[Debian-med-packaging] Bug#744421: clustalo: run dh-autoreconf to update config.{sub, guess} and {libtool, aclocal}.m4

[Matthias Klose]

Package: src:clustalo
Version: 1.2.0-1
User: debian-devel at lists.debian.org
Usertags: autoreconf

The package fails to build on arm64 (aarch64-linux-gnu), because the
config.{guess,sub} files are out of date, and are not updated during
the build.  If possible, please do not update these files directly,
but build-depend on autotools-dev instead, and use the tools provided
by autotools-dev to update these files.

  - For dh, call dh --with autoreconf.

  - For cdbs based build systems, include
    /usr/share/cdbs/1/rules/autoreconf.mk

  - For other rules files, call dh_autoreconf before calling
    configure (in the build or configure target), and call
    dh_autoreconf_clean before dh_clean in the clean target.

For combining autoreconf and autotools_dev, see bug #698765.

After the build on any architecture, and before a clean, a grep for
aarch64 in the config.sub file(s) should print some lines.

The full build log can be found at:
http://people.debian.org/~doko/logs/arm64-20140414/buildlog_ubuntu-trusty-arm64.clustalo_1.2.0-1_FAILEDTOBUILD.txt
The last lines of the build log are at the end of this report.

Please note that these builds were done in an Ubuntu development,
environment there may be a few false positives in these bug reports.

See https://wiki.debian.org/qa.debian.org/FTBFS for a guide how to
address these.

[...]
infodir='${prefix}/share/info'
install_sh='$(SHELL) /build/buildd/clustalo-1.2.0/install-sh'
libdir='${prefix}/lib/aarch64-linux-gnu'
libexecdir='${prefix}/lib/aarch64-linux-gnu'
localedir='${datarootdir}/locale'
localstatedir='/var'
lt_ECHO='echo'
mandir='${prefix}/share/man'
mkdir_p='/bin/mkdir -p'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

#define PACKAGE_NAME "Clustal Omega"
#define PACKAGE_TARNAME "clustal-omega"
#define PACKAGE_VERSION "1.2.0"
#define PACKAGE_STRING "Clustal Omega 1.2.0"
#define PACKAGE_BUGREPORT "clustalw at ucd.ie"
#define PACKAGE "clustal-omega"
#define VERSION "1.2.0"
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define __EXTENSIONS__ 1
#define _ALL_SOURCE 1
#define _GNU_SOURCE 1
#define _POSIX_PTHREAD_SEMANTICS 1
#define _TANDEM_SOURCE 1

configure: exit 1
dh_auto_configure: ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=${prefix}/include --mandir=${prefix}/share/man --infodir=${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --libdir=${prefix}/lib/aarch64-linux-gnu --libexecdir=${prefix}/lib/aarch64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking returned exit code 1
make: *** [build-arch] Error 255
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2