Re: RFP for bioperl's Bio-EUtilities
On Mon, Jan 23, 2017 at 08:57:35PM +0000, Fields, Christopher J wrote:
> Looks like there are two unrelated errors.
>
> The first is from a missing dependency (Bio::ASN1::EntrezGene), which is really optional (the comp test should skip that directory). The other is from XML::Simple, which is unusual; I’m wondering whether the underlying XML parser is checking the XML schema for the test reports. Any idea what the specific XML::SAX backend parser module used was?
Sorry, I've sended a wrong version of the log with missing
Build-Depends. Please check again.
Andreas.
> Hi Christopher,
>
> On Mon, Jan 23, 2017 at 07:25:38PM +0000, Fields, Christopher J wrote:
> > Just ran tests on a non-networked laptop (both latest from Github and the 1.75 release from CPAN) and they were fine, all passed and the relevant network tests are skipped. Can you be more specific as to the build failure?
>
> In the download tarball from CPAN the 1.75 release has only a t directory
> (no xt). I've attached the relevant part of the build log.
>
> Hope this helps
>
> Andreas.
>
> > On 1/23/17, 12:46 PM, "Fields, Christopher J" <cjfields@illinois.edu> wrote:
> >
> > Actually, when looking at this, the network tests are already in ‘xt’ on the repo, and should only tested when making a release:
> >
> > https://github.com/bioperl/Bio-EUtilities/tree/master/xt/release
> >
> > I’ll pull down the latest CPAN and run it from a non-networked computer to see if I can pinpoint what the problem is.
> >
> > chris
> >
> > On 1/23/17, 9:12 AM, "Fields, Christopher J" <cjfields@illinois.edu> wrote:
> >
> > My suggestion is to take the avenue of easiest solution first, then most stable solution long-term if needed.
> >
> > The easiest may be to move the network tests to ‘xt’, which as Carnė mentioned would be run upon release only. This should be easy enough w/ a Dist::Zilla release. Longer term a mock setup may be better.
> >
> > chris
> >
> > On 1/23/17, 9:03 AM, "carandraug@gmail.com on behalf of Carnë Draug" <carandraug@gmail.com on behalf of carandraug+dev@gmail.com> wrote:
> >
> > On 23 January 2017 at 12:40, Andreas Tille <andreas@an3as.eu> wrote:
> > > Hi Carnė,
> > >
> > > On Fri, Jan 20, 2017 at 05:44:00PM +0000, Carnė Draug wrote:
> > >> I have filled a RFP (bug # 852004) for bioperl's Bio-EUtilities
> > >> package [1]. Unlike Bio-Coordinate, which was split from bioperl and
> > >> was recently packaged in Debian, Bio-EUtilities development started
> > >> already after bioperl commenced its splitting.
> > >>
> > >> I was wondering if it was possible for the debian-med team to package
> > >> it. While I am not a debian maintainer, I am one of the
> > >> Bio-EUtilities developers, have an interest on seeing it packaged in
> > >> Debian, and I'm willing to support it upstream.
> > >
> > > I have commited some initial packaging to
> > >
> > > https://anonscm.debian.org/git/debian-med/libbio-eutilities-perl.git
> > >
> > > This build fails due to the failure of several tests - as far as I can
> > > see due to the attempt to access the internet. It would help if you
> > > could provide an option: "Just do all tests than can be done offline"
> > > since the Debian packaging process needs to run fully offline.
> > >
> > > Kind regards
> > >
> > > Andreas.
> >
> > I have asked on #debian-perl if there was any standard method or
> > debian preferred method to skip those tests and apparently there is
> > none. But there are some suggestions that seem to be common and
> > acceptable to the Debian.
> >
> > 1. check for an environment variable that defines whether network
> > tests should be skipped. Some variables used in Debian are
> > NO_NETWORK, NOINTERNET, TEST_INTERNET, and NETWORK_TESTING. See for
> > example discussion on debian bug #764868 [1]
> >
> > 2. mock EUtilities using Test::LWP::UserAgent. This is probably the
> > most involved but probably the technically most correct way. It has
> > the problem of not failing if upstream service ever changes (but maybe
> > if that happens and only the testsuite notices, then this whole module
> > is not needed).
> >
> > 3. move all tests from t/ to xt/ so that they are only ran at release
> > time by the package author "since obviously if the author isn't
> > running their own tests before releasing, you already have a bigger
> > problem"
> >
> > Note that the test must not even attempt network access [2] so
> > skipping the test because a ping to the entrez servers fails is also
> > not allowed.
> >
> > I'm CC'ing Chris Fields (also developer on Bio-EUtilities) to discuss
> > what would Debian and upstream prefer.
> >
> > Carnë
> >
> > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=764868
> > [2] https://www.debian.org/doc/debian-policy/
> >
> >
> >
> >
> >
> >
>
> --
> http://fam-tille.de
>
>
--
http://fam-tille.de
dh_auto_configure
perl -I. Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/build/libbio-eutilities-perl-1.75=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/libbio-eutilities-perl-1.75=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro"
Warning: prerequisite Text::CSV 0 not found.
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::EUtilities
Writing MYMETA.yml and MYMETA.json
dh_auto_build
make -j2
make[1]: Entering directory '/build/libbio-eutilities-perl-1.75'
cp bin/bp_genbank_ref_extractor blib/script/bp_genbank_ref_extractor
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank_ref_extractor
cp lib/Bio/Tools/EUtilities/EUtilDataI.pm blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm
cp lib/Bio/Tools/EUtilities/Summary/ItemContainerI.pm blib/lib/Bio/Tools/EUtilities/Summary/ItemContainerI.pm
cp lib/Bio/Tools/EUtilities/Link.pm blib/lib/Bio/Tools/EUtilities/Link.pm
cp lib/Bio/Tools/EUtilities/Summary/DocSum.pm blib/lib/Bio/Tools/EUtilities/Summary/DocSum.pm
cp lib/Bio/Tools/EUtilities/Query.pm blib/lib/Bio/Tools/EUtilities/Query.pm
cp lib/Bio/Tools/EUtilities/Info/FieldInfo.pm blib/lib/Bio/Tools/EUtilities/Info/FieldInfo.pm
cp lib/Bio/Tools/EUtilities/Link/UrlLink.pm blib/lib/Bio/Tools/EUtilities/Link/UrlLink.pm
cp lib/Bio/Tools/EUtilities/Summary.pm blib/lib/Bio/Tools/EUtilities/Summary.pm
cp lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm blib/lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm
cp lib/Bio/DB/EUtilities.pm blib/lib/Bio/DB/EUtilities.pm
cp lib/Bio/Tools/EUtilities/Link/LinkSet.pm blib/lib/Bio/Tools/EUtilities/Link/LinkSet.pm
cp lib/Bio/Tools/EUtilities/Info.pm blib/lib/Bio/Tools/EUtilities/Info.pm
cp lib/Bio/Tools/EUtilities.pm blib/lib/Bio/Tools/EUtilities.pm
cp lib/Bio/Tools/EUtilities/Info/LinkInfo.pm blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm
cp lib/Bio/Tools/EUtilities/HistoryI.pm blib/lib/Bio/Tools/EUtilities/HistoryI.pm
cp lib/Bio/Tools/EUtilities/Summary/Item.pm blib/lib/Bio/Tools/EUtilities/Summary/Item.pm
cp lib/Bio/Tools/EUtilities/EUtilParameters.pm blib/lib/Bio/Tools/EUtilities/EUtilParameters.pm
cp lib/Bio/Tools/EUtilities/History.pm blib/lib/Bio/Tools/EUtilities/History.pm
cp bin/bp_einfo blib/script/bp_einfo
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_einfo
Manifying 2 pod documents
Manifying 18 pod documents
make[1]: Leaving directory '/build/libbio-eutilities-perl-1.75'
dh_auto_test
make -j2 test TEST_VERBOSE=1
make[1]: Entering directory '/build/libbio-eutilities-perl-1.75'
PERL_DL_NONLAZY=1 PERL_USE_UNSAFE_INC=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t
t/00-compile.t ..............
1..20
ok 1 - Bio/DB/EUtilities.pm loaded ok
ok 2 - Bio/Tools/EUtilities.pm loaded ok
ok 3 - Bio/Tools/EUtilities/EUtilDataI.pm loaded ok
ok 4 - Bio/Tools/EUtilities/EUtilParameters.pm loaded ok
ok 5 - Bio/Tools/EUtilities/History.pm loaded ok
ok 6 - Bio/Tools/EUtilities/HistoryI.pm loaded ok
ok 7 - Bio/Tools/EUtilities/Info.pm loaded ok
ok 8 - Bio/Tools/EUtilities/Info/FieldInfo.pm loaded ok
ok 9 - Bio/Tools/EUtilities/Info/LinkInfo.pm loaded ok
ok 10 - Bio/Tools/EUtilities/Link.pm loaded ok
ok 11 - Bio/Tools/EUtilities/Link/LinkSet.pm loaded ok
ok 12 - Bio/Tools/EUtilities/Link/UrlLink.pm loaded ok
ok 13 - Bio/Tools/EUtilities/Query.pm loaded ok
ok 14 - Bio/Tools/EUtilities/Query/GlobalQuery.pm loaded ok
ok 15 - Bio/Tools/EUtilities/Summary.pm loaded ok
ok 16 - Bio/Tools/EUtilities/Summary/DocSum.pm loaded ok
ok 17 - Bio/Tools/EUtilities/Summary/Item.pm loaded ok
ok 18 - Bio/Tools/EUtilities/Summary/ItemContainerI.pm loaded ok
ok 19 - bin/bp_einfo compiled ok
ok 20 - bin/bp_genbank_ref_extractor compiled ok
ok
t/author-mojibake.t ......... skipped: these tests are for testing by the author
t/author-pod-syntax.t ....... skipped: these tests are for testing by the author
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 before it could output anything.
t/egquery.t .................
1..18
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 18/18 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 before it could output anything.
t/einfo.t ...................
1..49
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 49/49 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 just after 1.
t/elink_acheck.t ............
1..128
ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link'
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 127/128 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 just after 1.
t/elink_lcheck.t ............
1..62
ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link'
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 61/62 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 just after 1.
t/elink_llinks.t ............
1..84
ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link'
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 83/84 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 just after 1.
t/elink_ncheck.t ............
1..58
ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link'
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 57/58 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 just after 1.
t/elink_neighbor.t ..........
1..61
ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link'
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 60/61 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 just after 1.
t/elink_neighbor_history.t ..
1..63
ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link'
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 62/63 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 just after 1.
t/elink_scores.t ............
1..56
ok 1 - An object of class 'Bio::Tools::EUtilities::Link' isa 'Bio::Tools::EUtilities::Link'
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 55/56 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 just after 4.
t/epost.t ...................
1..15
ok 1 - An object of class 'Bio::Tools::EUtilities::Query' isa 'Bio::Tools::EUtilities::EUtilDataI'
ok 2 - An object of class 'Bio::Tools::EUtilities::Query' isa 'Bio::Tools::EUtilities::Query'
ok 3 - eutil
ok 4 - datatype
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 11/15 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 before it could output anything.
t/esearch.t .................
1..31
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 31/31 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 2 before it could output anything.
t/espell.t ..................
1..20
Dubious, test returned 2 (wstat 512, 0x200)
Failed 20/20 subtests
http error : connection refused
XML::Simple called at /build/libbio-eutilities-perl-1.75/blib/lib/Bio/Tools/EUtilities.pm line 140.
# Looks like your test exited with 255 just after 1.
t/esummary.t ................
1..81
ok 1 - An object of class 'Bio::Tools::EUtilities::Summary' isa 'Bio::Tools::EUtilities::Summary'
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 80/81 subtests
t/EUtilParameters.t .........
1..12
ok 1
ok 2 - An object of class 'HTTP::Request' isa 'HTTP::Request'
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - available_parameters
ok 10 - available_parameters
ok 11 - get_parameters
ok 12 - get_parameters
ok
t/release-eol.t ............. skipped: these tests are for release candidate testing
t/release-EUtilities.t ...... skipped: these tests are for release candidate testing
Test Summary Report
-------------------
t/egquery.t (Wstat: 65280 Tests: 0 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 18 tests but ran 0.
t/einfo.t (Wstat: 65280 Tests: 0 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 49 tests but ran 0.
t/elink_acheck.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 128 tests but ran 1.
t/elink_lcheck.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 62 tests but ran 1.
t/elink_llinks.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 84 tests but ran 1.
t/elink_ncheck.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 58 tests but ran 1.
t/elink_neighbor.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 61 tests but ran 1.
t/elink_neighbor_history.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 63 tests but ran 1.
t/elink_scores.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 56 tests but ran 1.
t/epost.t (Wstat: 65280 Tests: 4 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 15 tests but ran 4.
t/esearch.t (Wstat: 65280 Tests: 0 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 31 tests but ran 0.
t/espell.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 20 tests but ran 0.
t/esummary.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 81 tests but ran 1.
Files=19, Tests=44, 5 wallclock secs ( 0.08 usr 0.02 sys + 3.68 cusr 0.43 csys = 4.21 CPU)
Result: FAIL
Failed 13/19 test programs. 0/44 subtests failed.
Makefile:1003: recipe for target 'test_dynamic' failed
make[1]: *** [test_dynamic] Error 255
make[1]: Leaving directory '/build/libbio-eutilities-perl-1.75'
dh_auto_test: make -j2 test TEST_VERBOSE=1 returned exit code 2
debian/rules:4: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
[0mI: copying local configuration[0m
[0;31mE: Failed autobuilding of package[0m
[0mI: user script /var/cache/pbuilder/build/cow.2108/tmp/hooks/C99_failed_build starting[0m
Installing convenience apps: mc less bash-completion
[0mI: user script /var/cache/pbuilder/build/cow.2108/tmp/hooks/C99_failed_build finished[0m
[0mI: unmounting /var/cache/pbuilder/extra/release filesystem[0m
[0mI: unmounting /dev/shm filesystem[0m
[0mI: unmounting dev/pts filesystem[0m
[0mI: unmounting run/shm filesystem[0m
[0mI: unmounting proc filesystem[0m
[0mI: unmounting sys filesystem[0m
link_acheck.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 128 tests but ran 1.
t/elink_lcheck.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 62 tests but ran 1.
t/elink_llinks.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 84 tests but ran 1.
t/elink_ncheck.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 58 tests but ran 1.
t/elink_neighbor.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 61 tests but ran 1.
t/elink_neighbor_history.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 63 tests but ran 1.
t/elink_scores.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 56 tests but ran 1.
t/epost.t (Wstat: 65280 Tests: 4 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 15 tests but ran 4.
t/esearch.t (Wstat: 65280 Tests: 0 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 31 tests but ran 0.
t/espell.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 20 tests but ran 0.
t/esummary.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 81 tests but ran 1.
Files=19, Tests=44, 5 wallclock secs ( 0.08 usr 0.02 sys + 3.68 cusr 0.43 csys = 4.21 CPU)
Result: FAIL
Failed 13/19 test programs. 0/44 subtests failed.
Makefile:1003: recipe for target 'test_dynamic' failed
make[1]: *** [test_dynamic] Error 255
make[1]: Leaving directory '/build/libbio-eutilities-perl-1.75'
dh_auto_test: make -j2 test TEST_VERBOSE=1 returned exit code 2
debian/rules:4: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
[0mI: copying local configuration[0m
[0;31mE: Failed autobuilding of package[0m
[0mI: user script /var/cache/pbuilder/build/cow.2108/tmp/hooks/C99_failed_build starting[0m
Installing convenience apps: mc less bash-completion
[0mI: user script /var/cache/pbuilder/build/cow.2108/tmp/hooks/C99_failed_build finished[0m
[0mI: unmounting /var/cache/pbuilder/extra/release filesystem[0m
[0mI: unmounting /dev/shm filesystem[0m
[0mI: unmounting dev/pts filesystem[0m
[0mI: unmounting run/shm filesystem[0m
[0mI: unmounting proc filesystem[0m
[0mI: unmounting sys filesystem[0m
[0mI: Cleaning COW directory[0m
[0mI: forking: rm -rf /var/cache/pbuilder/build/cow.2108[0m
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