[med-svn] [Git][med-team/staden-io-lib][master] 6 commits: Switch to -O0 on armhf, mips.
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Jan 1 16:13:01 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / staden-io-lib
Commits:
d9476772 by Michael R. Crusoe at 2019-01-01T15:15:51Z
Switch to -O0 on armhf, mips.
- - - - -
0056fb47 by Michael R. Crusoe at 2019-01-01T15:16:36Z
Standards-Version: 4.3.0
- - - - -
30dd5e68 by Michael R. Crusoe at 2019-01-01T15:16:39Z
adjust substitution variables
- - - - -
129253be by Michael R. Crusoe at 2019-01-01T15:17:36Z
tweak patch to make `cme fix dpkg` happy
- - - - -
adf59b65 by Michael R. Crusoe at 2019-01-01T15:19:38Z
mark staden-io-lib-examples as Multi-Arch: foreign
- - - - -
b46425d0 by Michael R. Crusoe at 2019-01-01T15:29:33Z
Spelling: independant→independent
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/patches/1b28b6a.patch
- debian/patches/serial-tests.patch
- debian/patches/series
- + debian/patches/spelling
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,17 @@
+staden-io-lib (1.14.11-6) UNRELEASED; urgency=medium
+
+ * Switch to -O0 on armhf, mips. Closes: #916262
+ * Standards-Version: 4.3.0
+ * debian/control: mark staden-io-lib-examples as Multi-Arch: foreign
+ * changelog & debian/patches/spelling: spelling (independent)
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 01 Jan 2019 01:26:00 -0800
+
staden-io-lib (1.14.11-5) unstable; urgency=medium
* Fix hash table HASH_INT_KEYS on 32-bit platforms (thanks to
upstream Rob Davies)
- * Do not attempt to run test suite for architecture independant
+ * Do not attempt to run test suite for architecture independent
build.
* Use serial tests
=====================================
debian/control
=====================================
@@ -2,14 +2,15 @@ Source: staden-io-lib
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>,
- Thorsten Alteholz <debian at alteholz.de>
+ Thorsten Alteholz <debian at alteholz.de>,
+ Michael R. Crusoe <michael.crusoe at gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
zlib1g-dev,
libcurl4-gnutls-dev | libcurl4-nss-dev,
d-shlibs
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/staden-io-lib
Vcs-Git: https://salsa.debian.org/med-team/staden-io-lib.git
Homepage: https://github.com/jkbonfield/io_lib
@@ -34,7 +35,8 @@ Package: libstaden-read-dev
Architecture: any
Section: libdevel
Depends: libstaden-read13 (= ${binary:Version}),
- ${misc:Depends}
+ ${misc:Depends},
+ ${devlibs:Depends}
Description: development files for libstaden-read
This package contains the header and development files needed to build
programs and packages using the Staden io_lib.
@@ -62,8 +64,8 @@ Description: Staden library for reading and writing DNA sequencing results
Package: staden-io-lib-examples
Architecture: all
-Depends: ${shlibs:Depends},
- ${misc:Depends}
+Multi-Arch: foreign
+Depends: ${misc:Depends}
Recommends: staden-io-lib-utils
Description: programs for manipulating DNA sequencing files (usage examples)
The io_lib from the Staden package is a library of file reading and writing
=====================================
debian/patches/1b28b6a.patch
=====================================
@@ -6,7 +6,6 @@ Subject: [PATCH] Fix rANS codec on x32 architecture.
This is 32-bit usage of a 64-bit processor. See
https://wiki.debian.org/X32Port
-
Should fix the bug found here:
https://buildd.debian.org/status/fetch.php?pkg=staden-io-lib&arch=x32&ver=1.14.11-3&stamp=1543952038&raw=0
---
=====================================
debian/patches/serial-tests.patch
=====================================
@@ -2,9 +2,9 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Fri, 07 Dec 2018 12:55:44 +0100
Description: Use serial tests
---- a/configure.in
-+++ b/configure.in
-@@ -2,7 +2,7 @@ dnl Process this file with autoconf to p
+--- staden-io-lib.orig/configure.in
++++ staden-io-lib/configure.in
+@@ -2,7 +2,7 @@
AC_INIT(io_lib, 1.14.11)
AC_CONFIG_HEADERS([io_lib_config.h])
AC_CONFIG_MACRO_DIR([m4])
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ d4591b5.patch
1b28b6a.patch
242cd6b.patch
serial-tests.patch
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,46 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Spelling: independant→independent
+--- staden-io-lib.orig/io_lib/mach-io.c
++++ staden-io-lib/io_lib/mach-io.c
+@@ -81,7 +81,7 @@
+ */
+
+ /*
+- * Machine independant io:
++ * Machine independent io:
+ * For reading and writing to big-endian and little-endian files
+ *
+ * Routines available:
+--- staden-io-lib.orig/io_lib/mach-io.h
++++ staden-io-lib/io_lib/mach-io.h
+@@ -83,7 +83,7 @@
+ #ifndef _mach_io_h
+ #define _mach_io_h
+ /*
+- * Machine independant io
++ * Machine independent io
+ * For reading and writing to big-endian and little-endian files
+ *
+ * Routines available:
+--- staden-io-lib.orig/io_lib/seqIOABI.c
++++ staden-io-lib/io_lib/seqIOABI.c
+@@ -98,7 +98,7 @@
+ * 30.07.91 SD Those ole FWO_ field blues
+ * 17.09.91 LFW changed STLOUIS compilation flag to SAVE_EDITS
+ * and AUTO_CLIP
+- * 25.10.91 SD Machine independant I/O...removed BIGENDIAN flag
++ * 25.10.91 SD Machine independent I/O...removed BIGENDIAN flag
+ * 21.07.92 LFW Added finding of primer position
+ * 11.11.92 LFW added section to actually check that the trace it
+ * is trying to open is an ALF file using traceType sub
+--- staden-io-lib.orig/io_lib/seqIOALF.c
++++ staden-io-lib/io_lib/seqIOALF.c
+@@ -101,7 +101,7 @@
+ * We now treat them as unsigned.
+ * 17.09.91 LFW changed STLOUIS compilation flag to SAVE_EDITS
+ * and AUTO_CLIP
+- * 25.10.91 SD Machine independant I/O...removed BIGENDIAN flag
++ * 25.10.91 SD Machine independent I/O...removed BIGENDIAN flag
+ * 25.11.91 SD There was a hard limit (of 1024) for allocation of
+ * space for number of bases, yet program would
+ * read in more if there were any, causing nasties to happen.
=====================================
debian/rules
=====================================
@@ -5,6 +5,10 @@ devpkg=$(libpkg)-dev
srcname=staden-io-lib
testdir=debian/$(srcname)-examples/usr/share/doc/$(srcname)/test
+ifneq (,$(filter $(DEB_HOST_ARCH),armhf mips))
+ DEB_CFLAGS_MAINT_APPEND+=-O0
+endif
+
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
@@ -43,7 +47,7 @@ endif
override_dh_install-indep:
dh_install -i
mkdir -p $(testdir)
- # fix path to staden-io-lib executable in examples
+ # fix path to staden-io-lib executable in examples
for tst in `ls tests/*.test` ; do \
sed -e 's#\.\./$$top_builddir/progs/#/usr/bin/#' -e 's#$$top_builddir/progs/#/usr/bin/#' $${tst} > $(testdir)/`basename $${tst}` ; \
done
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/compare/2e04f013013b695d7eee3aaf1022f5f526725f29...b46425d0cef9d69ba59d7f27ba110c8ececb4918
--
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/compare/2e04f013013b695d7eee3aaf1022f5f526725f29...b46425d0cef9d69ba59d7f27ba110c8ececb4918
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