[Debian-med-packaging] Bug#890993: primer3 FTBFS on big endian: test failure
Adrian Bunk
bunk at debian.org
Wed Feb 21 12:03:43 UTC 2018
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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