Your message dated Tue, 29 May 2018 17:36:48 +0000 with message-id <e1fniyc-0006ze...@fasolo.debian.org> and subject line Bug#890993: fixed in primer3 2.4.0-2 has caused the Debian Bug report #890993, regarding primer3 FTBFS on big endian: test failure 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.) -- 890993: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890993 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: primer3 Version: 2.4.0-1 Severity: serious https://buildd.debian.org/status/package.php?p=primer3&suite=sid ... TESTING primer3_core Different number of lines [FAILED] make[2]: *** [Makefile:82: testmasker] Error 255 make[2]: *** Waiting for unfinished jobs.... mkdir: ../test/primer_list_tmp mkdir: ../test/primer1_list_tmp mkdir: ../test/primer1_th_list_tmp mkdir: ../test/th-w-other-tasks_list_tmp p3test.pl for primer3_core version 2.4.0 p3test.pl: testing ../src/primer3_core START, Wed Feb 21 09:45:45 2018 testing fatal errors... ./primer_global_err/bad_divalent_dntp_conc_1 Testing --output and --error flags on ../src/primer3_core --strict_tags ./primer_global_err/bad_divalent_dntp_conc_1.in --output ./primer_global_err/bad_divalent_dntp_conc_1.tmp --error ./primer_global_err/bad_divalent_dntp_conc_1.tmp2 ./primer_global_err/bad_divalent_dntp_conc_2 ./primer_global_err/bad_divalent_dntp_conc_3 ./primer_global_err/bad_divalent_dntp_conc_4 ./primer_global_err/bad_dna_conc ./primer_global_err/bad_first_base_index ./primer_global_err/bad_float_1 ./primer_global_err/bad_float_2 ./primer_global_err/bad_float_3 ./primer_global_err/bad_float_4 ./primer_global_err/bad_gc_1 ./primer_global_err/bad_gc_2 ./primer_global_err/bad_gc_3 ./primer_global_err/bad_gc_int_1 ./primer_global_err/bad_gc_int_2 ./primer_global_err/bad_gc_int_3 ./primer_global_err/bad_min_three_prime_distance ./primer_global_err/bad_num_ns ./primer_global_err/bad_num_ns_int ./primer_global_err/bad_product_sizes_1 ./primer_global_err/bad_product_sizes_2 ./primer_global_err/bad_product_sizes_3 ./primer_global_err/bad_product_sizes_4 ./primer_global_err/bad_salt_conc ./primer_global_err/bad_self_any ./primer_global_err/bad_self_any_int ./primer_global_err/bad_self_end ./primer_global_err/bad_self_end_int ./primer_global_err/bad_settings0 ./primer_global_err/bad_settings1 ./primer_global_err/bad_settings2 ./primer_global_err/bad_settings3 ./primer_global_err/bad_settings4 ./primer_global_err/bad_settings5 ./primer_global_err/bad_settings6 ./primer_global_err/empty_1 ./primer_global_err/empty_product_size ./primer_global_err/gc_clamp_min_size ./primer_global_err/incorrect_task ./primer_global_err/io_gc_content_obj_fn ./primer_global_err/io_obj_fn ./primer_global_err/junction_overlap_max_size ./primer_global_err/junction_overlap_min_size ./primer_global_err/max_min_tm ./primer_global_err/max_min_tm_int ./primer_global_err/max_opt_tm ./primer_global_err/max_opt_tm_int ./primer_global_err/MAX_PRIMER_LENGTH ./primer_global_err/max_size_limit_int ./primer_global_err/max_size_min_product ./primer_global_err/max_size_min_product_int ./primer_global_err/min_opt_tm ./primer_global_err/min_opt_tm_int ./primer_global_err/mishyb_obj_fn ./primer_global_err/mispr_obj_fn ./primer_global_err/must_match_length_0 ./primer_global_err/must_match_length_1 ./primer_global_err/must_match_length_10 ./primer_global_err/must_match_length_2 ./primer_global_err/must_match_length_3 ./primer_global_err/must_match_length_4 ./primer_global_err/must_match_length_5 ./primer_global_err/must_match_length_6 ./primer_global_err/must_match_length_7 ./primer_global_err/must_match_length_8 ./primer_global_err/must_match_length_9 ./primer_global_err/no_equal ./primer_global_err/no_terminal_equal ./primer_global_err/opt_max_size ./primer_global_err/opt_max_size_int ./primer_global_err/opt_min_size ./primer_global_err/opt_min_size_int ./primer_global_err/pair_mispr ./primer_global_err/pr_gc_content_obj_fn ./primer_global_err/product_size_obj_fn ./primer_global_err/product_tm_obj_fn ./primer_global_err/repeat_lib_err ./primer_global_err/repeat_lib_err1 ./primer_global_err/repeat_lib_err2 ./primer_global_err/repeat_lib_err3 ./primer_global_err/repeat_lib_err4 ./primer_global_err/repeat_lib_err5 ./primer_global_err/repeat_lib_err6 ./primer_global_err/repeat_lib_int_err ./primer_global_err/repeat_lib_int_err1 ./primer_global_err/repeat_lib_int_err2 ./primer_global_err/repeat_lib_int_err3 ./primer_global_err/repeat_lib_int_err4 ./primer_global_err/repeat_lib_int_err5 ./primer_global_err/repeat_lib_int_err6 ./primer_global_err/seq_quality1 ./primer_global_err/seq_quality2 ./primer_global_err/seq_quality3 ./primer_global_err/seq_quality4 ./primer_global_err/too_many_product_sizes ./primer_global_err/zero_min_size ./primer_global_err/zero_num_return [OK] primer_must_use_th...0s [OK] primer_task_th...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 2...[OK] Force _dpal_generic...5s [OK] primer_thal_args...[OK] Force _dpal_long_nopath_generic 1...2s [OK] primer_thal_max_seq_error...[OK] Default implementations + NO alignment 2...2s [OK] primer_first_base_index...[OK] Force _dpal_long_nopath_generic 2...0s [OK] primer_must_match...[OK] Force long maxgap1 functions 1...0s [OK] primer_masker...../src/primer3_core: Given file is not a list file: ../kmer_lists/homo_sapiens_11.list; Given file is not a list file: ../kmer_lists/homo_sapiens_16.list NON-0 EXIT: 252 [FAILED] primer_masker_formatted...../src/primer3_core: Given file is not a list file: ../kmer_lists/homo_sapiens_11.list; Given file is not a list file: ../kmer_lists/homo_sapiens_16.list NON-0 EXIT: 252 [FAILED] test_compl_error...0s [OK] test_left_to_right_of_right...0s [OK] dv_conc_vs_dntp_conc...0s [OK] primer_boundary...0s [OK] primer_boundary1...0s [OK] primer_boundary_formatted...0s [OK] primer_boundary1_formatted...1s [OK] primer3_v1_1_4_default_settings...0s [OK] primer3web_v0_4_0_default_settings...[OK] 0s [OK] primer3web_v3_0_0_default_settings...[OK] Force long maxgap1 functions 2...[OK] 9s [OK] primer3web_v4_0_0_default_settings...0s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...0s [OK] primer_internal1_formatted...1s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] primer_ok_regions2...61s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...2s [OK] primer_task...0s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_new_tasks...1s [OK] primer_new_tasks_formatted...1s [OK] primer_must_overlap_point...7s [OK] primer_overlap_junction...0s [OK] primer_all_settingsfiles...0s [OK] primer_high_tm_load_set...0s [OK] primer_high_gc_load_set...0s [OK] primer_gc_end...0s [OK] primer_check...1s [OK] primer_must_use...0s [OK] primer_must_use_formatted...0s [OK] primer_syntax...0s [OK] primer_end_pathology...0s [OK] primer_num_best...0s [OK] primer_quality_boundary...0s [OK] primer...4s [OK] primer_list_files...[OK] primer1...1s [OK] primer1_list_files...[OK] primer_mispriming...2s [OK] primer_mispriming_formatted...2s [OK] primer_mispriming_boundary1...1s [OK] primer_mispriming_boundary1_formatted...0s [OK] primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...2s [OK] primer_human...5s [OK] long_seq...1s [OK] primer_position_penalty...4s [OK] primer_position_penalty_formatted...4s [OK] p3-tmpl-mispriming...0s [OK] primer_three_prime_distance...0s [OK] primer_obj_fn...10s [OK] p3_3_prime_n...0s [OK] primer_masker...../src/primer3_core: Given file is not a list file: ../kmer_lists/homo_sapiens_11.list; Given file is not a list file: ../kmer_lists/homo_sapiens_16.list NON-0 EXIT: 252 [FAILED] primer_masker_formatted...../src/primer3_core: Given file is not a list file: ../kmer_lists/homo_sapiens_11.list; Given file is not a list file: ../kmer_lists/homo_sapiens_16.list NON-0 EXIT: 252 [FAILED] primer_mispriming_th...55s [OK] th-w-other-tasks...67s [OK] th-w-other-tasks_list_files...[OK] primer_new_tasks_th...101s [OK] primer_thermod_align...240s [OK] primer_thermod_align_formatted...239s [OK] primer1_th...727s [OK] primer1_th_list_files...[OK] primer_lib_amb_codes... NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more). starting primer_lib_amb_codes at Wed Feb 21 10:11:46 2018...1939s [OK] Tests in p3test.pl ran for 3500 s (58.3333333333333 min) DONE Wed Feb 21 10:44:05 2018 At least one test failed - [FAILED] make[2]: Leaving directory '/<<PKGBUILDDIR>>/test' dh_auto_test: cd test && make -j4 test returned exit code 2 make[1]: *** [debian/rules:16: override_dh_auto_test] Error 2
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--- Begin Message ---Source: primer3 Source-Version: 2.4.0-2 We believe that the bug you reported is fixed in the latest version of primer3, 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 890...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Liubov Chuprikova <chuprikov...@gmail.com> (supplier of updated primer3 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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 28 May 2018 13:44:30 +0000 Source: primer3 Binary: primer3 primer3-examples Architecture: source Version: 2.4.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Liubov Chuprikova <chuprikov...@gmail.com> Description: primer3 - tool to design flanking oligo nucleotides for DNA amplification primer3-examples - tool to design flanking oligo nucleotides for DNA amplification ( Closes: 890993 Changes: primer3 (2.4.0-2) unstable; urgency=medium . [ Liubov Chuprikova ] * Team upload. * Skip tests that fail on big endian Closes: #890993 * Added d/README.source with explanation why some tests are skipped * debian/patches/p3test_fix_exit_status.patch: Fix test to show correct exit status . [ Andreas Tille ] * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 Checksums-Sha1: ed7288049fca41a312d5d528d3e57e0b51be9bdc 2117 primer3_2.4.0-2.dsc 9d7f7874ef42796bd45181a610ad4d2d9193ef02 12060 primer3_2.4.0-2.debian.tar.xz 60fe57fc774ab8b537785d4c6d07e54647aabd70 5964 primer3_2.4.0-2_amd64.buildinfo Checksums-Sha256: 541ec07c9092995dd359620326630c45135321868ee2c2350ef61e1d4d67628d 2117 primer3_2.4.0-2.dsc 96247e4223393e0056a8886209b1bb37abfa7dc7fb00eca4e3e695daf62dd71e 12060 primer3_2.4.0-2.debian.tar.xz 9efe00a2d1781bee2b2cef34dbbe268dd743812b8d1a2fc232915eb20b7ef909 5964 primer3_2.4.0-2_amd64.buildinfo Files: e818c1100ac8d9bbd7785be93d6a6a35 2117 science optional primer3_2.4.0-2.dsc 94f8c7a3847e87211ecac64492ed834f 12060 science optional primer3_2.4.0-2.debian.tar.xz 1f789e2a7739fefb45e659ebd565b390 5964 science optional primer3_2.4.0-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJCBAEBCgAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlsNiusOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtH5Gw//aY7xpnFua27y6O+DCQPhbsv8Q62+N7Jmq2kX fJFdT7UL969kMAR/ZPcF44nQslVUnUR//e5Kay7Au/6tMLM1jQur5YZqCIIX97LT 3ZBaCY4dzwgx1nxQm2NGnj6msN+RDvVoYPOXoDjII04WxziyQ0jTWXnvucrXowpE OfUnnsJSCoSNVYBkBk+rNAhUZE+iuGaEy3HtE/853sgMgByTLCWkSVsV887MKijx jYLNEgNDaPkYgHkzk1j/ZwzcGywx5Hl/7lMPmccbV4PgiuSPizx3SWh1kpNfJNyM EY+vl8iGXOGzKfqInvFwgHDx51ax8VnHHeEDT6AFJNE93ajJ3RyNCorSC8vTrXtk M1uir31wKKaA7XZypOaR43wy81hTwTjum3UK6kpGX9PAE0taGvlCfEFEAZObmwI6 XqptSGxqToPQQpueOgzhFfFur+WgNbhmG5giRc7I20Y0ZJI8GYRZcm6kNrPJwtEA ugPJjN23fpnpjkKe9e2U3JauZS/UILkrxSez14dRQdCHYJGJuRe08YhZtfF+Pj7O 1KGC2bW6YML+NbyKz44tDns4OR9tzyIMs0axyi3D9xO1KjJbXicqJ7/c0f5DuwOL IZAtiYDUgVNAKLAnCRcjWLvHtRvoooECU8FEknaMGoWkRIw+FhEuGKZ3RNhCCHR7 XDMBu+s= =1S6Y -----END PGP SIGNATURE-----
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