Hi again, sorry for nagging again but what else than I did in
https://salsa.debian.org/med-team/snakemake/blob/master/debian/rules can I do to set PATH in pbuilder. Possibly I've understand all your hints incorrectly - the PATH is just not set inside pbuilder chroot. :-( Kind regards Andreas. On Mon, Apr 30, 2018 at 11:13:44PM +0200, Andreas Tille wrote: > On Mon, Apr 30, 2018 at 08:29:13PM +0200, Piotr Ożarowski wrote: > > [Andreas Tille, 2018-04-30] > > > Hmmm, inside pbuilder chroot the files are installed to > > > > > > > > > /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build/bin/snakemake > > > > > > while > > > > > > # pybuild --print build_dir --interpreter python3 > > > /build/snakemake-4.8.0/.pybuild/cpython3_3.6/build > > > > you invoked it outside debian/rules, without --name or PYBUILD_NAME set, > > right? > > Yes, that's right. > > > > I have no idea why since some dh-python version things are different > > > than before but wouldn't it be the best idea to let pybuild set PATH and > > > PYTHONPATH instead of setting it manually by some manual command? > > > > I meant to fix also debian/rules line 11 (you fixed line 21 only) > > I commited my last attemt to Git fixing PATH on both lines. > > I get with this d/rules: > > > ... > raise Exception("snakemake not in PATH. For testing, install snakemake > with " > Exception: snakemake not in PATH. For testing, install snakemake with 'pip > install -e .'. You should do this in a separate environment (via conda or > virtualenv). > > ---------------------------------------------------------------------- > Ran 4 tests in 0.187s > > FAILED (errors=1) > E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1: cd > /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build; python3.6 -m > nose tests > dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 returned > exit code 13 > make: *** [debian/rules:17: build] Error 25 > dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 > I: copying local configuration > E: Failed autobuilding of package > I: user script /var/cache/pbuilder/build/cow.11501/tmp/hooks/C99_failed_build > starting > root:/# echo $PATH > /usr/sbin:/usr/bin:/sbin:/bin > > > I have no idea why but the PATH does not make it through. > > I confirm if I set > > root:/build/snakemake-4.8.0# export PYBUILD_NAME=snakemake > root:/build/snakemake-4.8.0# pybuild --print build_dir --interpreter > python3 > /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build > > But why does these variables not end up in the chroot? > > Kind regards > > Andreas. > > -- > http://fam-tille.de > > -- http://fam-tille.de