primer3-2.6.1
checks.x86_64-linux.pkgs-primer3
· build #65
· 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.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.a88libprimer3.cc: In function 'char* strstr_nocase(char*, char*)':89libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free]90 6168 | else {free(tmp); return p;}91 | ^92libprimer3.cc:6168:15: note: call to 'void free(void*)' here93 6168 | else {free(tmp); return p;}94 | ~~~~^~~~~95ar rv libamplicontm.a amplicontm.o96ar: creating libamplicontm.a97a - amplicontm.o98ranlib libamplicontm.a99cc -g -Wall -O2 -o amplicon3_core amplicontm_main.c libamplicontm.a -lm100ar rv libdpal.a dpal_primer.o101ar: creating libdpal.a102a - dpal_primer.o103ranlib libdpal.a104cc -g -o ntdpal ntdpal_main.o dpal.o105ar rv libthal.a thal_primer.o106ar: creating libthal.a107a - thal_primer.o108ranlib libthal.a109cc -g -o ntthal thal_main.o thal.o thal_parameters.o -lm110ar 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 ;127make[2]: Entering directory '/build/source/src'128no windows129130131TESTING ALIGNMENT CALCS132133echo; echo; echo 'TESTING amplicon3_core'; echo; perl a3test.pl 134135136TESTING THERMODYNAMIC ALIGNMENT CALCS137138139140TESTING MASKER141142make[2]: Nothing to be done for 'all'.143make[2]: Leaving directory '/build/source/src'144145146TESTING amplicon3_core147148echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl 149150151TESTING primer3_core152153154TESTING Tm CALCULATIONS155156Tm tests nr 1-Error handling of too-long sequence...Default implementations...157158TESTING command line arguments159160Test 1... a3test.pl for amplicon3_core version 2.5.0161162163a3test.pl: testing ../src/amplicon3_core164165START, Sun Sep 6 08:47:09 2026166[OK]167Default implementations + alignment...plain_WNT9B...Error handling of too-long sequence...1680s [OK]169plain_TBX18...1................................... [OK]170Default implementations + alignment...[OK]171Test 2... 0s [OK]172plain_RYK...mkdir: ../test/primer_list_tmp173mkdir: ../test/primer1_list_tmp174mkdir: ../test/primer1_th_list_tmp175mkdir: ../test/th-w-other-tasks_list_tmp176p3test.pl for primer3_core version 2.6.1177178179p3test.pl: testing ../src/primer3_core180181START, Sun Sep 6 08:47:09 20261820s [OK]183184testing fatal errors...185plain_WNT2... ./primer_global_err/annealing_temp_salt186Testing --output and --error flags on187../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.tmp2188[OK]189Test 3... 0s [OK]190plain_ROCK2...[OK]191Test 4... ./primer_global_err/bad_divalent_dntp_conc_11920s [OK]193plain_SFRP3...[OK]194Test 5... 0s [OK]195plain_IFT20... ./primer_global_err/bad_divalent_dntp_conc_2196[OK]197Passed all tests - [OK]1981992000s [OK]201plain_DVL1... ./primer_global_err/bad_divalent_dntp_conc_32020s [OK]203plain_IFT88...0s [OK]204plain_FZD2... ./primer_global_err/bad_divalent_dntp_conc_42050s [OK]206plain_GAPDH... ./primer_global_err/bad_dna_conc2070s [OK]208plain_WNT1...0s [OK]209plain_MYH6... ./primer_global_err/bad_first_base_index2100s [OK]211plain_on_command_line_WNT9B... ./primer_global_err/bad_float_12120s [OK]213plain_on_command_line_TBX18... ./primer_global_err/bad_float_22140s [OK]215plain_on_command_line_RYK... ./primer_global_err/bad_float_32160s [OK]217plain_on_command_line_WNT2...0s [OK]218plain_on_command_line_ROCK2... ./primer_global_err/bad_float_42190s [OK]220plain_on_command_line_SFRP3... ./primer_global_err/bad_gc_12210s [OK]222plain_on_command_line_IFT20...0s [OK]223plain_on_command_line_DVL1...0s [OK]224plain_on_command_line_IFT88... ./primer_global_err/bad_gc_2225 ./primer_global_err/bad_gc_32260s [OK]227plain_on_command_line_FZD2...0s [OK]228plain_on_command_line_GAPDH...0s [OK]229plain_on_command_line_WNT1... ./primer_global_err/bad_gc_int_1230 ./primer_global_err/bad_gc_int_22310s [OK]232plain_on_command_line_MYH6...50: [OK]2332342350s [OK]236classic_WNT9B... ./primer_global_err/bad_gc_int_32370s [OK]238classic_TBX18...0s [OK]239classic_RYK... ./primer_global_err/bad_min_three_prime_distance2400s [OK]241classic_WNT2...0s [OK]242classic_ROCK2... ./primer_global_err/bad_num_ns2430s [OK]244classic_SFRP3... ./primer_global_err/bad_num_ns_int2450s [OK]246classic_IFT20...0s [OK]247classic_DVL1...0s [OK]248classic_IFT88... ./primer_global_err/bad_product_sizes_12490s [OK]250classic_FZD2... ./primer_global_err/bad_product_sizes_22510s [OK]252classic_GAPDH...0s [OK]253 ./primer_global_err/bad_product_sizes_3254classic_WNT1...0s [OK]255classic_MYH6...1s [OK]256heli_WNT9B... ./primer_global_err/bad_product_sizes_4257 ./primer_global_err/bad_salt_conc258 ./primer_global_err/bad_self_any259 ./primer_global_err/bad_self_any_int2600s [OK]261heli_TBX18... ./primer_global_err/bad_self_end262 ./primer_global_err/bad_self_end_int263 ./primer_global_err/bad_settings0264 ./primer_global_err/bad_settings1265 ./primer_global_err/bad_settings22660s [OK]267heli_RYK... ./primer_global_err/bad_settings3268 ./primer_global_err/bad_settings4269 ./primer_global_err/bad_settings5270 ./primer_global_err/bad_settings6271 ./primer_global_err/empty_12720s [OK]273heli_WNT2... ./primer_global_err/empty_product_size274 ./primer_global_err/gc_clamp_min_size2750s [OK]276heli_ROCK2... ./primer_global_err/incorrect_task277 ./primer_global_err/io_gc_content_obj_fn278 ./primer_global_err/io_obj_fn2790s [OK]280heli_SFRP3... ./primer_global_err/junction_overlap_max_size281 ./primer_global_err/junction_overlap_min_size282 ./primer_global_err/max_annealing_temp283 ./primer_global_err/max_min_bound2840s [OK]285heli_IFT20... ./primer_global_err/max_min_bound_int286 ./primer_global_err/max_min_tm287 ./primer_global_err/max_min_tm_int2880s [OK]289heli_DVL1... ./primer_global_err/max_opt_bound290 ./primer_global_err/max_opt_bound_int2910s [OK]292heli_IFT88... ./primer_global_err/max_opt_tm293 ./primer_global_err/max_opt_tm_int294 ./primer_global_err/MAX_PRIMER_LENGTH2950s [OK]296heli_FZD2... ./primer_global_err/max_size_limit_int297 ./primer_global_err/max_size_limit_with_overhang298 ./primer_global_err/max_size_min_product2990s [OK]300heli_GAPDH... ./primer_global_err/max_size_min_product_int301 ./primer_global_err/min_opt_tm302 ./primer_global_err/min_opt_tm_int3030s [OK]304heli_WNT1... ./primer_global_err/mishyb_obj_fn305 ./primer_global_err/mispr_obj_fn306 ./primer_global_err/must_match_length_0307 ./primer_global_err/must_match_length_13080s [OK]309heli_MYH6... ./primer_global_err/must_match_length_10310 ./primer_global_err/must_match_length_2311 ./primer_global_err/must_match_length_3312 ./primer_global_err/must_match_length_4313 ./primer_global_err/must_match_length_5314 ./primer_global_err/must_match_length_6315 ./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_equal3190s [OK]320long_WNT9B...0s [OK]321long_TBX18... ./primer_global_err/no_terminal_equal3220s [OK]323long_RYK...0s [OK]324long_WNT2... ./primer_global_err/opt_max_size3250s [OK]326long_ROCK2... ./primer_global_err/opt_max_size_int3270s [OK]328long_SFRP3... ./primer_global_err/opt_min_size3290s [OK]330long_IFT20... ./primer_global_err/opt_min_size_int3310s [OK]332long_DVL1... ./primer_global_err/pair_mispr3330s [OK]334long_IFT88...0s [OK]335long_FZD2... ./primer_global_err/pr_gc_content_obj_fn3360s [OK]337long_GAPDH... ./primer_global_err/product_size_obj_fn3380s [OK]339long_WNT1... ./primer_global_err/product_tm_obj_fn3400s [OK]341long_MYH6... ./primer_global_err/repeat_lib_err3420s [OK]343optimal_WNT9B...0s [OK]344optimal_TBX18... ./primer_global_err/repeat_lib_err1345 ./primer_global_err/repeat_lib_err23460s [OK]347optimal_RYK...0s [OK]348optimal_WNT2... ./primer_global_err/repeat_lib_err33490s [OK]350optimal_ROCK2... ./primer_global_err/repeat_lib_err43510s [OK]352optimal_SFRP3... ./primer_global_err/repeat_lib_err53530s [OK]354optimal_IFT20...0s [OK]355optimal_DVL1... ./primer_global_err/repeat_lib_err63560s [OK]357optimal_IFT88... ./primer_global_err/repeat_lib_int_err3580s [OK]359optimal_FZD2...0s [OK]360optimal_GAPDH... ./primer_global_err/repeat_lib_int_err13610s [OK]362optimal_WNT1... ./primer_global_err/repeat_lib_int_err23630s [OK]364optimal_MYH6... ./primer_global_err/repeat_lib_int_err33650s [OK]366only_mv_WNT9B...0s [OK]367only_mv_TBX18... ./primer_global_err/repeat_lib_int_err4368 ./primer_global_err/repeat_lib_int_err53690s [OK]370only_mv_RYK... ./primer_global_err/repeat_lib_int_err63710s [OK]372only_mv_WNT2...0s [OK]373only_mv_ROCK2... ./primer_global_err/seq_quality13740s [OK]375only_mv_SFRP3... ./primer_global_err/seq_quality23760s [OK]377only_mv_IFT20... ./primer_global_err/seq_quality33780s [OK]379only_mv_DVL1... ./primer_global_err/seq_quality43800s [OK]381only_mv_IFT88... ./primer_global_err/too_many_product_sizes3820s [OK]383only_mv_FZD2...0s [OK]384only_mv_GAPDH... ./primer_global_err/zero_min_size385 ./primer_global_err/zero_num_return3860s [OK]387only_mv_WNT1...0s [OK]388only_mv_MYH6...[OK]389primer_must_use_th...0s [OK]390no_dmso_WNT9B...0s [OK]391no_dmso_TBX18...0s [OK]392no_dmso_RYK...0s [OK]393no_dmso_WNT2...0s [OK]394no_dmso_ROCK2...0s [OK]395no_dmso_SFRP3...0s [OK]396no_dmso_IFT20...0s [OK]397no_dmso_DVL1...0s [OK]398no_dmso_IFT88...0s [OK]399no_dmso_FZD2...0s [OK]400no_dmso_GAPDH...0s [OK]401primer_sec_struct_dpal...0s [OK]402no_dmso_WNT1...0s [OK]403no_dmso_MYH6...0s [OK]404405Tests in a3test.pl ran for 1 s (0.0166666666666667 min)406407DONE Sun Sep 6 08:47:10 2026 Passed all tests - [OK]4084094100s [OK]411primer_task_th...[OK]412Default implementations + NO alignment 1...[OK]413[OK]414Default implementations + NO alignment 1...0s [OK]415primer_thal_args...[OK]416Default implementations + NO alignment 2...[OK]417Force _dpal_generic...1s [OK]418primer_thal_max_seq_error...0s [OK]419primer_first_base_index...0s [OK]420primer_must_match...0s [OK]421test_compl_error...0s [OK]422test_left_to_right_of_right...[OK]423Default implementations + NO alignment 2...0s [OK]424dv_conc_vs_dntp_conc...0s [OK]425primer_boundary...0s [OK]426primer_boundary1...[OK]427Force _dpal_long_nopath_generic 1...0s [OK]428primer_boundary_formatted...0s [OK]429primer_boundary1_formatted...0s [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]4371s [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]4506s [OK]451primer_tm_lc_masking...0s [OK]452primer_tm_lc_masking_formatted...0s [OK]453primer_start_codon...0s [OK]454primer_task...1s [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...0s [OK]461primer_annealing_temp...0s [OK]462primer_windows_newlines...1s [OK]463primer_must_overlap_point...0s [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...1s [OK]477primer_list_files...[OK]478primer1...0s [OK]479primer1_list_files...[OK]480primer_mispriming...0s [OK]481primer_mispriming_formatted...0s [OK]482primer_mispriming_boundary1...1s [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...1s [OK]499primer_overhang...0s [OK]500primer_overhang_th...25s [OK]501primer_mispriming_th...14s [OK]502th-w-other-tasks...10s [OK]503th-w-other-tasks_list_files...[OK]504primer_new_tasks_th...11s [OK]505primer_sec_struct_thal...9s [OK]506primer_thermod_align...22s [OK]507primer_thermod_align_formatted...23s [OK]508primer1_th...58s [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 Sun Sep 6 08:50:18 2026...63s [OK]513514Tests in p3test.pl ran for 252 s (4.2 min)515516DONE Sun Sep 6 08:51:21 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 12 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