On 20.09.17 15:44, Andreas Tille wrote: > [switching back to list discussion also involving debian-mentors. > Please see the gdb output below I get when installing gdb inside the > pbuilder chroot.] > > Hi Steffen, > > On Wed, Sep 20, 2017 at 02:26:20PM +0200, Steffen Möller wrote: >>>> /build/bowtie-1.2.1.1+dfsg# ./bowtie -a -v 2 e_coli --suppress 1,5,6,7 -c >>>> ATGCATCATGCGCCAT >>>> Segmentation fault >>>> >>>> >>>> I intended to open an issue on Github but when doing so I wanted to leave >>>> a proof that we are using the latest upstream version: >>>> >>>> >>>> /build/bowtie-1.2.1.1+dfsg# ./bowtie -v >>>> Segmentation fault >>>> >>>> >>>> Hups, I think something is wrong at our side and the build has a problem. >>>> >>>> Has anybody some spare cylces to track this down? >>> Any volunteer? >> >> Not really, except that on my virtual machine "bowtie -v" shows the >> expected (long) usage information. > I guess you try to test the *existing* bowtie package. Please note > that I was talking about the new version in Git which I try to build > and the segfault happens in the pbuilder chroot (I just learned that > you are rarely using pbuilder - see subsequent fast5 uploads :-P ).
I was using it (for -2 and later versions at least), but for some weird reason that issue did not surface in pbulder (if you allow me to point to your -5 upload) or was only spotted during my building of a reverse dependency. > So please try to build latest Git (git.debian.org seems to be offline > currently). It is back. > I get: > > ... > 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 ;) > >> So, I cannot immediately reproduce >> the behaviour you observe. What does "bowtie --version" do for you? > See above - but we are most probably talking about different things. Hm. So, I get this: example5 OK # reads processed: 5 # reads with at least one reported alignment: 5 (100.00%) # reads that failed to align: 0 (0.00%) Reported 5 alignments to 1 output stream(s) debian/tests/run-unit-test: 18: debian/tests/run-unit-test: ---: not found Error testing example --- tests/example6.out 2017-09-20 22:18:16.708036897 +0200 +++ example6.out 2017-09-20 22:25:50.634724676 +0200 @@ -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 '/home/moeller/git/debian-med/bowtie' debian/rules:14: recipe for target 'binary' failed make: *** [binary] Error 2 I interpret this like the first 5 examples being fine, just the 6th failing. When executign directly, I get $ ./bowtie -a --best --strata -v 2 --suppress 1,5,6,7 e_coli -c ATGCATCATGCGCCAT - 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 # reads processed: 5 # reads with at least one reported alignment: 5 (100.00%) # reads that failed to align: 0 (0.00%) So, this works, basically. But the tests/example6.out file has only the first line of the five returned. > >> Should we add "bowtie -v" as an autotest, just testing that it does not >> crash but that it exits with a bad code ( == 1) ? > I assume this test will not be necessary since it is not really > `bowtie -v` which breaks but *any* call of bowtie segfaults inside > the pbuilder environment. I cannot confirm that - but I had not built inside pbuilder. >> Another question to me is why we do not have a bowtie-dbgsym package. >> Where is it? > No idea but hey, I installed gdb into the pbuilder environment and did: > > 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? Many thanks and greetings Steffen
