Your message dated Fri, 27 Apr 2018 12:00:24 +0000
with message-id <[email protected]>
and subject line Bug#892066: fixed in ruby-crb-blast 0.6.9-2
has caused the Debian Bug report #892066,
regarding ruby-crb-blast FTBFS: test failures
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.
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--
892066: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=892066
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ruby-crb-blast
Version: 0.6.9-1
Severity: serious
https://buildd.debian.org/status/fetch.php?pkg=ruby-crb-blast&arch=all&ver=0.6.9-1&stamp=1520009847&raw=0
...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Run tests for ruby2.3 from debian/ruby-tests.rake │
└──────────────────────────────────────────────────────────────────────────────┘
RUBYLIB=/<<PKGBUILDDIR>>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby:.
GEM_PATH=debian/ruby-crb-blast/usr/share/rubygems-integration/all:/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 -w -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"
"test/test_test3.rb" -v
/<<PKGBUILDDIR>>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:348:
warning: shadowing outer local variable - name
/<<PKGBUILDDIR>>/debian/ruby-crb-blast/usr/lib/ruby/vendor_ruby/crb-blast/crb-blast.rb:348:
warning: shadowing outer local variable - seq
/usr/lib/ruby/vendor_ruby/fixwhich.rb:3: warning: assigned but unused variable
- e
/usr/lib/ruby/vendor_ruby/threach.rb:7: warning: `*' interpreted as argument
prefix
/usr/lib/ruby/vendor_ruby/threach.rb:13: warning: shadowing outer local
variable - i
/<<PKGBUILDDIR>>/test/test_test3.rb:28: warning: assigned but unused variable -
blaster
/<<PKGBUILDDIR>>/test/test_test3.rb:44: warning: assigned but unused variable -
dbs
/<<PKGBUILDDIR>>/test/test_test3.rb:45: warning: assigned but unused variable -
run
/<<PKGBUILDDIR>>/test/test_test3.rb:46: warning: assigned but unused variable -
load
Loaded suite /usr/lib/ruby/vendor_ruby/rake/rake_test_loader
Started
Test2CRBBlast:
test: crb-blast should add secondary hits. : E
===============================================================================
Error: test: crb-blast should add secondary hits. (Test2CRBBlast):
RuntimeError: BLAST Error:
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-perc_identity float_value]
[-qcov_hsp_perc float_value] [-max_hsps int_value]
[-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-version]
DESCRIPTION
Nucleotide-Nucleotide BLAST 2.7.1+
--- End Message ---
--- Begin Message ---
Source: ruby-crb-blast
Source-Version: 0.6.9-2
We believe that the bug you reported is fixed in the latest version of
ruby-crb-blast, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <[email protected]> (supplier of updated
ruby-crb-blast package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 16 Mar 2018 15:09:31 -0700
Source: ruby-crb-blast
Binary: ruby-crb-blast
Architecture: source all
Version: 0.6.9-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Ruby Extras Maintainers
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Description:
ruby-crb-blast - Run conditional reciprocal best blast
Closes: 892066
Changes:
ruby-crb-blast (0.6.9-2) unstable; urgency=medium
.
* Run tests with actual number of cores, not 6. (Closes: 892066)
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--- End Message ---
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