[med-svn] [Git][med-team/murasaki][master] 9 commits: d/changelog: trim trailing whitespace.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Nov 20 21:28:29 GMT 2025
Étienne Mollier pushed to branch master at Debian Med / murasaki
Commits:
1d60ca44 by Étienne Mollier at 2025-11-20T21:41:43+01:00
d/changelog: trim trailing whitespace.
- - - - -
32859112 by Étienne Mollier at 2025-11-20T22:11:20+01:00
buildflags.patch: new: propagate build flags.
Closes: #1119494
- - - - -
8e926592 by Étienne Mollier at 2025-11-20T22:11:57+01:00
d/rules: activate full hardening.
The relocation bug documented in comment is now fixed apparently.
- - - - -
1035eaca by Étienne Mollier at 2025-11-20T22:13:57+01:00
d/copyright: drop the old FSF mail address.
- - - - -
8467155e by Étienne Mollier at 2025-11-20T22:15:22+01:00
d/control: murasaki depends by default on gnuplot-nox.
This may be revisited for gnuplot-x11 if deemed more appropriate.
- - - - -
272d0bd4 by Étienne Mollier at 2025-11-20T22:24:01+01:00
d/copyright: document the origin of debian-tests-data.
- - - - -
dea0ae8d by Étienne Mollier at 2025-11-20T22:24:47+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
b65426ff by Étienne Mollier at 2025-11-20T22:26:44+01:00
buildflags.patch: accomodate to C++ code.
Gbp-Dch: ignore
- - - - -
6eb5b25c by Étienne Mollier at 2025-11-20T22:27:59+01:00
d/changelog: ready for upload to unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/buildflags.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+murasaki (1.68.6-16) unstable; urgency=medium
+
+ * Team upload.
+ * d/changelog: trim trailing whitespace.
+ * buildflags.patch: new: propagate build flags. (Closes: #1119494)
+ * d/rules: activate full hardening.
+ The relocation bug documented in comment is now fixed apparently.
+ * d/copyright: drop the old FSF mail address.
+ * d/control: murasaki depends by default on gnuplot-nox.
+ This may be revisited for gnuplot-x11 if deemed more appropriate.
+ * d/copyright: document the origin of debian-tests-data.
+ * d/control: drop redundant Rules-Requires-Root: no.
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 20 Nov 2025 22:27:17 +0100
+
murasaki (1.68.6-15) unstable; urgency=medium
* Team Upload.
@@ -28,7 +43,7 @@ murasaki (1.68.6-13) unstable; urgency=medium
murasaki (1.68.6-12) unstable; urgency=medium
* Team Upload.
- * Remove recommends on murasaki-examples which is non-existent
+ * Remove recommends on murasaki-examples which is non-existent
-- Nilesh Patra <nilesh at debian.org> Sat, 20 Mar 2021 00:16:09 +0530
=====================================
debian/control
=====================================
@@ -16,7 +16,6 @@ Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/murasaki
Vcs-Git: https://salsa.debian.org/med-team/murasaki.git
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
-Rules-Requires-Root: no
Package: murasaki
Architecture: any
@@ -66,7 +65,7 @@ Package: murasaki-common
Architecture: all
Depends: ${misc:Depends},
${misc:perl},
- gnuplot | gnuplot5,
+ gnuplot-nox | gnuplot,
libbio-perl-perl,
r-cran-rocr,
imagemagick
=====================================
debian/copyright
=====================================
@@ -14,6 +14,20 @@ Files: debian/*
Copyright: © 2008-2015 Andreas Tille <tille at debian.org>
License: GPL-3+
+Files: debian-tests-data/*
+Copyright: NCBI: National Center for Biotechnology Information
+License: Public
+ You have reached the NCBI ftp server. NOTE: ALL DATA HERE IS PUBLIC,
+ NON-SENSITIVE, UNRESTRICTED SCIENTIFIC DATA SHARING AMONG SCIENTIFIC
+ COMMUNITIES. THESE SERVERS ARE INTENTIONALLY PUBLIC.
+Comment:
+ The data for tests has been referenced from NCBI FTP servers[1]. Terms
+ of use were identified in the README.ftp file at the root of the data
+ server[2].
+ .
+ [1]: https://ftp.ncbi.nlm.nih.gov/genomes/HUMAN_MICROBIOM/Bacteria/Acinetobacter_lwoffii_SH145_uid38343
+ [2]: https://ftp.ncbi.nlm.nih.gov/README.ftp
+
License: GPL-3+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
@@ -25,10 +39,6 @@ License: GPL-3+
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- .
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL-3'.
@@ -43,10 +53,6 @@ License: GPL-2+
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- .
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL-2'.
=====================================
debian/patches/buildflags.patch
=====================================
@@ -0,0 +1,19 @@
+Description: propagate Debian build flags.
+ This patch depends heavily on the rest of the patch queue and cannot
+ really be forwarded as-is without more extensive rework.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1119494
+Forwarded: not-needed
+Last-Update: 2025-11-20
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- murasaki.orig/src/Makefile
++++ murasaki/src/Makefile
+@@ -18,6 +18,7 @@
+ ##some systems might use this boost naming scheme, but they're a minority at this point
+ #LDLIBS = -lboost_regex -lboost_filesystem -lboost_iostreams
+ CPPFLAGS += $(OPTIM) $(INCLUDE) -Wall $(MARCH)
++CPPFLAGS += $(CXXFLAGS) # fix/workaround missing build flags.
+ LDFLAGS += $(LIBPATH)
+
+ ## if you're really strapped for memory, commenting this out may save you a little memory at the cost of losing the ability to handle >2Gbp sequences
=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ freebsd.patch
gcc-6.patch
fix_mpi.patch
boost-1.88.patch
+buildflags.patch
=====================================
debian/rules
=====================================
@@ -10,10 +10,7 @@ MANDIR := debian/$(DEB_SOURCE)/usr/share/man/man1
CMANDIR := debian/$(DEB_SOURCE)-common/usr/share/man/man1
MMANDIR := debian/$(DEB_SOURCE)-mpi/usr/share/man/man1
-# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-# leads to linking failure:
-# /usr/bin/ld: murasaki.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
-export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@
View it on GitLab: https://salsa.debian.org/med-team/murasaki/-/compare/e6e9596221408f416b49b85b8f5e9123e66ea39e...6eb5b25c4943dd40662e3503ebd9b85a797a522c
--
View it on GitLab: https://salsa.debian.org/med-team/murasaki/-/compare/e6e9596221408f416b49b85b8f5e9123e66ea39e...6eb5b25c4943dd40662e3503ebd9b85a797a522c
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