On Thu, 2017-09-21 at 15:12 +0200, Andreas Tille wrote:
> Hi Phil,
>
> thanks for your attempt to help.
>
> On Thu, Sep 21, 2017 at 12:15:50PM +0100, Phil Wyett wrote:
> > 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.
>
> That's redundant since debian/compat=10 is used.
>
> > 2. At error the unit tests should dump a diff to std error.
> >
> > The script is very old style and has errors.
>
> Well, its old style but you replaced `` by $() which has the same
> result und adding "" around variables is probably better style but
> not solving any problem here. Or am I missing something?
>
> > // 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.
>
> That's no change at all. The point is that *after* outputting the
> diff (which is the very same as without your changes) the segfault
> happens again. The *very* strange thing is that the test suite
> works until example5 bit if I force an error before running the
> script and run it manually inside the chroot
>
>
> 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# sh debian/tests/run-unit-test
> test_at_build_time
> Segmentation fault
> debian/tests/run-unit-test: 18: debian/tests/run-unit-test: ---: not found
> Error testing example
> --- tests/example1.out 2017-09-21 12:55:02.000000000 +0000
> +++ example1.out 2017-09-21 13:07:54.755536757 +0000
> @@ -1,5 +0,0 @@
> -- gi|110640213|ref|NC_008253.1| 148810 10:A>G,13:C>G
> -- gi|110640213|ref|NC_008253.1| 2852852 8:T>A
> -- gi|110640213|ref|NC_008253.1| 4930433 4:G>T,6:C>G
> -- gi|110640213|ref|NC_008253.1| 905664 6:A>G,7:G>T
> -+ gi|110640213|ref|NC_008253.1| 1093035 2:T>G,15:A>T
> root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# bash debian/tests/run-unit-test
> test_at_build_time
> debian/tests/run-unit-test: line 27: 24652 Segmentation fault bowtie -a
> -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT > example1.out
> debian/tests/run-unit-test: line 18: ---: command not found
> Error testing example
> --- tests/example1.out 2017-09-21 12:55:02.000000000 +0000
> +++ example1.out 2017-09-21 13:08:04.855722853 +0000
> @@ -1,5 +0,0 @@
> -- gi|110640213|ref|NC_008253.1| 148810 10:A>G,13:C>G
> -- gi|110640213|ref|NC_008253.1| 2852852 8:T>A
> -- gi|110640213|ref|NC_008253.1| 4930433 4:G>T,6:C>G
> -- gi|110640213|ref|NC_008253.1| 905664 6:A>G,7:G>T
> -+ gi|110640213|ref|NC_008253.1| 1093035 2:T>G,15:A>T
>
>
>
> The problem happens even for example1. So I keep on thinking that
> running inside the chroot is evident to reproduce the problem and
> the script itself is not the problem even if it produces strange
> effects. I would love to hear further opinions to the gdb output
> I provided in my first mail to this thread on debian-mentors.
>
> Kind regards
>
> Andreas.
> Hi, True with compat 10 --parallel nor needed. The shell script changes were due to getting garbled output at end of pbuilder builds. The changes rectify that. Still looking at why I get seg faults sometimes and not others. I have added a few post release git fixes to my tree and will test later. https://github.com/BenLangmead/bowtie/commit/1f37e940f3df319b78eee0e0f0f87c3d30a d95de https://github.com/BenLangmead/bowtie/commit/e31c2e127a5605f7105bd6c31a13a895310 9fa3f 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
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