"
"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
"Last-Translator: FULL NAME <EMAIL at ADDRESS>\n"
"Language-Team: LANGUAGE <LL at li.org>\n"
@@ -28,8 +28,8 @@ msgstr ""
#: ../arb-common.templates:2001
msgid ""
"The default configuration of PT-server slots in /etc/arb/arb_tcp.dat gives "
-"ARB three global slots accessible by all users (connecting to localhost:"
-"${PORT}), as well as three slots to give private per-user access (connecting "
+"ARB three global slots accessible by all users (connecting to localhost:$"
+"{PORT}), as well as three slots to give private per-user access (connecting "
"to ~/.arb_pts/${USER}${NUMBER}.socket)."
msgstr ""
View it on GitLab: https://salsa.debian.org/med-team/arb/-/compare/2a6b970ea2f3d27f04d571007ba4ceb0f2907b4a...cb2c88d8bcb2da582e05f9f32a71ddfdd107bc82
--
View it on GitLab: https://salsa.debian.org/med-team/arb/-/compare/2a6b970ea2f3d27f04d571007ba4ceb0f2907b4a...cb2c88d8bcb2da582e05f9f32a71ddfdd107bc82
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