Your message dated Thu, 22 Dec 2016 07:29:21 +0100 with message-id <20161222062920.ga27...@percival.namespace.at> and subject line Re: #822702: 0.6.8-1 now builds has caused the Debian Bug report #822702, regarding ruby-crb-blast: FTBFS: Failure: test: crb-blast should get number of reciprocals. (TestCRBBlast) to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 822702: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822702 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: ruby-crb-blast Version: 0.6.4-1 Severity: serious Justification: fails to build from source User: reproducible-bui...@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org Dear Maintainer, ruby-crb-blast fails to build from source in unstable/amd64: [..] Get:10 http://httpredir.debian.org/debian sid/main amd64 libruby2.3 amd64 2.3.0-5 [3089 kB] Get:11 http://httpredir.debian.org/debian sid/main amd64 ruby2.3 amd64 2.3.0-5 [167 kB] Get:12 http://httpredir.debian.org/debian sid/main amd64 ruby amd64 1:2.3.0+4 [10.5 kB] Get:13 http://httpredir.debian.org/debian sid/main amd64 rake all 10.5.0-2 [49.4 kB] Get:14 http://httpredir.debian.org/debian sid/main amd64 gem2deb-test-runner all 0.30.1 [19.4 kB] Get:15 http://httpredir.debian.org/debian sid/main amd64 python3-pkg-resources all 20.10.1-1 [112 kB] Get:16 http://httpredir.debian.org/debian sid/main amd64 python3-chardet all 2.3.0-2 [96.0 kB] Get:17 http://httpredir.debian.org/debian sid/main amd64 python3-six all 1.10.0-3 [14.4 kB] Get:18 http://httpredir.debian.org/debian sid/main amd64 python3-debian all 0.1.27 [50.9 kB] Get:19 http://httpredir.debian.org/debian sid/main amd64 libgmpxx4ldbl amd64 2:6.1.0+dfsg-2 [22.2 kB] Get:20 http://httpredir.debian.org/debian sid/main amd64 libgmp-dev amd64 2:6.1.0+dfsg-2 [628 kB] Get:21 http://httpredir.debian.org/debian sid/main amd64 ruby2.3-dev amd64 2.3.0-5 [1159 kB] Get:22 http://httpredir.debian.org/debian sid/main amd64 ruby-all-dev amd64 1:2.3.0+4 [9996 B] Get:23 http://httpredir.debian.org/debian sid/main amd64 ruby-setup all 3.4.1-9 [34.2 kB] Get:24 http://httpredir.debian.org/debian sid/main amd64 gem2deb all 0.30.1 [55.3 kB] Get:25 http://httpredir.debian.org/debian sid/main amd64 ruby-bio all 1.5.0-2 [701 kB] Get:26 http://httpredir.debian.org/debian sid/main amd64 ruby-facade all 1.0.7-1 [7868 B] Get:27 http://httpredir.debian.org/debian sid/main amd64 ruby-pathname2 all 1.7.4-1 [17.7 kB] Get:28 http://httpredir.debian.org/debian sid/main amd64 ruby-fixwhich all 1.0.2-1 [4014 B] Get:29 http://httpredir.debian.org/debian sid/main amd64 ruby-threach all 0.2.0-1 [5020 B] Get:30 http://httpredir.debian.org/debian sid/main amd64 ruby-trollop all 2.0-2 [16.8 kB] Get:31 http://httpredir.debian.org/debian sid/main amd64 ruby-shoulda-context all 1.2.0-1 [13.1 kB] Get:32 http://httpredir.debian.org/debian sid/main amd64 ruby-shoulda-matchers all 1.0.0~beta2-1 [18.1 kB] Get:33 http://httpredir.debian.org/debian sid/main amd64 ruby-shoulda all 3.5.0-3 [5216 B] Get:34 http://httpredir.debian.org/debian sid/main amd64 ncbi-data all 6.1.20120620-10 [3291 kB] Get:35 http://httpredir.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.3.0-1 [9278 kB] Get:36 http://httpredir.debian.org/debian sid/main amd64 help2man amd64 1.47.3 [154 kB] Fetched 20.1 MB in 0s (96.8 MB/s) Selecting previously unselected package openssl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23040 files and directories currently installed.) Preparing to unpack .../openssl_1.0.2g-2_amd64.deb ... Unpacking openssl (1.0.2g-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../ca-certificates_20160104_all.deb ... Unpacking ca-certificates (20160104) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../rubygems-integration_1.10_all.deb ... Unpacking rubygems-integration (1.10) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../ruby-did-you-mean_1.0.0-2_all.deb ... Unpacking ruby-did-you-mean (1.0.0-2) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../ruby-minitest_5.8.4-2_all.deb ... Unpacking ruby-minitest (5.8.4-2) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../ruby-power-assert_0.2.7-1_all.deb ... Unpacking ruby-power-assert (0.2.7-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../ruby-test-unit_3.1.7-2_all.deb ... Unpacking ruby-test-unit (3.1.7-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../libyaml-0-2_0.1.6-3_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.1.6-3) ... Selecting previously unselected package libruby2.3:amd64. Preparing to unpack .../libruby2.3_2.3.0-5_amd64.deb ... Unpacking libruby2.3:amd64 (2.3.0-5) ... Selecting previously unselected package ruby2.3. Preparing to unpack .../ruby2.3_2.3.0-5_amd64.deb ... Unpacking ruby2.3 (2.3.0-5) ... Selecting previously unselected package ruby. Preparing to unpack .../ruby_1%3a2.3.0+4_amd64.deb ... Unpacking ruby (1:2.3.0+4) ... Selecting previously unselected package rake. Preparing to unpack .../archives/rake_10.5.0-2_all.deb ... Unpacking rake (10.5.0-2) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../gem2deb-test-runner_0.30.1_all.deb ... Unpacking gem2deb-test-runner (0.30.1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../python3-pkg-resources_20.10.1-1_all.deb ... Unpacking python3-pkg-resources (20.10.1-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../python3-chardet_2.3.0-2_all.deb ... Unpacking python3-chardet (2.3.0-2) ... Selecting previously unselected package python3-six. Preparing to unpack .../python3-six_1.10.0-3_all.deb ... Unpacking python3-six (1.10.0-3) ... Selecting previously unselected package python3-debian. Preparing to unpack .../python3-debian_0.1.27_all.deb ... Unpacking python3-debian (0.1.27) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../libgmpxx4ldbl_2%3a6.1.0+dfsg-2_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.1.0+dfsg-2) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../libgmp-dev_2%3a6.1.0+dfsg-2_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.1.0+dfsg-2) ... Selecting previously unselected package ruby2.3-dev:amd64. Preparing to unpack .../ruby2.3-dev_2.3.0-5_amd64.deb ... Unpacking ruby2.3-dev:amd64 (2.3.0-5) ... Selecting previously unselected package ruby-all-dev:amd64. Preparing to unpack .../ruby-all-dev_1%3a2.3.0+4_amd64.deb ... Unpacking ruby-all-dev:amd64 (1:2.3.0+4) ... Selecting previously unselected package ruby-setup. Preparing to unpack .../ruby-setup_3.4.1-9_all.deb ... Unpacking ruby-setup (3.4.1-9) ... Selecting previously unselected package gem2deb. Preparing to unpack .../gem2deb_0.30.1_all.deb ... Unpacking gem2deb (0.30.1) ... Selecting previously unselected package ruby-bio. Preparing to unpack .../ruby-bio_1.5.0-2_all.deb ... Unpacking ruby-bio (1.5.0-2) ... Selecting previously unselected package ruby-facade. Preparing to unpack .../ruby-facade_1.0.7-1_all.deb ... Unpacking ruby-facade (1.0.7-1) ... Selecting previously unselected package ruby-pathname2. Preparing to unpack .../ruby-pathname2_1.7.4-1_all.deb ... Unpacking ruby-pathname2 (1.7.4-1) ... Selecting previously unselected package ruby-fixwhich. Preparing to unpack .../ruby-fixwhich_1.0.2-1_all.deb ... Unpacking ruby-fixwhich (1.0.2-1) ... Selecting previously unselected package ruby-threach. Preparing to unpack .../ruby-threach_0.2.0-1_all.deb ... Unpacking ruby-threach (0.2.0-1) ... Selecting previously unselected package ruby-trollop. Preparing to unpack .../ruby-trollop_2.0-2_all.deb ... Unpacking ruby-trollop (2.0-2) ... Selecting previously unselected package ruby-shoulda-context. Preparing to unpack .../ruby-shoulda-context_1.2.0-1_all.deb ... Unpacking ruby-shoulda-context (1.2.0-1) ... Selecting previously unselected package ruby-shoulda-matchers. Preparing to unpack .../ruby-shoulda-matchers_1.0.0~beta2-1_all.deb ... Unpacking ruby-shoulda-matchers (1.0.0~beta2-1) ... Selecting previously unselected package ruby-shoulda. Preparing to unpack .../ruby-shoulda_3.5.0-3_all.deb ... Unpacking ruby-shoulda (3.5.0-3) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../ncbi-data_6.1.20120620-10_all.deb ... Unpacking ncbi-data (6.1.20120620-10) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../ncbi-blast+_2.3.0-1_amd64.deb ... Unpacking ncbi-blast+ (2.3.0-1) ... Selecting previously unselected package help2man. Preparing to unpack .../help2man_1.47.3_amd64.deb ... Unpacking help2man (1.47.3) ... Processing triggers for man-db (2.7.5-1) ... Processing triggers for libc-bin (2.22-7) ... Setting up openssl (1.0.2g-2) ... Setting up ca-certificates (20160104) ... Setting up rubygems-integration (1.10) ... Setting up ruby-did-you-mean (1.0.0-2) ... Setting up ruby-minitest (5.8.4-2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up ruby-power-assert (0.2.7-1) ... Setting up ruby-test-unit (3.1.7-2) ... Setting up libyaml-0-2:amd64 (0.1.6-3) ... Setting up python3-pkg-resources (20.10.1-1) ... Setting up python3-chardet (2.3.0-2) ... Setting up python3-six (1.10.0-3) ... Setting up python3-debian (0.1.27) ... Setting up libgmpxx4ldbl:amd64 (2:6.1.0+dfsg-2) ... Setting up libgmp-dev:amd64 (2:6.1.0+dfsg-2) ... Setting up ncbi-data (6.1.20120620-10) ... Setting up ncbi-blast+ (2.3.0-1) ... Setting up help2man (1.47.3) ... Setting up rake (10.5.0-2) ... Setting up libruby2.3:amd64 (2.3.0-5) ... Setting up ruby2.3 (2.3.0-5) ... Setting up gem2deb-test-runner (0.30.1) ... Setting up ruby2.3-dev:amd64 (2.3.0-5) ... Setting up ruby-all-dev:amd64 (1:2.3.0+4) ... Setting up ruby-setup (3.4.1-9) ... Setting up ruby-bio (1.5.0-2) ... Setting up ruby-facade (1.0.7-1) ... Setting up ruby-pathname2 (1.7.4-1) ... Setting up ruby-fixwhich (1.0.2-1) ... Setting up ruby-threach (0.2.0-1) ... Setting up ruby-trollop (2.0-2) ... Setting up ruby-shoulda-context (1.2.0-1) ... Setting up ruby-shoulda-matchers (1.0.0~beta2-1) ... Setting up ruby-shoulda (3.5.0-3) ... Setting up ruby (1:2.3.0+4) ... Setting up gem2deb (0.30.1) ... Setting up ruby-crb-blast-build-deps (0.6.4-1) ... Processing triggers for ca-certificates (20160104) ... Updating certificates in /etc/ssl/certs... 173 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for libc-bin (2.22-7) ... dpkg-buildpackage -rfakeroot -D -us -uc -b dpkg-buildpackage: source package ruby-crb-blast dpkg-buildpackage: source version 0.6.4-1 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Michael R. Crusoe <cru...@ucdavis.edu> dpkg-source --before-build ruby-crb-blast-0.6.4 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem=ruby --with ruby dh_testdir -O--buildsystem=ruby dh_auto_clean -O--buildsystem=ruby dh_ruby --clean dh_ruby --clean dh_clean -O--buildsystem=ruby debian/rules build make: 'build' is up to date. fakeroot debian/rules binary dh binary --buildsystem=ruby --with ruby dh_testdir -O--buildsystem=ruby dh_update_autotools_config -O--buildsystem=ruby dh_auto_configure -O--buildsystem=ruby dh_ruby --configure debian/rules override_dh_auto_build make[1]: Entering directory '/home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4' dh_auto_build dh_ruby --build dh_ruby --build RUBYLIB=lib help2man --no-info --name='Conditional Reciprocal Best BLAST' \ bin/crb-blast > debian/crb-blast.1 make[1]: Leaving directory '/home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4' dh_auto_test -O--buildsystem=ruby dh_ruby --test dh_testroot -O--buildsystem=ruby dh_prep -O--buildsystem=ruby dh_auto_install -O--buildsystem=ruby dh_ruby --install /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast dh_ruby --install ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install files │ └──────────────────────────────────────────────────────────────────────────────┘ install -d /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/bin install -D -m755 /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/bin/crb-blast /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/bin/crb-blast install -d /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby install -D -m644 /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/lib/crb-blast/version.rb /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/version.rb install -D -m644 /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/lib/crb-blast/crb-blast.rb /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb install -D -m644 /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/lib/crb-blast/hit.rb /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/hit.rb install -D -m644 /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/lib/crb-blast/cmd.rb /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/cmd.rb install -D -m644 /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/lib/crb-blast.rb /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast.rb Rewriting shebang line of /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/bin/crb-blast ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/share/rubygems-integration/all/specifications/crb-blast-0.6.4.gemspec /usr/bin/ruby2.3 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby2.3 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby:. GEM_PATH=debian/ruby-crb-blast/usr/share/rubygems-integration/all:/home/lamby/.gem/ruby/2.3.0:/var/lib/gems/2.3.0:/usr/lib/x86_64-linux-gnu/rubygems-integration/2.3.0:/usr/share/rubygems-integration/2.3.0:/usr/share/rubygems-integration/all ruby2.3 -S rake -f debian/ruby-tests.rake /usr/bin/ruby2.3 -I"test" "/usr/lib/ruby/vendor_ruby/rake/rake_test_loader.rb" "test/test_test.rb" "test/test_bin.rb" "test/test_test.rb" "test/test_test2.rb" -v Loaded suite /usr/lib/ruby/vendor_ruby/rake/rake_test_loader Started Test2CRBBlast: test: crb-blast should add secondary hits. : .: (0.439440) test: crb-blast should break input file into no more pieces than there are sequences. :.: (0.397928) test: crb-blast should break input file into pieces. :.: (0.382934) test: crb-blast should find reciprocals. : .: (0.427060) test: crb-blast should get non reciprocal hits. : .: (0.423871) test: crb-blast should load output should check if the databases exist. :.: (0.362060) test: crb-blast should run blast should check if the databases exist yet. :.: (0.399319) test: crb-blast should setup2 should run ok. : .: (0.450815) TestBinary: test: crb-blast should run binary. : .: (0.091697) TestCRBBlast: test: crb-blast should check if contig has reciprocal hit. :.: (0.477356) test: crb-blast should determine that the target is a protein sequence. :.: (0.436480) test: crb-blast should find reciprocals. : .: (0.447236) test: crb-blast should get number of reciprocals. : F =============================================================================== Failure: test: crb-blast should get number of reciprocals. (TestCRBBlast) /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/test/test_test.rb:96:in `block (2 levels) in <class:TestCRBBlast>' <11> expected but was <10> diff: ? 11 ? 0 =============================================================================== : (0.487708) test: crb-blast should get query results. : .: (0.528858) test: crb-blast should load outputs. : .: (0.529476) test: crb-blast should not find fake scaffold name. : .: (0.574174) test: crb-blast should output all reciprocal hits. : .: (0.458777) test: crb-blast should raise error when files don't exist. :.: (0.440840) test: crb-blast should run blast. : .: (0.495463) test: crb-blast should run. : .: (0.522633) test: crb-blast should setup should run ok. : .: (0.556309) Finished in 9.332857226 seconds. ------ 21 tests, 38 assertions, 1 failures, 0 errors, 0 pendings, 0 omissions, 0 notifications 95.2381% passed ------ 2.25 tests/s, 4.07 assertions/s rake aborted! Command failed with status (1): [ruby -I"test" "/usr/lib/ruby/vendor_ruby/rake/rake_test_loader.rb" "test/test_test.rb" "test/test_bin.rb" "test/test_test.rb" "test/test_test2.rb" -v] Tasks: TOP => default (See full trace by running task with --trace) ERROR: Test "ruby2.3" failed. Exiting. dh_auto_install: dh_ruby --install /home/lamby/temp/cdt.20160426185902.AbZmPxe6Mi.ruby-crb-blast/ruby-crb-blast-0.6.4/debian/ruby-crb-blast returned exit code 1 debian/rules:18: recipe for target 'binary' failed make: *** [binary] Error 1 [..] The full build log is attached. Regards, -- ,''`. : :' : Chris Lamb `. `'` la...@debian.org / chris-lamb.co.uk `-
ruby-crb-blast.0.6.4-1.unstable.amd64.log.txt.gz
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--- Begin Message ---Version: 0.6.8-1 New version builds on the buildds.
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