primer3-2.6.1
checks.x86_64-linux.pkgs-primer3
· build #63
· raw
unpackPhase
1unpacking source archive /nix/store/p69aqq50wyh98ycsdmqxfh9bwj5wx4p7-source2source root is source/srcconfigurePhase
3no configure script, doing nothingbuildPhase
4build flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash CC=cc CXX=c++ AR=ar RANLIB=ranlib5no windows6cc -c -g -Wall -O2 primer3_boulder_main.c7cc -c -g -Wall -O2 -o format_output.o format_output.c8cc -c -g -Wall -O2 -o read_boulder.o read_boulder.c9cc -c -g -Wall -O2 -o print_boulder.o print_boulder.c10c++ -c -g -Wall -O2 -std=c++11 -o libprimer3.o libprimer3.cc11cc -c -g -Wall -O2 -o p3_seq_lib.o p3_seq_lib.c12cc -c -g -Wall -O2 -o dpal_primer.o dpal.c13cc -c -g -Wall -O2 -ffloat-store -o thal_primer.o thal.c14cc -c -g -Wall -O2 -ffloat-store -o thal_parameters.o thal_parameters.c15cc -g -Wall -O2 -c -o oligotm.o oligotm.c16cc -g -Wall -O2 -c -o amplicontm.o amplicontm.c17cc -c -g -Wall -O2 masker.c18cc -c -g -Wall -o ntdpal_main.o ntdpal_main.c19cc -c -g -Wall -O2 -o dpal.o dpal.c20cc -c -g -Wall -O2 -o thal_main.o thal_main.c21cc -c -g -Wall -O2 -ffloat-store -o thal.o thal.c22format_output.c: In function 'print_seq':23format_output.c:418:61: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress]24 418 | if (pa->pick_right_primer && (&retval->rev) != NULL25 | ^~26In file included from format_output.h:41,27 from format_output.c:40:28libprimer3.h:927:26: note: 'rev' declared here29 927 | oligo_array fwd, intl, rev;30 | ^~~31format_output.c:429:60: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress]32 429 | if (pa->pick_left_primer && (&retval->fwd) != NULL33 | ^~34libprimer3.h:927:15: note: 'fwd' declared here35 927 | oligo_array fwd, intl, rev;36 | ^~~37format_output.c: In function 'format_oligos':38format_output.c:851:51: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress]39 851 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL )40 | ^~41libprimer3.h:927:15: note: 'fwd' declared here42 927 | oligo_array fwd, intl, rev;43 | ^~~44format_output.c:858:55: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress]45 858 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL )46 | ^~47libprimer3.h:927:20: note: 'intl' declared here48 927 | oligo_array fwd, intl, rev;49 | ^~~~50format_output.c:865:52: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress]51 865 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL )52 | ^~53libprimer3.h:927:26: note: 'rev' declared here54 927 | oligo_array fwd, intl, rev;55 | ^~~56format_output.c:888:49: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress]57 888 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL )58 | ^~59libprimer3.h:927:15: note: 'fwd' declared here60 927 | oligo_array fwd, intl, rev;61 | ^~~62format_output.c:907:53: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress]63 907 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL )64 | ^~65libprimer3.h:927:20: note: 'intl' declared here66 927 | oligo_array fwd, intl, rev;67 | ^~~~68format_output.c:926:50: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress]69 926 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL )70 | ^~71libprimer3.h:927:26: note: 'rev' declared here72 927 | oligo_array fwd, intl, rev;73 | ^~~74ar rv libthalpara.a thal_parameters.o75ar: creating libthalpara.a76a - thal_parameters.o77ranlib libthalpara.a78libprimer3.cc: In function 'char* strstr_nocase(char*, char*)':79libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free]80 6168 | else {free(tmp); return p;}81 | ^82libprimer3.cc:6168:15: note: call to 'void free(void*)' here83 6168 | else {free(tmp); return p;}84 | ~~~~^~~~~85ar rv liboligotm.a oligotm.o86cc -g -Wall -O2 -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm87ar: creating liboligotm.a88a - oligotm.o89ranlib liboligotm.a90cc -g -Wall -O2 -o oligotm oligotm_main.c liboligotm.a -lm91ar rv libamplicontm.a amplicontm.o92ar: creating libamplicontm.a93a - amplicontm.o94ranlib libamplicontm.a95cc -g -Wall -O2 -o amplicon3_core amplicontm_main.c libamplicontm.a -lm96ar rv libmasker.a masker.o97ar: creating libmasker.a98a - masker.o99ranlib libmasker.a100cc -g -o ntdpal ntdpal_main.o dpal.o101ar rv libdpal.a dpal_primer.o102ar: creating libdpal.a103a - dpal_primer.o104ranlib libdpal.a105cc -g -o ntthal thal_main.o thal.o thal_parameters.o -lm106ar rv libthal.a thal_primer.o107ar: creating libthal.a108a - thal_primer.o109ranlib libthal.a110ar rv libprimer3.a libprimer3.o p3_seq_lib.o111ar: creating libprimer3.a112a - libprimer3.o113a - p3_seq_lib.o114ranlib libprimer3.a115c++ -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 -lm116c++ -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 -lmcheckPhase
117check flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash CC=cc CXX=c++ AR=ar RANLIB=ranlib VERBOSE=y test118no windows119cd ../test; make test120make[1]: Entering directory '/build/source/test'121cd ../src; make122perl cmdline_test.pl 123perl oligotm_test.pl 124echo; echo; echo 'TESTING ALIGNMENT CALCS'; echo; perl dpal_test.pl ; 125echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ;126echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ;127echo; echo; echo 'TESTING amplicon3_core'; echo; perl a3test.pl 128echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl 129make[2]: Entering directory '/build/source/src'130no windows131132133TESTING ALIGNMENT CALCS134135136137TESTING THERMODYNAMIC ALIGNMENT CALCS138139140141TESTING MASKER142143144145TESTING amplicon3_core146147148149TESTING primer3_core150make[2]: Nothing to be done for 'all'.151152make[2]: Leaving directory '/build/source/src'153Error handling of too-long sequence...154TESTING Tm CALCULATIONS155156157158TESTING command line arguments159160Test 1... Tm tests nr 1-[OK]161Default implementations + alignment...Default implementations...a3test.pl for amplicon3_core version 2.5.0162163164a3test.pl: testing ../src/amplicon3_core165166START, Sat Sep 5 12:13:48 2026167plain_WNT9B...mkdir: ../test/primer_list_tmp168mkdir: ../test/primer1_list_tmp169mkdir: ../test/primer1_th_list_tmp170mkdir: ../test/th-w-other-tasks_list_tmp171p3test.pl for primer3_core version 2.6.1172[OK]173Test 2... 174175p3test.pl: testing ../src/primer3_core176177START, Sat Sep 5 12:13:48 20261780s [OK]179plain_TBX18...Error handling of too-long sequence...180181testing fatal errors...182 ./primer_global_err/annealing_temp_salt183Testing --output and --error flags on184../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.tmp21851................................... [OK]186Default implementations + alignment...0s [OK]187plain_RYK... ./primer_global_err/bad_divalent_dntp_conc_1188[OK]189Test 3... 0s [OK]190plain_WNT2...[OK]191Test 4... 0s [OK]192plain_ROCK2... ./primer_global_err/bad_divalent_dntp_conc_21930s [OK]194plain_SFRP3...[OK]195Test 5... ./primer_global_err/bad_divalent_dntp_conc_31960s [OK]197plain_IFT20...[OK]198Passed all tests - [OK]199200201 ./primer_global_err/bad_divalent_dntp_conc_42020s [OK]203plain_DVL1... ./primer_global_err/bad_dna_conc2040s [OK]205plain_IFT88... ./primer_global_err/bad_first_base_index2060s [OK]207plain_FZD2...0s [OK]208plain_GAPDH... ./primer_global_err/bad_float_12090s [OK]210plain_WNT1... ./primer_global_err/bad_float_22110s [OK]212plain_MYH6... ./primer_global_err/bad_float_32130s [OK]214plain_on_command_line_WNT9B... ./primer_global_err/bad_float_42150s [OK]216plain_on_command_line_TBX18... ./primer_global_err/bad_gc_12170s [OK]218plain_on_command_line_RYK...0s [OK]219plain_on_command_line_WNT2... ./primer_global_err/bad_gc_22200s [OK]221plain_on_command_line_ROCK2... ./primer_global_err/bad_gc_32220s [OK]223plain_on_command_line_SFRP3... ./primer_global_err/bad_gc_int_12240s [OK]225plain_on_command_line_IFT20...0s [OK]226plain_on_command_line_DVL1... ./primer_global_err/bad_gc_int_22270s [OK]228plain_on_command_line_IFT88... ./primer_global_err/bad_gc_int_32290s [OK]230plain_on_command_line_FZD2...50: [OK]2312322330s [OK]234plain_on_command_line_GAPDH... ./primer_global_err/bad_min_three_prime_distance2350s [OK]236plain_on_command_line_WNT1... ./primer_global_err/bad_num_ns2370s [OK]238plain_on_command_line_MYH6... ./primer_global_err/bad_num_ns_int2390s [OK]240classic_WNT9B...0s [OK]241classic_TBX18... ./primer_global_err/bad_product_sizes_12420s [OK]243classic_RYK... ./primer_global_err/bad_product_sizes_22440s [OK]245classic_WNT2...0s [OK]246classic_ROCK2...0s [OK]247classic_SFRP3... ./primer_global_err/bad_product_sizes_32480s [OK]249classic_IFT20...0s [OK]250classic_DVL1... ./primer_global_err/bad_product_sizes_42510s [OK]252classic_IFT88... ./primer_global_err/bad_salt_conc2530s [OK]254classic_FZD2...0s [OK]255 ./primer_global_err/bad_self_any256classic_GAPDH...0s [OK]257classic_WNT1... ./primer_global_err/bad_self_any_int2580s [OK]259classic_MYH6...0s [OK]260heli_WNT9B... ./primer_global_err/bad_self_end261 ./primer_global_err/bad_self_end_int262 ./primer_global_err/bad_settings0263 ./primer_global_err/bad_settings12640s [OK]265heli_TBX18... ./primer_global_err/bad_settings2266 ./primer_global_err/bad_settings3267 ./primer_global_err/bad_settings4268 ./primer_global_err/bad_settings52690s [OK]270heli_RYK... ./primer_global_err/bad_settings6271 ./primer_global_err/empty_1272 ./primer_global_err/empty_product_size273 ./primer_global_err/gc_clamp_min_size274 ./primer_global_err/incorrect_task2750s [OK]276heli_WNT2... ./primer_global_err/io_gc_content_obj_fn277 ./primer_global_err/io_obj_fn278 ./primer_global_err/junction_overlap_max_size2790s [OK]280heli_ROCK2... ./primer_global_err/junction_overlap_min_size281 ./primer_global_err/max_annealing_temp282 ./primer_global_err/max_min_bound283 ./primer_global_err/max_min_bound_int2840s [OK]285heli_SFRP3... ./primer_global_err/max_min_tm286 ./primer_global_err/max_min_tm_int287 ./primer_global_err/max_opt_bound288 ./primer_global_err/max_opt_bound_int2890s [OK]290heli_IFT20... ./primer_global_err/max_opt_tm291 ./primer_global_err/max_opt_tm_int292 ./primer_global_err/MAX_PRIMER_LENGTH293 ./primer_global_err/max_size_limit_int294 ./primer_global_err/max_size_limit_with_overhang2950s [OK]296heli_DVL1... ./primer_global_err/max_size_min_product297 ./primer_global_err/max_size_min_product_int298 ./primer_global_err/min_opt_tm2990s [OK]300heli_IFT88... ./primer_global_err/min_opt_tm_int301 ./primer_global_err/mishyb_obj_fn302 ./primer_global_err/mispr_obj_fn303 ./primer_global_err/must_match_length_03040s [OK]305heli_FZD2... ./primer_global_err/must_match_length_1306 ./primer_global_err/must_match_length_10307 ./primer_global_err/must_match_length_23080s [OK]309heli_GAPDH... ./primer_global_err/must_match_length_3310 ./primer_global_err/must_match_length_4311 ./primer_global_err/must_match_length_5312 ./primer_global_err/must_match_length_63130s [OK]314heli_WNT1... ./primer_global_err/must_match_length_7315 ./primer_global_err/must_match_length_8316 ./primer_global_err/must_match_length_9317 ./primer_global_err/no_equal3180s [OK]319heli_MYH6... ./primer_global_err/no_terminal_equal320 ./primer_global_err/opt_max_size321 ./primer_global_err/opt_max_size_int322 ./primer_global_err/opt_min_size323 ./primer_global_err/opt_min_size_int324 ./primer_global_err/pair_mispr325 ./primer_global_err/pr_gc_content_obj_fn326 ./primer_global_err/product_size_obj_fn327 ./primer_global_err/product_tm_obj_fn328 ./primer_global_err/repeat_lib_err329 ./primer_global_err/repeat_lib_err13300s [OK]331long_WNT9B... ./primer_global_err/repeat_lib_err23320s [OK]333long_TBX18... ./primer_global_err/repeat_lib_err33340s [OK]335long_RYK... ./primer_global_err/repeat_lib_err43360s [OK]337long_WNT2... ./primer_global_err/repeat_lib_err53380s [OK]339long_ROCK2...0s [OK]340long_SFRP3... ./primer_global_err/repeat_lib_err63410s [OK]342long_IFT20... ./primer_global_err/repeat_lib_int_err3430s [OK]344long_DVL1... ./primer_global_err/repeat_lib_int_err13450s [OK]346long_IFT88...0s [OK]347long_FZD2... ./primer_global_err/repeat_lib_int_err23480s [OK]349long_GAPDH... ./primer_global_err/repeat_lib_int_err33500s [OK]351long_WNT1... ./primer_global_err/repeat_lib_int_err43520s [OK]353long_MYH6... ./primer_global_err/repeat_lib_int_err53540s [OK]355optimal_WNT9B... ./primer_global_err/repeat_lib_int_err63560s [OK]357optimal_TBX18... ./primer_global_err/seq_quality13580s [OK]359optimal_RYK... ./primer_global_err/seq_quality23600s [OK]361optimal_WNT2... ./primer_global_err/seq_quality33620s [OK]363optimal_ROCK2... ./primer_global_err/seq_quality43640s [OK]365optimal_SFRP3... ./primer_global_err/too_many_product_sizes3660s [OK]367optimal_IFT20... ./primer_global_err/zero_min_size3680s [OK]369optimal_DVL1...0s [OK]370optimal_IFT88... ./primer_global_err/zero_num_return3710s [OK]372optimal_FZD2...[OK]373primer_must_use_th...0s [OK]374optimal_GAPDH...0s [OK]375optimal_WNT1...0s [OK]376optimal_MYH6...0s [OK]377only_mv_WNT9B...0s [OK]378only_mv_TBX18...0s [OK]379only_mv_RYK...0s [OK]380only_mv_WNT2...0s [OK]381only_mv_ROCK2...0s [OK]382only_mv_SFRP3...0s [OK]383only_mv_IFT20...0s [OK]384only_mv_DVL1...0s [OK]385only_mv_IFT88...0s [OK]386primer_sec_struct_dpal...0s [OK]387only_mv_FZD2...0s [OK]388only_mv_GAPDH...0s [OK]389only_mv_WNT1...0s [OK]390only_mv_MYH6...0s [OK]391no_dmso_WNT9B...0s [OK]392no_dmso_TBX18...0s [OK]393no_dmso_RYK...0s [OK]394no_dmso_WNT2...0s [OK]395no_dmso_ROCK2...0s [OK]396no_dmso_SFRP3...0s [OK]397no_dmso_IFT20...0s [OK]398no_dmso_DVL1...0s [OK]399no_dmso_IFT88...0s [OK]400no_dmso_FZD2...0s [OK]401no_dmso_GAPDH...0s [OK]402no_dmso_WNT1...1s [OK]403no_dmso_MYH6...1s [OK]404primer_task_th...0s [OK]405406Tests in a3test.pl ran for 1 s (0.0166666666666667 min)407408DONE Sat Sep 5 12:13:49 2026 Passed all tests - [OK]409410411[OK]412[OK]413Default implementations + NO alignment 1...[OK]414Default implementations + NO alignment 1...0s [OK]415primer_thal_args...[OK]416Default implementations + NO alignment 2...[OK]417Force _dpal_generic...0s [OK]418primer_thal_max_seq_error...0s [OK]419primer_first_base_index...[OK]420Default implementations + NO alignment 2...0s [OK]421primer_must_match...0s [OK]422test_compl_error...0s [OK]423test_left_to_right_of_right...0s [OK]424dv_conc_vs_dntp_conc...[OK]425Force _dpal_long_nopath_generic 1...0s [OK]426primer_boundary...0s [OK]427primer_boundary1...0s [OK]428primer_boundary_formatted...0s [OK]429primer_boundary1_formatted...1s [OK]430primer3_v1_1_4_default_settings...0s [OK]431primer3web_v0_4_0_default_settings...0s [OK]432primer3web_v3_0_0_default_settings...[OK]433Default implementations + alignment (interactive)...[OK]434Force _dpal_long_nopath_generic 2...[OK]435Force long maxgap1 functions 1...[OK]436Force long maxgap1 functions 2...[OK]4370s [OK]438primer3web_v4_0_0_default_settings...0s [OK]439primer_internal...0s [OK]440primer_internal1...0s [OK]441primer_internal_formatted...0s [OK]442primer_internal1_formatted...0s [OK]443primer_ok_regions...0s [OK]444primer_ok_regions_formatted...0s [OK]445primer_ok_regions2...[OK]446Default implementations + NO alignment 1 (interactive)...[OK]447Default implementations + NO alignment 2 (interactive)...[OK]448Default implementations + alignment (interactive batch inputs)...[OK]449Default implementations + alignment + HAIRPIN (interactive batch inputs)...[OK]4507s [OK]451primer_tm_lc_masking...0s [OK]452primer_tm_lc_masking_formatted...0s [OK]453primer_start_codon...0s [OK]454primer_task...0s [OK]455primer_task_formatted...0s [OK]456primer_renewed_tasks...0s [OK]457primer_dmso_formamide...0s [OK]458primer_new_tasks...0s [OK]459primer_new_tasks_formatted...1s [OK]460primer_internal_position...0s [OK]461primer_annealing_temp...0s [OK]462primer_windows_newlines...0s [OK]463primer_must_overlap_point...1s [OK]464primer_overlap_junction...0s [OK]465primer_all_settingsfiles...0s [OK]466primer_high_tm_load_set...0s [OK]467primer_high_gc_load_set...0s [OK]468primer_gc_end...0s [OK]469primer_check...0s [OK]470primer_must_use...0s [OK]471primer_must_use_formatted...0s [OK]472primer_syntax...0s [OK]473primer_end_pathology...0s [OK]474primer_num_best...0s [OK]475primer_quality_boundary...0s [OK]476primer...0s [OK]477primer_list_files...[OK]478primer1...0s [OK]479primer1_list_files...[OK]480primer_mispriming...1s [OK]481primer_mispriming_formatted...0s [OK]482primer_mispriming_boundary1...0s [OK]483primer_mispriming_boundary1_formatted...0s [OK]484primer_mispriming_boundary2...0s [OK]485primer_mispriming_boundary2_formatted...0s [OK]486primer_mispriming_long_lib...0s [OK]487primer_rat...0s [OK]488primer_human...0s [OK]489long_seq...0s [OK]490primer_position_penalty...1s [OK]491primer_position_penalty_formatted...0s [OK]492p3-tmpl-mispriming...0s [OK]493primer_poly_x...0s [OK]494primer_three_prime_distance...0s [OK]495primer_obj_fn...1s [OK]496p3_3_prime_n...0s [OK]497primer_masker...1s [OK]498primer_masker_formatted...3s [OK]499primer_overhang...0s [OK]500primer_overhang_th...35s [OK]501primer_mispriming_th...15s [OK]502th-w-other-tasks...9s [OK]503th-w-other-tasks_list_files...[OK]504primer_new_tasks_th...10s [OK]505primer_sec_struct_thal...8s [OK]506primer_thermod_align...22s [OK]507primer_thermod_align_formatted...22s [OK]508primer1_th...56s [OK]509primer1_th_list_files...[OK]510primer_lib_amb_codes...511NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more).512starting primer_lib_amb_codes at Sat Sep 5 12:17:03 2026...64s [OK]513514Tests in p3test.pl ran for 259 s (4.31666666666667 min)515516DONE Sat Sep 5 12:18:07 2026 Passed all tests - [OK]517518519echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo;520521522Testing completed. You must check the test output for the string FAILED523524525make[1]: Leaving directory '/build/source/test'526checkPhase completed in 4 minutes 19 secondsfixupPhase
527shrinking RPATHs of ELF executables and libraries in /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1528shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/amplicon3_core529shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/long_seq_tm_test530shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/ntdpal531shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/ntthal532shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/oligotm533shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/primer3_core534shrinking /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin/primer3_masker535checking for references to /build/ in /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1...536patching script interpreter paths in /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1537stripping (with command strip and flags -S -p) in /nix/store/3y31nrxwv72d6bqjgh24vjaljskni793-primer3-2.6.1/bin