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

On Thu, 2017-09-21 at 12:15 +0100, Phil Wyett wrote:

On Thu, 2017-09-21 at 08:27 +0200, Andreas Tille wrote:

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.

Hi,

Not part of the project and saw this on mentors.

  1. Parallel build.

// Diff starts  on line below. diff --git a/debian/rules b/debian/rules index 7919361..b536ce7 100755 --- a/debian/rules +++ b/debian/rules @@ -11,7 +11,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all  pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')    %: -       dh $@ +       dh $@ --parallel    override_dh_auto_build:         $(MAKE) allall // Diff ends on line above.

  1. At error the unit tests should dump a diff to std error.

The script is very old style and has errors.

// Diff starts  on line below. diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test index dfcb0e5..1335a4b 100644 --- a/debian/tests/run-unit-test +++ b/debian/tests/run-unit-test @@ -5,19 +5,19 @@ if [ "$1" = "test_at_build_time" ] ; then  else      pkg=bowtie      if [ "$ADTTMP" = "" ] ; then -      ADTTMP=mktemp -d /tmp/${pkg}-test.XXXXXX +      ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)      fi -    mkdir -p $ADTTMP/tests -    cp -a debian/tests/example* $ADTTMP/tests -    cd $ADTTMP -    cp -a /usr/share/doc/bowtie/examples/indexes $ADTTMP +    mkdir -p "$ADTTMP"/tests +    cp -a debian/tests/example* "$ADTTMP"/tests +    cd "$ADTTMP" +    cp -a /usr/share/doc/bowtie/examples/indexes "$ADTTMP"  fi    check_result () { -    EDIFF=diff -u tests/$1.out $1.out +    EDIFF=$(diff -u tests/"$1".out "$1".out)      if ! $EDIFF ; then          echo "Error testing example" -        echo $EDIFF +        echo "$EDIFF"          exit 1      else          echo "$1 OK" // Diff ends on line above.

A diff is now outputted at example6.

Regards

Phil

Hi,

There is a live upstream issue when using --best and --strata.

https://github.com/BenLangmead/bowtie/issues/58https://github.com/BenLangmead/bo wtie/issues/58

Maybe you should seek help with example6 upstream.

Regards

Phil

-- *** If this is a mailing list, I am subscribed, no need to CC me.***

Playing the game for the games sake.

Web: https://kathenas.org

GitLab: https://gitlab.com/kathenas

Twitter: kathenasorg

Instagram: kathenasorg

GPG: 1B97 6556 913F 73F3 9C9B 25C4 2961 D9B6 2017 A57A

Attachment:signature.asc
Description: This is a digitally signed message part

Reply to: