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
Description: Binary data