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" <[email protected]>
> 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"
> <[email protected]> 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, "[email protected] on behalf of Carnë
> Draug" <[email protected] on behalf of [email protected]> wrote:
> >
> > On 23 January 2017 at 12:40, Andreas Tille
> <[email protected]> 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
