Re: Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie) (original) (raw)

Hi Steffen,

On Wed, Sep 20, 2017 at 10:52:55PM +0200, Steffen Möller wrote:

... Error testing example --- tests/example6.out 2017-09-20 13:07:01.000000000 +0000 +++ example6.out 2017-09-20 13:13:53.186064608 +0000 @@ -1 +1,5 @@ - gi|110640213|ref|NC_008253.1| 2852852 8:T>A +- gi|110640213|ref|NC_008253.1| 148810 10:A>G,13:C>G ++ gi|110640213|ref|NC_008253.1| 1093035 2:T>G,15:A>T +- gi|110640213|ref|NC_008253.1| 905664 6:A>G,7:G>T +- gi|110640213|ref|NC_008253.1| 4930433 4:G>T,6:C>G debian/rules:46: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 1 make[1]: Leaving directory '/build/bowtie-1.2.1.1+dfsg' debian/rules:14: recipe for target 'build' failed make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 I: copying local configuration E: Failed autobuilding of package I: user script /var/cache/pbuilder/build/cow.8814/tmp/hooks/C99_failed_build starting root@wr-linux01:/# cd build/bowtie-1.2.1.1+dfsg/ root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# ./bowtie Segmentation fault root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# ./bowtie --version Segmentation fault

You need to setup a pbuilder hook to be able to stop the build and end up inside the pbuilder chroot.

Hm. I feel like building that outside the chroot ;)

root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# apt-get install gdb Reading package lists... Done Building dependency tree
Reading state information... Done The following additional packages will be installed: libbabeltrace-ctf1 libbabeltrace1 libdw1 libelf1 libmpdec2 libpopt0 libpython3.5 libpython3.5-minimal libpython3.5-stdlib ... root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# gdb --args bowtie-align-s --wrapper basic-0 GNU gdb (Debian 7.12-6) 7.12.0.20161007-git ... Type "apropos word" to search for commands related to "word"... Reading symbols from bowtie-align-s...done. (gdb) run Starting program: /build/bowtie-1.2.1.1+dfsg/bowtie-align-s --wrapper basic-0 [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

Program received signal SIGSEGV, Segmentation fault. 0x00007ffff652003e in dlsym () from /lib/x86_64-linux-gnu/libdl.so.2 (gdb)

Same happens when testing bowtie-align-l.

Does this ring a bell somehow?

Sounds like a missing dynamic library?

ldd bowtie-align-l gives me

        linux-vdso.so.1 (0x00007ffcb73f3000)         libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007faf4d456000)         libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007faf4d239000)         libtbb.so.2 => /usr/lib/x86_64-linux-gnu/libtbb.so.2 (0x00007faf4cffb000)         libtbbmalloc_proxy.so.2 => /usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2 (0x00007faf4cdf7000)         libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007faf4ca78000)         libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007faf4c774000)         libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007faf4c55d000)         libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007faf4c1c0000)         /lib64/ld-linux-x86-64.so.2 (0x00007faf4d94c000)         libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007faf4bfbc000)         librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007faf4bdb4000)         libatomic.so.1 => /usr/lib/x86_64-linux-gnu/libatomic.so.1 (0x00007faf4bbac000)         libtbbmalloc.so.2 => /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2 (0x00007faf4b96e000)

anything reported missing by ldd in your pbuilder environment?

Inside pbuilder chroot:

root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# ldd bowtie-align-l
linux-vdso.so.1 (0x00007ffe9511a000) /usr/lib/cowdancer/libcowdancer.so (0x00007f56d5209000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f56d4feb000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f56d4dce000) libtbb.so.2 => /lib/x86_64-linux-gnu/libtbb.so.2 (0x00007f56d4b90000) libtbbmalloc_proxy.so.2 => /lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2 (0x00007f56d498c000) libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f56d460b000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f56d4307000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f56d40f0000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f56d3d53000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f56d3b4f000) libncurses.so.5 => /lib/x86_64-linux-gnu/libncurses.so.5 (0x00007f56d392b000) libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 (0x00007f56d36ff000) /lib64/ld-linux-x86-64.so.2 (0x0000561b175bb000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f56d34f7000) libatomic.so.1 => /lib/x86_64-linux-gnu/libatomic.so.1 (0x00007f56d32ef000) libtbbmalloc.so.2 => /lib/x86_64-linux-gnu/libtbbmalloc.so.2 (0x00007f56d30b1000)

That looks pretty similar and no visible missing.

Kind regards

 Andreas.

-- http://fam-tille.de

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