debian/changelog

+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@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@lists.alioth.debian.org>
 Uploaders: Charles Plessy <plessy@debian.org>,
            Andreas Tille <tille@debian.org>,
-           Thorsten Alteholz <debian@alteholz.de>
+           Thorsten Alteholz <debian@alteholz.de>,
+	   Michael R. Crusoe <michael.crusoe@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@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

+From: Michael R. Crusoe <michael.crusoe@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
 
 %: