[Debian-med-packaging] Bug#744664: staden-io-lib: run dh-autoreconf to update config.{sub, guess} and {libtool, aclocal}.m4

[Matthias Klose]

Package: src:staden-io-lib
Version: 1.13.2-3
User: debian-devel at lists.debian.org
Usertags: autoreconf

The package fails to build on ppc64el (powerpc64le-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the config.{guess,sub} files are out of date, and are not updated during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
powerpc64le in the configure, aclocal.m4 and/or libtool.m4 file(s)
should print some lines. It is not enough to just update the
config.guess and config.sub files.

The full build log can be found at:
http://people.debian.org/~doko/logs/ppc64el-20140414/buildlog_ubuntu-trusty-ppc64el.staden-io-lib_1.13.2-3ubuntu1_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.

[...]
libtool: install: /usr/bin/install -c scramble /build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/bin/scramble
libtool: install: /usr/bin/install -c scram_merge /build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/bin/scram_merge
libtool: install: /usr/bin/install -c scram_pileup /build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/bin/scram_pileup
libtool: install: /usr/bin/install -c scram_flagstat /build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/bin/scram_flagstat
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/build/buildd/staden-io-lib-1.13.2/progs'
make[2]: Leaving directory `/build/buildd/staden-io-lib-1.13.2/progs'
Making install in tests
make[2]: Entering directory `/build/buildd/staden-io-lib-1.13.2/tests'
make[3]: Entering directory `/build/buildd/staden-io-lib-1.13.2/tests'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/build/buildd/staden-io-lib-1.13.2/tests'
make[2]: Leaving directory `/build/buildd/staden-io-lib-1.13.2/tests'
make[2]: Entering directory `/build/buildd/staden-io-lib-1.13.2'
make[3]: Entering directory `/build/buildd/staden-io-lib-1.13.2'
test -z "/usr/bin" || /bin/mkdir -p "/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/bin"
 /usr/bin/install -c io_lib-config '/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/bin'
test -z "/usr/share/man/man1" || /bin/mkdir -p "/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/share/man/man1"
 /usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/share/man/man1'
test -z "/usr/share/man/man3" || /bin/mkdir -p "/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/share/man/man3"
 /usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/share/man/man3'
test -z "/usr/share/man/man4" || /bin/mkdir -p "/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/share/man/man4"
 /usr/bin/install -c -m 644 man/man4/Read.4 '/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/share/man/man4'
test -z "/usr/include/io_lib" || /bin/mkdir -p "/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/include/io_lib"
 /usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/seqIOCTF.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h '/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/include/io_lib'
 /usr/bin/install -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib_config.h io_lib/md5.h io_lib/thread_pool.h '/build/buildd/staden-io-lib-1.13.2/debian/tmp/usr/include/io_lib'
make[3]: Leaving directory `/build/buildd/staden-io-lib-1.13.2'
make[2]: Leaving directory `/build/buildd/staden-io-lib-1.13.2'
make[1]: Leaving directory `/build/buildd/staden-io-lib-1.13.2'
   debian/rules override_dh_install
make[1]: Entering directory `/build/buildd/staden-io-lib-1.13.2'
dh_install
mkdir -p /build/buildd/staden-io-lib-1.13.2/debian/libstaden-read-dev/usr/bin
mv /build/buildd/staden-io-lib-1.13.2/debian/staden-io-lib-utils/usr/bin/io_lib-config /build/buildd/staden-io-lib-1.13.2/debian/libstaden-read-dev/usr/bin
find debian/tmp -name "*.la" -delete
# Call d-shlibmove to comply with library packaging guide
d-shlibmove --commit \
		    --multiarch \
		    --devunversioned \
		    --override s/libbz2-1.0-dev/libbz2-dev/ \
		    --override s/libcurl-gnutls4-dev/libcurl4-gnutls-dev/ \
		    --movedev "debian/tmp/usr/include" usr \
		    debian/tmp/usr/lib/*/libstaden-read.so
Library package automatic movement utility
/usr/bin/d-shlibmove: expected [debian/tmp/usr/lib/*/libstaden-read.so] to be a symlink, but it is not
make[1]: *** [override_dh_install] Error 1
make[1]: Leaving directory `/build/buildd/staden-io-lib-1.13.2'
make: *** [binary-arch] Error 2
dpkg-buildpackage: error: /usr/bin/fakeroot debian/rules binary-arch gave error exit status 2