[Reproducible-builds] Bug#822702: ruby-crb-blast: FTBFS: Failure: test: crb-blast should get number of reciprocals. (TestCRBBlast)
Chris Lamb
lamby at debian.org
Tue Apr 26 18:04:21 UTC 2016
Source: ruby-crb-blast
Version: 0.6.4-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at 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.
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(Reading database ... 23040 files and directories currently installed.)
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Unpacking openssl (1.0.2g-2) ...
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Unpacking ca-certificates (20160104) ...
Selecting previously unselected package rubygems-integration.
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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.
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Selecting previously unselected package ruby-power-assert.
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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) ...
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Unpacking rake (10.5.0-2) ...
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Unpacking gem2deb-test-runner (0.30.1) ...
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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.
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Unpacking python3-six (1.10.0-3) ...
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Selecting previously unselected package libgmpxx4ldbl:amd64.
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Unpacking libgmpxx4ldbl:amd64 (2:6.1.0+dfsg-2) ...
Selecting previously unselected package libgmp-dev:amd64.
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Unpacking libgmp-dev:amd64 (2:6.1.0+dfsg-2) ...
Selecting previously unselected package ruby2.3-dev:amd64.
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Unpacking ruby2.3-dev:amd64 (2.3.0-5) ...
Selecting previously unselected package ruby-all-dev:amd64.
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Unpacking ruby-all-dev:amd64 (1:2.3.0+4) ...
Selecting previously unselected package ruby-setup.
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Unpacking gem2deb (0.30.1) ...
Selecting previously unselected package ruby-bio.
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Unpacking ruby-bio (1.5.0-2) ...
Selecting previously unselected package ruby-facade.
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Unpacking ruby-facade (1.0.7-1) ...
Selecting previously unselected package ruby-pathname2.
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Unpacking ruby-pathname2 (1.7.4-1) ...
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Selecting previously unselected package ruby-threach.
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Unpacking ruby-threach (0.2.0-1) ...
Selecting previously unselected package ruby-trollop.
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Selecting previously unselected package ruby-shoulda-context.
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Selecting previously unselected package ruby-shoulda-matchers.
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Unpacking ruby-shoulda (3.5.0-3) ...
Selecting previously unselected package ncbi-data.
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Unpacking ncbi-data (6.1.20120620-10) ...
Selecting previously unselected package ncbi-blast+.
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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 <crusoe at 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
`. `'` lamby at debian.org / chris-lamb.co.uk
`-
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