Running phase: unpackPhase unpacking source archive /nix/store/p69aqq50wyh98ycsdmqxfh9bwj5wx4p7-source source root is source/src Running phase: patchPhase Running phase: updateAutotoolsGnuConfigScriptsPhase Running phase: configurePhase no configure script, doing nothing Running phase: buildPhase build flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash CC=cc CXX=c++ AR=ar RANLIB=ranlib no windows cc -c -g -Wall -O2 primer3_boulder_main.c cc -c -g -Wall -O2 -o format_output.o format_output.c cc -c -g -Wall -O2 -o read_boulder.o read_boulder.c cc -c -g -Wall -O2 -o print_boulder.o print_boulder.c c++ -c -g -Wall -O2 -std=c++11 -o libprimer3.o libprimer3.cc cc -c -g -Wall -O2 -o p3_seq_lib.o p3_seq_lib.c cc -c -g -Wall -O2 -o dpal_primer.o dpal.c cc -c -g -Wall -O2 -ffloat-store -o thal_primer.o thal.c cc -c -g -Wall -O2 -ffloat-store -o thal_parameters.o thal_parameters.c cc -g -Wall -O2 -c -o oligotm.o oligotm.c cc -g -Wall -O2 -c -o amplicontm.o amplicontm.c cc -c -g -Wall -O2 masker.c cc -c -g -Wall -o ntdpal_main.o ntdpal_main.c cc -c -g -Wall -O2 -o dpal.o dpal.c cc -c -g -Wall -O2 -o thal_main.o thal_main.c cc -c -g -Wall -O2 -ffloat-store -o thal.o thal.c format_output.c: In function 'print_seq': format_output.c:418:61: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 418 | if (pa->pick_right_primer && (&retval->rev) != NULL | ^~ In file included from format_output.h:41, from format_output.c:40: libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:429:60: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 429 | if (pa->pick_left_primer && (&retval->fwd) != NULL | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c: In function 'format_oligos': format_output.c:851:51: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 851 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL ) | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:858:55: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress] 858 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL ) | ^~ libprimer3.h:927:20: note: 'intl' declared here 927 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:865:52: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 865 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:888:49: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 888 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL ) | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:907:53: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress] 907 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL ) | ^~ libprimer3.h:927:20: note: 'intl' declared here 927 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:926:50: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 926 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a libprimer3.cc: In function 'char* strstr_nocase(char*, char*)': libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free] 6168 | else {free(tmp); return p;} | ^ libprimer3.cc:6168:15: note: call to 'void free(void*)' here 6168 | else {free(tmp); return p;} | ~~~~^~~~~ ar rv liboligotm.a oligotm.o cc -g -Wall -O2 -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm ar: creating liboligotm.a a - oligotm.o ranlib liboligotm.a cc -g -Wall -O2 -o oligotm oligotm_main.c liboligotm.a -lm ar rv libamplicontm.a amplicontm.o ar: creating libamplicontm.a a - amplicontm.o ranlib libamplicontm.a cc -g -Wall -O2 -o amplicon3_core amplicontm_main.c libamplicontm.a -lm ar rv libmasker.a masker.o ar: creating libmasker.a a - masker.o ranlib libmasker.a cc -g -o ntdpal ntdpal_main.o dpal.o ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o ranlib libdpal.a cc -g -o ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating libprimer3.a a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a c++ -g -Wall -O2 -std=c++11 -lstdc++ -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm c++ -g -Wall -O2 -std=c++11 -lstdc++ -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm Running phase: checkPhase check flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash CC=cc CXX=c++ AR=ar RANLIB=ranlib VERBOSE=y test no windows cd ../test; make test make[1]: Entering directory '/build/source/test' cd ../src; make perl cmdline_test.pl perl oligotm_test.pl echo; echo; echo 'TESTING ALIGNMENT CALCS'; echo; perl dpal_test.pl ; echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ; echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ; echo; echo; echo 'TESTING amplicon3_core'; echo; perl a3test.pl echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl make[2]: Entering directory '/build/source/src' no windows TESTING ALIGNMENT CALCS TESTING THERMODYNAMIC ALIGNMENT CALCS TESTING MASKER TESTING amplicon3_core TESTING primer3_core make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/source/src' Error handling of too-long sequence... TESTING Tm CALCULATIONS TESTING command line arguments Test 1... Tm tests nr 1-[OK] Default implementations + alignment...Default implementations...a3test.pl for amplicon3_core version 2.5.0 a3test.pl: testing ../src/amplicon3_core START, Sat Sep 5 12:13:48 2026 plain_WNT9B...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 2.6.1 [OK] Test 2... p3test.pl: testing ../src/primer3_core START, Sat Sep 5 12:13:48 2026 0s [OK] plain_TBX18...Error handling of too-long sequence... testing fatal errors... ./primer_global_err/annealing_temp_salt Testing --output and --error flags on ../src/primer3_core --strict_tags ./primer_global_err/annealing_temp_salt.in --output ./primer_global_err/annealing_temp_salt.tmp --error ./primer_global_err/annealing_temp_salt.tmp2 1................................... [OK] Default implementations + alignment...0s [OK] plain_RYK... ./primer_global_err/bad_divalent_dntp_conc_1 [OK] Test 3... 0s [OK] plain_WNT2...[OK] Test 4... 0s [OK] plain_ROCK2... ./primer_global_err/bad_divalent_dntp_conc_2 0s [OK] plain_SFRP3...[OK] Test 5... ./primer_global_err/bad_divalent_dntp_conc_3 0s [OK] plain_IFT20...[OK] Passed all tests - [OK] ./primer_global_err/bad_divalent_dntp_conc_4 0s [OK] plain_DVL1... ./primer_global_err/bad_dna_conc 0s [OK] plain_IFT88... ./primer_global_err/bad_first_base_index 0s [OK] plain_FZD2...0s [OK] plain_GAPDH... ./primer_global_err/bad_float_1 0s [OK] plain_WNT1... ./primer_global_err/bad_float_2 0s [OK] plain_MYH6... ./primer_global_err/bad_float_3 0s [OK] plain_on_command_line_WNT9B... ./primer_global_err/bad_float_4 0s [OK] plain_on_command_line_TBX18... ./primer_global_err/bad_gc_1 0s [OK] plain_on_command_line_RYK...0s [OK] plain_on_command_line_WNT2... ./primer_global_err/bad_gc_2 0s [OK] plain_on_command_line_ROCK2... ./primer_global_err/bad_gc_3 0s [OK] plain_on_command_line_SFRP3... ./primer_global_err/bad_gc_int_1 0s [OK] plain_on_command_line_IFT20...0s [OK] plain_on_command_line_DVL1... ./primer_global_err/bad_gc_int_2 0s [OK] plain_on_command_line_IFT88... ./primer_global_err/bad_gc_int_3 0s [OK] plain_on_command_line_FZD2...50: [OK] 0s [OK] plain_on_command_line_GAPDH... ./primer_global_err/bad_min_three_prime_distance 0s [OK] plain_on_command_line_WNT1... ./primer_global_err/bad_num_ns 0s [OK] plain_on_command_line_MYH6... ./primer_global_err/bad_num_ns_int 0s [OK] classic_WNT9B...0s [OK] classic_TBX18... ./primer_global_err/bad_product_sizes_1 0s [OK] classic_RYK... ./primer_global_err/bad_product_sizes_2 0s [OK] classic_WNT2...0s [OK] classic_ROCK2...0s [OK] classic_SFRP3... ./primer_global_err/bad_product_sizes_3 0s [OK] classic_IFT20...0s [OK] classic_DVL1... ./primer_global_err/bad_product_sizes_4 0s [OK] classic_IFT88... ./primer_global_err/bad_salt_conc 0s [OK] classic_FZD2...0s [OK] ./primer_global_err/bad_self_any classic_GAPDH...0s [OK] classic_WNT1... ./primer_global_err/bad_self_any_int 0s [OK] classic_MYH6...0s [OK] heli_WNT9B... ./primer_global_err/bad_self_end ./primer_global_err/bad_self_end_int ./primer_global_err/bad_settings0 ./primer_global_err/bad_settings1 0s [OK] heli_TBX18... ./primer_global_err/bad_settings2 ./primer_global_err/bad_settings3 ./primer_global_err/bad_settings4 ./primer_global_err/bad_settings5 0s [OK] heli_RYK... ./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 0s [OK] heli_WNT2... ./primer_global_err/io_gc_content_obj_fn ./primer_global_err/io_obj_fn ./primer_global_err/junction_overlap_max_size 0s [OK] heli_ROCK2... ./primer_global_err/junction_overlap_min_size ./primer_global_err/max_annealing_temp ./primer_global_err/max_min_bound ./primer_global_err/max_min_bound_int 0s [OK] heli_SFRP3... ./primer_global_err/max_min_tm ./primer_global_err/max_min_tm_int ./primer_global_err/max_opt_bound ./primer_global_err/max_opt_bound_int 0s [OK] heli_IFT20... ./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_limit_with_overhang 0s [OK] heli_DVL1... ./primer_global_err/max_size_min_product ./primer_global_err/max_size_min_product_int ./primer_global_err/min_opt_tm 0s [OK] heli_IFT88... ./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 0s [OK] heli_FZD2... ./primer_global_err/must_match_length_1 ./primer_global_err/must_match_length_10 ./primer_global_err/must_match_length_2 0s [OK] heli_GAPDH... ./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 0s [OK] heli_WNT1... ./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 0s [OK] heli_MYH6... ./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 0s [OK] long_WNT9B... ./primer_global_err/repeat_lib_err2 0s [OK] long_TBX18... ./primer_global_err/repeat_lib_err3 0s [OK] long_RYK... ./primer_global_err/repeat_lib_err4 0s [OK] long_WNT2... ./primer_global_err/repeat_lib_err5 0s [OK] long_ROCK2...0s [OK] long_SFRP3... ./primer_global_err/repeat_lib_err6 0s [OK] long_IFT20... ./primer_global_err/repeat_lib_int_err 0s [OK] long_DVL1... ./primer_global_err/repeat_lib_int_err1 0s [OK] long_IFT88...0s [OK] long_FZD2... ./primer_global_err/repeat_lib_int_err2 0s [OK] long_GAPDH... ./primer_global_err/repeat_lib_int_err3 0s [OK] long_WNT1... ./primer_global_err/repeat_lib_int_err4 0s [OK] long_MYH6... ./primer_global_err/repeat_lib_int_err5 0s [OK] optimal_WNT9B... ./primer_global_err/repeat_lib_int_err6 0s [OK] optimal_TBX18... ./primer_global_err/seq_quality1 0s [OK] optimal_RYK... ./primer_global_err/seq_quality2 0s [OK] optimal_WNT2... ./primer_global_err/seq_quality3 0s [OK] optimal_ROCK2... ./primer_global_err/seq_quality4 0s [OK] optimal_SFRP3... ./primer_global_err/too_many_product_sizes 0s [OK] optimal_IFT20... ./primer_global_err/zero_min_size 0s [OK] optimal_DVL1...0s [OK] optimal_IFT88... ./primer_global_err/zero_num_return 0s [OK] optimal_FZD2...[OK] primer_must_use_th...0s [OK] optimal_GAPDH...0s [OK] optimal_WNT1...0s [OK] optimal_MYH6...0s [OK] only_mv_WNT9B...0s [OK] only_mv_TBX18...0s [OK] only_mv_RYK...0s [OK] only_mv_WNT2...0s [OK] only_mv_ROCK2...0s [OK] only_mv_SFRP3...0s [OK] only_mv_IFT20...0s [OK] only_mv_DVL1...0s [OK] only_mv_IFT88...0s [OK] primer_sec_struct_dpal...0s [OK] only_mv_FZD2...0s [OK] only_mv_GAPDH...0s [OK] only_mv_WNT1...0s [OK] only_mv_MYH6...0s [OK] no_dmso_WNT9B...0s [OK] no_dmso_TBX18...0s [OK] no_dmso_RYK...0s [OK] no_dmso_WNT2...0s [OK] no_dmso_ROCK2...0s [OK] no_dmso_SFRP3...0s [OK] no_dmso_IFT20...0s [OK] no_dmso_DVL1...0s [OK] no_dmso_IFT88...0s [OK] no_dmso_FZD2...0s [OK] no_dmso_GAPDH...0s [OK] no_dmso_WNT1...1s [OK] no_dmso_MYH6...1s [OK] primer_task_th...0s [OK] Tests in a3test.pl ran for 1 s (0.0166666666666667 min) DONE Sat Sep 5 12:13:49 2026 Passed all tests - [OK] [OK] [OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 1...0s [OK] primer_thal_args...[OK] Default implementations + NO alignment 2...[OK] Force _dpal_generic...0s [OK] primer_thal_max_seq_error...0s [OK] primer_first_base_index...[OK] Default implementations + NO alignment 2...0s [OK] primer_must_match...0s [OK] test_compl_error...0s [OK] test_left_to_right_of_right...0s [OK] dv_conc_vs_dntp_conc...[OK] Force _dpal_long_nopath_generic 1...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...0s [OK] primer3web_v3_0_0_default_settings...[OK] Default implementations + alignment (interactive)...[OK] Force _dpal_long_nopath_generic 2...[OK] Force long maxgap1 functions 1...[OK] Force long maxgap1 functions 2...[OK] 0s [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...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] primer_ok_regions2...[OK] Default implementations + NO alignment 1 (interactive)...[OK] Default implementations + NO alignment 2 (interactive)...[OK] Default implementations + alignment (interactive batch inputs)...[OK] Default implementations + alignment + HAIRPIN (interactive batch inputs)...[OK] 7s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...0s [OK] primer_task...0s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...0s [OK] primer_new_tasks...0s [OK] primer_new_tasks_formatted...1s [OK] primer_internal_position...0s [OK] primer_annealing_temp...0s [OK] primer_windows_newlines...0s [OK] primer_must_overlap_point...1s [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...0s [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...0s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...1s [OK] primer_mispriming_formatted...0s [OK] primer_mispriming_boundary1...0s [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...0s [OK] primer_human...0s [OK] long_seq...0s [OK] primer_position_penalty...1s [OK] primer_position_penalty_formatted...0s [OK] p3-tmpl-mispriming...0s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] primer_obj_fn...1s [OK] p3_3_prime_n...0s [OK] primer_masker...1s [OK] primer_masker_formatted...3s [OK] primer_overhang...0s [OK] primer_overhang_th...35s [OK] primer_mispriming_th...15s [OK] th-w-other-tasks...9s [OK] th-w-other-tasks_list_files...[OK] primer_new_tasks_th...10s [OK] primer_sec_struct_thal...8s [OK] primer_thermod_align...22s [OK] primer_thermod_align_formatted...22s [OK] primer1_th...56s [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 Sat Sep 5 12:17:03 2026...64s [OK] Tests in p3test.pl ran for 259 s (4.31666666666667 min) DONE Sat Sep 5 12:18:07 2026 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; Testing completed. You must check the test output for the string FAILED make[1]: Leaving directory '/build/source/test' checkPhase completed in 4 minutes 19 seconds Running phase: installPhase Running phase: fixupPhase shrinking RPATHs of ELF executables and libraries in /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1 shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/amplicon3_core shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/long_seq_tm_test shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/ntdpal shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/ntthal shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/oligotm shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/primer3_core shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/primer3_masker checking for references to /build/ in /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1... patching script interpreter paths in /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1 stripping (with command strip and flags -S -p) in /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin Running phase: installCheckPhase