Bug#719484: boost1.54: FTBFS: assertion fail in bjam, possibly invalid/unportable alignment assumptions
Source: boost1.54
Version: 1.54.0-2
Severity: important
Justification: fails to build from source (but built successfully in the past)
Hi,
I’ve not yet had time to look at this, but my guess is
that bjam assumes natural alignment / struct padding,
which is not portable – implicit alignment assumptions
should be made explicit, usually by adding padding
members to structs, if they are to be relied upon.
Full build log attached.
-- System Information:
Debian Release: jessie/sid
APT prefers unreleased
APT policy: (500, 'unreleased'), (500, 'unstable')
Architecture: m68k
Kernel: Linux 3.10-1-m68k
Locale: LANG=C, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/mksh-static
I: Using pkgname logfile
I: Current time: Sun Aug 11 22:51:50 UTC 2013
I: pbuilder-time-stamp: 1376261511
I: Obtaining the cached apt archive contents
I: Installing the build-deps
W: no hooks of type D found -- ignoring
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: m68k
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper (>= 9), dpkg-dev (>= 1.16.1~), zlib1g-dev, libbz2-dev, libicu-dev, mpi-default-dev, bison, flex, docbook-to-man, help2man, xsltproc, doxygen, python, python-all-dev, python3, python3-all-dev (>= 3.1)
Conflicts: libopenmpi-dev (= 1.3.2-2)
dpkg-deb: building package `pbuilder-satisfydepends-dummy' in `/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 12645 files and directories currently installed.)
Unpacking pbuilder-satisfydepends-dummy (from .../pbuilder-satisfydepends-dummy.deb) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
Package libbz2-dev is not installed.
pbuilder-satisfydepends-dummy depends on libicu-dev; however:
Package libicu-dev is not installed.
pbuilder-satisfydepends-dummy depends on mpi-default-dev; however:
Package mpi-default-dev is not installed.
pbuilder-satisfydepends-dummy depends on bison; however:
Package bison is not installed.
pbuilder-satisfydepends-dummy depends on flex; however:
Package flex is not installed.
pbuilder-satisfydepends-dummy depends on docbook-to-man; however:
Package docbook-to-man is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on xsltproc; however:
Package xsltproc is not installed.
pbuilder-satisfydepends
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
The following NEW packages will be installed:
bison{a} dh-python{a} docbook{a} docbook-to-man{a} doxygen{a} flex{a}
help2man{a} libbison-dev{a} libbz2-dev{a} libexpat1{a} libexpat1-dev{a}
libicu-dev{a} libicu48{a} libmpich2-3{a} libmpich2-dev{a}
libpython-all-dev{a} libpython-dev{a} libpython-stdlib{a} libpython2.7{a}
libpython2.7-dev{a} libpython2.7-minimal{a} libpython2.7-stdlib{a}
libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a}
libpython3.3{a} libpython3.3-dev{a} libpython3.3-minimal{a}
libpython3.3-stdlib{a} libsigsegv2{a} libsp1c2{a} libssl1.0.0{a}
libxslt1.1{a} m4{a} mime-support{a} mpi-default-dev{a} python{a}
python-all{a} python-all-dev{a} python-dev{a} python-minimal{a}
python2.7{a} python2.7-dev{a} python2.7-minimal{a} python3{a}
python3-all{a} python3-all-dev{a} python3-dev{a} python3-minimal{a}
python3.3{a} python3.3-dev{a} python3.3-minimal{a} sgml-base{a}
sgml-data{a} sp{a} xml-core{a} xsltproc{a} zlib1g-dev{a}
0 packages upgraded, 58 newly installed, 0 to remove and 0 not upgraded.
Need to get 35.3 MB/38.7 MB of archives. After unpacking 138 MB will be used.
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Get: 1 http://ftp.de.debian.org/debian-ports/ unstable/main flex m68k 2.5.35-10.1 [300 kB]
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Get: 4 http://ftp.de.debian.org/debian-ports/ unstable/main mime-support all 3.54 [36.4 kB]
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Get: 31 http://ftp.de.debian.org/debian-ports/ unstable/main doxygen m68k 1.8.4-1 [2294 kB]
Get: 32 http://ftp.de.debian.org/debian-ports/ unstable/main help2man m68k 1.43.3 [104 kB]
Get: 33 http://ftp.de.debian.org/debian-ports/ unstable/main libbz2-dev m68k 1.0.6-4 [29.4 kB]
Get: 34 http://ftp.de.debian.org/debian-ports/ unstable/main libicu-dev m68k 4.8.1.1-12 [5456 kB]
Get: 35 http://ftp.de.debian.org/debian-ports/ unstable/main libpython-dev m68k 2.7.5-3 [18.6 kB]
Get: 36 http://ftp.de.debian.org/debian-ports/ unstable/main libpython-all-dev m68k 2.7.5-3 [956 B]
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Get: 40 http://ftp.de.debian.org/debian-ports/ unstable/main python2.7-dev m68k 2.7.5-6 [260 kB]
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Get: 42 http://ftp.de.debian.org/debian-ports/ unstable/main python-all-dev m68k 2.7.5-3 [946 B]
Get: 43 http://ftp.de.debian.org/debian-ports/ unstable/main python3-all m68k 3.3.2-13 [922 B]
Get: 44 http://ftp.de.debian.org/debian-ports/ unstable/main python3.3-dev m68k 3.3.2-4 [376 kB]
Get: 45 http://ftp.de.debian.org/debian-ports/ unstable/main python3-dev m68k 3.3.2-13 [1156 B]
Get: 46 http://ftp.de.debian.org/debian-ports/ unstable/main python3-all-dev m68k 3.3.2-13 [950 B]
Get: 47 http://ftp.de.debian.org/debian-ports/ unstable/main xsltproc m68k 1.1.28-2 [120 kB]
Get: 48 http://ftp.de.debian.org/debian-ports/ unstable/main libmpich2-3 m68k 1.4.1-4.2 [767 kB]
Get: 49 http://ftp.de.debian.org/debian-ports/ unstable/main libmpich2-dev m68k 1.4.1-4.2 [979 kB]
Get: 50 http://ftp.de.debian.org/debian-ports/ unstable/main mpi-default-dev m68k 1.0.1 [3622 B]
Fetched 35.3 MB in 9min 54s (59.4 kB/s)
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0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Copying back the cached apt archive contents
I: new cache content python2.7_2.7.5-6_m68k.deb added
I: new cache content python3-minimal_3.3.2-13_m68k.deb added
I: new cache content python-minimal_2.7.5-3_m68k.deb added
I: new cache content python3.3-minimal_3.3.2-4_m68k.deb added
I: new cache content libpython-all-dev_2.7.5-3_m68k.deb added
I: new cache content libicu-dev_4.8.1.1-12_m68k.deb added
I: new cache content python3.3_3.3.2-4_m68k.deb added
I: new cache content libpython3-stdlib_3.3.2-13_m68k.deb added
I: new cache content libpython2.7-stdlib_2.7.5-6_m68k.deb added
I: new cache content python-all-dev_2.7.5-3_m68k.deb added
I: new cache content mime-support_3.54_all.deb added
I: new cache content libpython3.3-minimal_3.3.2-4_m68k.deb added
I: new cache content libicu48_4.8.1.1-12_m68k.deb added
I: new cache content libmpich2-dev_1.4.1-4.2_m68k.deb added
I: new cache content flex_2.5.35-10.1_m68k.deb added
I: new cache content libpython2.7-dev_2.7.5-6_m68k.deb added
I: new cache content python3-dev_3.3.2-13_m68k.deb added
I: new cache content libpython3.3-stdlib_3.3.2-4_m68k.deb added
I: new cache content libxslt1.1_1.1.28-2_m68k.deb added
I: new cache content python_2.7.5-3_m68k.deb added
I: new cache content python-dev_2.7.5-3_m68k.deb added
I: new cache content help2man_1.43.3_m68k.deb added
I: new cache content python3-all_3.3.2-13_m68k.deb added
I: new cache content libbison-dev_2%3a2.7.1.dfsg-1_m68k.deb added
I: new cache content python3_3.3.2-13_m68k.deb added
I: new cache content xsltproc_1.1.28-2_m68k.deb added
I: new cache content python-all_2.7.5-3_m68k.deb added
I: new cache content libpython2.7_2.7.5-6_m68k.deb added
I: new cache content docbook_4.5-5.1_all.deb added
I: new cache content libpython3-all-dev_3.3.2-13_m68k.deb added
I: new cache content python2.7-minimal_2.7.5-6_m68k.deb added
I: new cache content mpi-default-dev_1.0.1_m68k.deb added
I: new cache content doxygen_1.8.4-1_m68k.deb added
I: new cache content python3-all-dev_3.3.2-13_m68k.deb added
I: new cache content sgml-base_1.26+nmu4_all.deb added
I: new cache content libpython3.3_3.3.2-4_m68k.deb added
I: new cache content docbook-to-man_1%3a2.0.0-31_m68k.deb added
I: new cache content libpython3.3-dev_3.3.2-4_m68k.deb added
I: new cache content sgml-data_2.0.9-1_all.deb added
I: new cache content libpython-stdlib_2.7.5-3_m68k.deb added
I: new cache content libpython3-dev_3.3.2-13_m68k.deb added
I: new cache content libpython-dev_2.7.5-3_m68k.deb added
I: new cache content python3.3-dev_3.3.2-4_m68k.deb added
I: new cache content python2.7-dev_2.7.5-6_m68k.deb added
I: new cache content bison_2%3a2.7.1.dfsg-1_m68k.deb added
I: new cache content xml-core_0.13+nmu2_all.deb added
I: new cache content libpython2.7-minimal_2.7.5-6_m68k.deb added
I: new cache content libmpich2-3_1.4.1-4.2_m68k.deb added
I: new cache content dh-python_1.20130807-1_all.deb added
I: new cache content libbz2-dev_1.0.6-4_m68k.deb added
I: Copying source file
I: copying [/root/boost1.54_1.54.0-2.dsc]
I: copying [/root/boost1.54_1.54.0.orig.tar.bz2]
I: copying [/root/boost1.54_1.54.0-2.debian.tar.gz]
I: Extracting source
gpgv: keyblock resource `/tmp/buildd/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun Jul 7 05:54:06 2013 UTC using DSA key ID 21DB31C5
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./boost1.54_1.54.0-2.dsc
dpkg-source: info: extracting boost1.54 in boost1.54-1.54.0
dpkg-source: info: unpacking boost1.54_1.54.0.orig.tar.bz2
dpkg-source: info: unpacking boost1.54_1.54.0-2.debian.tar.gz
dpkg-source: info: applying 001-coroutine.patch
dpkg-source: info: applying 002-date-time.patch
dpkg-source: info: applying chrono-duration.patch
dpkg-source: info: applying boost-python-examples.patch
dpkg-source: info: applying endian.patch
dpkg-source: info: applying boost-1.44-py3.1.patch
dpkg-source: info: applying pythonid.patch
dpkg-source: info: applying mpi-allocator-c++0x.patch
dpkg-source: info: applying fix-ftbfs-python-3.3.patch
dpkg-source: info: applying hurd-clock-gettime.patch
I: Building the package
W: no hooks of type A found -- ignoring
I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" dpkg-buildpackage -us -uc -B -m'Thorsten Glaser <tg@mirbsd.de>' -B -m'Thorsten Glaser <tg@mirbsd.de>' -B -rfakeroot
dpkg-buildpackage: source package boost1.54
dpkg-buildpackage: source version 1.54.0-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build boost1.54-1.54.0
dpkg-buildpackage: host architecture m68k
fakeroot debian/rules clean
pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
py3versions: no X-Python3-Version in control file, using supported versions
dh clean --with python2 --with python3
dh_testdir
debian/rules override_dh_auto_clean
pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
py3versions: no X-Python3-Version in control file, using supported versions
make[1]: Entering directory `/tmp/buildd/boost1.54-1.54.0'
rm -rf debian/*.install
rm -rf debian/*.links
rm -rf debian/*.lintian-overrides
cd tools && /tmp/buildd/boost1.54-1.54.0/bjam -d2 --layout=system --ignore-site-config --user-config=/tmp/buildd/boost1.54-1.54.0/user-config.jam debug-symbols=on clean
/bin/sh: 1: /tmp/buildd/boost1.54-1.54.0/bjam: not found
make[1]: [override_dh_auto_clean] Error 127 (ignored)
/tmp/buildd/boost1.54-1.54.0/bjam -d2 --layout=system --ignore-site-config --user-config=/tmp/buildd/boost1.54-1.54.0/user-config.jam debug-symbols=on clean
make[1]: /tmp/buildd/boost1.54-1.54.0/bjam: Command not found
make[1]: [override_dh_auto_clean] Error 127 (ignored)
cd libs/python/pyste/install && python setup.py clean
/usr/lib/python2.7/distutils/dist.py:251: UserWarning: 'licence' distribution option is deprecated; use 'license'
warnings.warn(msg)
running clean
rm -rf libs/python/pyste/install/build
rm -rf tools/jam/src/bootstrap
rm -rf tools/jam/src/bin.*
rm -ff tools/jam/src/bjam
rm -rf tools/regression/build/bin
rm -rf bin.v2 dist
rm -rf user-config.jam
rm -rf debian/bjam.1
dh_auto_clean
make[1]: Leaving directory `/tmp/buildd/boost1.54-1.54.0'
dh_clean
debian/rules build-arch
pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
py3versions: no X-Python3-Version in control file, using supported versions
dh build-arch --with python2 --with python3
dh_testdir -a
debian/rules override_dh_auto_configure
pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
py3versions: no X-Python3-Version in control file, using supported versions
pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
py3versions: no X-Python3-Version in control file, using supported versions
make[1]: Entering directory `/tmp/buildd/boost1.54-1.54.0'
echo 'using gcc : : : <compileflags>"-D_FORTIFY_SOURCE=2" <cflags>"-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" <cxxflags>"-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" <linkflags>"-Wl,-z,relro" ;' > user-config.jam
echo "using mpi ;" >> user-config.jam
for pyver in 3.3; do \
echo "using python : $pyver : /usr ;" >> user-config.jam; \
done
rm -rf debian/*.install
rm -rf debian/*.links
rm -rf debian/*.lintian-overrides
sed -e 's/@PKGVERSION@/1.54/g' < debian/libboost-doc.doc-base.in > debian/libboost-doc.doc-base
sed -e 's/@PKGVERSION@/1.54/g' < debian/libboost-python-dev.postinst.in > debian/libboost-python-dev.postinst
sed -e 's/@PKGVERSION@/1.54/g' < debian/libboost-python-dev.prerm.in > debian/libboost-python-dev.prerm
making debhelper files for atomic...
making debhelper files for chrono...
making debhelper files for date-time...
making debhelper files for exception...
making debhelper files for filesystem...
making debhelper files for graph...
making debhelper files for graph-parallel...
making debhelper files for iostreams...
making debhelper files for locale...
making debhelper files for log...
making debhelper files for math...
making debhelper files for mpi...
making debhelper files for mpi-python...
making debhelper files for program-options...
making debhelper files for python...
making debhelper files for random...
making debhelper files for regex...
making debhelper files for serialization...
making debhelper files for signals...
making debhelper files for system...
making debhelper files for test...
making debhelper files for thread...
making debhelper files for timer...
making debhelper files for wave...
dh override_dh_auto_configure --with python2 --with python3
make[1]: Leaving directory `/tmp/buildd/boost1.54-1.54.0'
debian/rules override_dh_auto_build
pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
py3versions: no X-Python3-Version in control file, using supported versions
make[1]: Entering directory `/tmp/buildd/boost1.54-1.54.0'
../bootstrap.sh --with-icu --prefix=/tmp/buildd/boost1.54-1.54.0/debian/tmp/usr \
|| cat bootstrap.log
Building Boost.Build engine with toolset gcc...
Failed to build Boost.Build build engine
Consult 'bootstrap.log' for more details
###
### Using 'gcc' toolset.
###
rm -rf bootstrap
mkdir bootstrap
gcc -o bootstrap/jam0 command.c compile.c constants.c debug.c execcmd.c frames.c function.c glob.c hash.c hdrmacro.c headers.c jam.c jambase.c jamgram.c lists.c make.c make1.c object.c option.c output.c parse.c pathsys.c pathunix.c regexp.c rules.c scan.c search.c subst.c timestamp.c variable.c modules.c strings.c filesys.c builtins.c class.c cwd.c native.c md5.c w32_getreg.c modules/set.c modules/path.c modules/regex.c modules/property-set.c modules/sequence.c modules/order.c execunix.c fileunix.c
../bootstrap/jam0 -f build.jam --toolset=gcc --toolset-root= clean
jam0: function.c:233: check_alignment: Assertion `(size_t)s->data % sizeof( LIST * ) == 0' failed.
Aborted
help2man --name 'software build tool' --no-info ./bjam > debian/bjam.1
help2man: can't get `--help' info from ./bjam
Try `--no-discard-stderr' if option outputs to stderr
make[1]: *** [debian/bjam.1] Error 127
make[1]: Leaving directory `/tmp/buildd/boost1.54-1.54.0'
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
E: Failed autobuilding of package
I: user script /var/cache/pbuilder/build/cow.17712/tmp/hooks/C80shell-jupp starting
I: Current time: Mon Aug 12 02:08:05 UTC 2013
Build failed. Trying to invoke a shell.
Reading package lists...
Building dependency tree...
Reading state information...
Starting pkgProblemResolver with broken count: 0
Starting 2 pkgProblemResolver with broken count: 0
Done
The following NEW packages will be installed:
ed jupp less mksh
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/894 kB of archives.
After this operation, 1738 kB of additional disk space will be used.
Selecting previously unselected package less.
(Reading database ... 16171 files and directories currently installed.)
Unpacking less (from .../archives/less_458-2_m68k.deb) ...
Selecting previously unselected package ed.
Unpacking ed (from .../apt/archives/ed_1.9-2_m68k.deb) ...
Selecting previously unselected package jupp.
Unpacking jupp (from .../jupp_3.1.24-1_m68k.deb) ...
Selecting previously unselected package mksh.
Unpacking mksh (from .../archives/mksh_46-2+b1_m68k.deb) ...
Processing triggers for man-db ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for mime-support ...
Setting up less (458-2) ...
Setting up ed (1.9-2) ...
Setting up jupp (3.1.24-1) ...
update-alternatives: using /usr/bin/jupp to provide /usr/bin/editor (editor) in auto mode
Setting up mksh (46-2+b1) ...
update-alternatives: using /bin/mksh to provide /bin/ksh (ksh) in auto mode
I: user script /var/cache/pbuilder/build/cow.17712/tmp/hooks/C80shell-jupp finished
I: unmounting /run/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
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