primer3-2.6.1
checks.x86_64-linux.pkgs-primer3
· build #79
· raw
unpackPhase
1unpacking source archive /nix/store/p69aqq50wyh98ycsdmqxfh9bwj5wx4p7-source2source root is source/srcconfigurePhase
3no configure script, doing nothingbuildPhase
4build flags: -j48 SHELL=/nix/store/svx59425zxp552p2b8gm11qj5r09b56i-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.a78ar rv liboligotm.a oligotm.o79cc -g -Wall -O2 -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm80ar: creating liboligotm.a81a - oligotm.o82ranlib liboligotm.a83cc -g -Wall -O2 -o oligotm oligotm_main.c liboligotm.a -lm84ar rv libmasker.a masker.o85ar: creating libmasker.a86a - masker.o87ranlib libmasker.a88ar rv libamplicontm.a amplicontm.o89ar: creating libamplicontm.a90a - amplicontm.o91ranlib libamplicontm.a92cc -g -Wall -O2 -o amplicon3_core amplicontm_main.c libamplicontm.a -lm93libprimer3.cc: In function 'char* strstr_nocase(char*, char*)':94libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free]95 6168 | else {free(tmp); return p;}96 | ^97libprimer3.cc:6168:15: note: call to 'void free(void*)' here98 6168 | else {free(tmp); return p;}99 | ~~~~^~~~~100cc -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/svx59425zxp552p2b8gm11qj5r09b56i-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 ;127128129TESTING ALIGNMENT CALCS130131make[2]: Entering directory '/build/source/src'132no windows133134135TESTING THERMODYNAMIC ALIGNMENT CALCS136137echo; echo; echo 'TESTING amplicon3_core'; echo; perl a3test.pl 138echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl 139140141TESTING MASKER142143make[2]: Nothing to be done for 'all'.144make[2]: Leaving directory '/build/source/src'145146147148149TESTING primer3_core150TESTING amplicon3_core151152153154TESTING Tm CALCULATIONS155156Tm tests nr 1-Error handling of too-long sequence...157Default implementations...Error handling of too-long sequence...1................................... [OK]158Default implementations + alignment...[OK]159Default implementations + alignment...mkdir: ../test/primer_list_tmp160mkdir: ../test/primer1_list_tmp161mkdir: ../test/primer1_th_list_tmp162mkdir: ../test/th-w-other-tasks_list_tmp163p3test.pl for primer3_core version 2.6.1164165166TESTING command line arguments167168Test 1... 169170p3test.pl: testing ../src/primer3_core171172START, Mon Sep 21 12:16:40 2026173174testing fatal errors...175 ./primer_global_err/annealing_temp_salt176Testing --output and --error flags on177../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.tmp2178 ./primer_global_err/bad_divalent_dntp_conc_1179a3test.pl for amplicon3_core version 2.5.0180181182a3test.pl: testing ../src/amplicon3_core183184START, Mon Sep 21 12:16:40 2026185plain_WNT9B...[OK]186Test 2... ./primer_global_err/bad_divalent_dntp_conc_21870s [OK]188plain_TBX18...0s [OK]189plain_RYK... ./primer_global_err/bad_divalent_dntp_conc_31900s [OK]191plain_WNT2...[OK]192Test 3... 0s [OK]193plain_ROCK2... ./primer_global_err/bad_divalent_dntp_conc_4194[OK]195Test 4... 0s [OK]196plain_SFRP3... ./primer_global_err/bad_dna_conc197[OK]198Test 5... 0s [OK]199plain_IFT20...[OK]200Passed all tests - [OK]2012022030s [OK]204plain_DVL1... ./primer_global_err/bad_first_base_index2050s [OK]206plain_IFT88... ./primer_global_err/bad_float_12070s [OK]208plain_FZD2...0s [OK]209plain_GAPDH... ./primer_global_err/bad_float_22100s [OK]211plain_WNT1... ./primer_global_err/bad_float_32120s [OK]213plain_MYH6... ./primer_global_err/bad_float_42140s [OK]215plain_on_command_line_WNT9B... ./primer_global_err/bad_gc_12160s [OK]217plain_on_command_line_TBX18... ./primer_global_err/bad_gc_22180s [OK]219plain_on_command_line_RYK...0s [OK]220plain_on_command_line_WNT2... ./primer_global_err/bad_gc_32210s [OK]222plain_on_command_line_ROCK2... ./primer_global_err/bad_gc_int_12230s [OK]224plain_on_command_line_SFRP3...50: [OK]2252262270s [OK]228plain_on_command_line_IFT20... ./primer_global_err/bad_gc_int_22290s [OK]230plain_on_command_line_DVL1... ./primer_global_err/bad_gc_int_32310s [OK]232plain_on_command_line_IFT88...0s [OK]233plain_on_command_line_FZD2... ./primer_global_err/bad_min_three_prime_distance2340s [OK]235plain_on_command_line_GAPDH... ./primer_global_err/bad_num_ns2360s [OK]237plain_on_command_line_WNT1... ./primer_global_err/bad_num_ns_int2380s [OK]239plain_on_command_line_MYH6... ./primer_global_err/bad_product_sizes_12400s [OK]241classic_WNT9B... ./primer_global_err/bad_product_sizes_22420s [OK]243classic_TBX18... ./primer_global_err/bad_product_sizes_32440s [OK]245classic_RYK...0s [OK]246classic_WNT2... ./primer_global_err/bad_product_sizes_42470s [OK]248classic_ROCK2... ./primer_global_err/bad_salt_conc2490s [OK]250classic_SFRP3...0s [OK]251classic_IFT20... ./primer_global_err/bad_self_any2520s [OK]253classic_DVL1... ./primer_global_err/bad_self_any_int2540s [OK]255classic_IFT88...0s [OK]256classic_FZD2... ./primer_global_err/bad_self_end2570s [OK]258classic_GAPDH...0s [OK]259classic_WNT1... ./primer_global_err/bad_self_end_int2600s [OK]261classic_MYH6... ./primer_global_err/bad_settings02620s [OK]263heli_WNT9B... ./primer_global_err/bad_settings1264 ./primer_global_err/bad_settings2265 ./primer_global_err/bad_settings32660s [OK]267heli_TBX18... ./primer_global_err/bad_settings4268 ./primer_global_err/bad_settings5269 ./primer_global_err/bad_settings62700s [OK]271heli_RYK... ./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_bound2830s [OK]284heli_SFRP3... ./primer_global_err/max_min_bound_int285 ./primer_global_err/max_min_tm286 ./primer_global_err/max_min_tm_int2870s [OK]288heli_IFT20... ./primer_global_err/max_opt_bound289 ./primer_global_err/max_opt_bound_int290 ./primer_global_err/max_opt_tm2910s [OK]292heli_DVL1... ./primer_global_err/max_opt_tm_int293 ./primer_global_err/MAX_PRIMER_LENGTH2940s [OK]295heli_IFT88... ./primer_global_err/max_size_limit_int296 ./primer_global_err/max_size_limit_with_overhang297 ./primer_global_err/max_size_min_product298 ./primer_global_err/max_size_min_product_int2990s [OK]300heli_FZD2... ./primer_global_err/min_opt_tm301 ./primer_global_err/min_opt_tm_int302 ./primer_global_err/mishyb_obj_fn303 ./primer_global_err/mispr_obj_fn3040s [OK]305heli_GAPDH... ./primer_global_err/must_match_length_0306 ./primer_global_err/must_match_length_1307 ./primer_global_err/must_match_length_10308 ./primer_global_err/must_match_length_2309 ./primer_global_err/must_match_length_33100s [OK]311heli_WNT1... ./primer_global_err/must_match_length_4312 ./primer_global_err/must_match_length_5313 ./primer_global_err/must_match_length_63141s [OK]315heli_MYH6... ./primer_global_err/must_match_length_7316 ./primer_global_err/must_match_length_8317 ./primer_global_err/must_match_length_9318 ./primer_global_err/no_equal319 ./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_mispr3250s [OK]326long_WNT9B... ./primer_global_err/pr_gc_content_obj_fn3270s [OK]328long_TBX18... ./primer_global_err/product_size_obj_fn3290s [OK]330long_RYK... ./primer_global_err/product_tm_obj_fn3310s [OK]332long_WNT2... ./primer_global_err/repeat_lib_err3330s [OK]334long_ROCK2... ./primer_global_err/repeat_lib_err13350s [OK]336long_SFRP3...0s [OK]337long_IFT20... ./primer_global_err/repeat_lib_err23380s [OK]339long_DVL1... ./primer_global_err/repeat_lib_err33400s [OK]341long_IFT88... ./primer_global_err/repeat_lib_err43420s [OK]343long_FZD2...0s [OK]344long_GAPDH... ./primer_global_err/repeat_lib_err53450s [OK]346long_WNT1... ./primer_global_err/repeat_lib_err63470s [OK]348long_MYH6... ./primer_global_err/repeat_lib_int_err3490s [OK]350optimal_WNT9B... ./primer_global_err/repeat_lib_int_err13510s [OK]352optimal_TBX18... ./primer_global_err/repeat_lib_int_err23530s [OK]354optimal_RYK... ./primer_global_err/repeat_lib_int_err33550s [OK]356optimal_WNT2...0s [OK]357optimal_ROCK2... ./primer_global_err/repeat_lib_int_err43580s [OK]359optimal_SFRP3... ./primer_global_err/repeat_lib_int_err53600s [OK]361optimal_IFT20... ./primer_global_err/repeat_lib_int_err63620s [OK]363optimal_DVL1...0s [OK]364optimal_IFT88... ./primer_global_err/seq_quality13650s [OK]366optimal_FZD2... ./primer_global_err/seq_quality23670s [OK]368optimal_GAPDH... ./primer_global_err/seq_quality33690s [OK]370optimal_WNT1... ./primer_global_err/seq_quality43710s [OK]372optimal_MYH6... ./primer_global_err/too_many_product_sizes3730s [OK]374only_mv_WNT9B... ./primer_global_err/zero_min_size3750s [OK]376only_mv_TBX18... ./primer_global_err/zero_num_return3770s [OK]378only_mv_RYK...[OK]379primer_must_use_th...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]386only_mv_FZD2...0s [OK]387only_mv_GAPDH...0s [OK]388only_mv_WNT1...0s [OK]389only_mv_MYH6...0s [OK]390primer_sec_struct_dpal...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]397primer_task_th...0s [OK]398no_dmso_IFT20...0s [OK]399no_dmso_DVL1...0s [OK]400no_dmso_IFT88...0s [OK]401no_dmso_FZD2...0s [OK]402no_dmso_GAPDH...0s [OK]403no_dmso_WNT1...0s [OK]404no_dmso_MYH6...0s [OK]405406Tests in a3test.pl ran for 1 s (0.0166666666666667 min)407408DONE Mon Sep 21 12:16:41 2026 Passed all tests - [OK]409410411[OK]412Default implementations + NO alignment 1...[OK]4131s [OK]414primer_thal_args...[OK]415Default implementations + NO alignment 1...0s [OK]416primer_thal_max_seq_error...[OK]417Default implementations + NO alignment 2...[OK]418Force _dpal_generic...1s [OK]419primer_first_base_index...0s [OK]420primer_must_match...0s [OK]421test_compl_error...0s [OK]422test_left_to_right_of_right...0s [OK]423dv_conc_vs_dntp_conc...0s [OK]424primer_boundary...0s [OK]425primer_boundary1...0s [OK]426primer_boundary_formatted...0s [OK]427primer_boundary1_formatted...0s [OK]428primer3_v1_1_4_default_settings...1s [OK]429primer3web_v0_4_0_default_settings...0s [OK]430primer3web_v3_0_0_default_settings...[OK]431Default implementations + NO alignment 2...[OK]432Force _dpal_long_nopath_generic 1...[OK]433Default implementations + alignment (interactive)...[OK]434Force _dpal_long_nopath_generic 2...[OK]435Force long maxgap1 functions 1...1s [OK]436primer3web_v4_0_0_default_settings...0s [OK]437primer_internal...0s [OK]438primer_internal1...0s [OK]439primer_internal_formatted...0s [OK]440primer_internal1_formatted...0s [OK]441primer_ok_regions...0s [OK]442primer_ok_regions_formatted...0s [OK]443primer_ok_regions2...[OK]444Force long maxgap1 functions 2...[OK]445[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]4504s [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...0s [OK]460primer_internal_position...1s [OK]461primer_annealing_temp...0s [OK]462primer_windows_newlines...1s [OK]463primer_must_overlap_point...2s [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...2s [OK]477primer_list_files...[OK]478primer1...0s [OK]479primer1_list_files...[OK]480primer_mispriming...1s [OK]481primer_mispriming_formatted...1s [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...1s [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...2s [OK]496p3_3_prime_n...0s [OK]497primer_masker...2s [OK]498primer_masker_formatted...3s [OK]499primer_overhang...0s [OK]500primer_overhang_th...8s [OK]501primer_mispriming_th...17s [OK]502th-w-other-tasks...32s [OK]503th-w-other-tasks_list_files...[OK]504primer_new_tasks_th...13s [OK]505primer_sec_struct_thal...9s [OK]506primer_thermod_align...26s [OK]507primer_thermod_align_formatted...22s [OK]508primer1_th...65s [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 Mon Sep 21 12:20:18 2026...155s [OK]513514Tests in p3test.pl ran for 373 s (6.21666666666667 min)515516DONE Mon Sep 21 12:22:53 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 6 minutes 13 secondsfixupPhase
527shrinking RPATHs of ELF executables and libraries in /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1528shrinking /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1/bin/amplicon3_core529shrinking /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1/bin/long_seq_tm_test530shrinking /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1/bin/ntdpal531shrinking /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1/bin/ntthal532shrinking /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1/bin/oligotm533shrinking /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1/bin/primer3_core534shrinking /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1/bin/primer3_masker535checking for references to /build/ in /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1...536patching script interpreter paths in /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1537stripping (with command strip and flags -S -p) in /nix/store/w1l48127psssh9bm3yc39jzq06179kz1-primer3-2.6.1/bin