[Debian-med-packaging] Bug#727491: pdb2pqr: update config.{sub, guess} for the AArch64 port

[Matthias Klose]

Package: src:pdb2pqr
Version: 1.8-1
Severity: normal
User: debian-arm at lists.debian.org
Usertags: arm64

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config.{guess,sub} files are out of date, and are not updated during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 autotools_dev (yes, underscore).

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

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/arm64-20131023/logs/buildlog_ubuntu-trusty-arm64.pdb2pqr_1.8-1_FAILEDTOBUILD.txt
The last lines of the build log are at the end of this report.

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

[...]
host_alias=''
host_cpu=''
host_os=''
host_vendor=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${prefix}/share/info'
install_dir_var=''
install_sh=''
last_prefix=''
last_website_install=''
libdir='${prefix}/lib/aarch64-linux-gnu'
libexecdir='${prefix}/lib/aarch64-linux-gnu'
localedir='${datarootdir}/locale'
localstatedir='/var'
mandir='${prefix}/share/man'
mkdir_p=''
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr'
program_transform_name='s,x,x,'
psdir='${docdir}'
py_path=''
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='/etc'
target=''
target_alias=''
target_cpu=''
target_os=''
target_vendor=''
website_install_var=''
with_pdb2pka=''

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

#define PACKAGE_NAME "PDB2PQR"
#define PACKAGE_TARNAME "pdb2pqr"
#define PACKAGE_VERSION "1.8"
#define PACKAGE_STRING "PDB2PQR 1.8"
#define PACKAGE_BUGREPORT "baker at biochem.wustl.edu"

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 CFLAGS=-g -O2 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy CPPFLAGS=-D_FORTIFY_SOURCE=2 -fPIC -I/usr/share/pyshared/numpy/core/include/numpy CXXFLAGS=-g -O2 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy FFLAGS=-g -O2 -fPIC LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro returned exit code 1
make[1]: *** [override_dh_auto_configure] Error 255
make[1]: Leaving directory `/build/buildd/pdb2pqr-1.8'
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2