primer3-2.6.1
checks.x86_64-linux.pkgs-primer3
· build #95
· raw
unpackPhase
1unpacking source archive /nix/store/p69aqq50wyh98ycsdmqxfh9bwj5wx4p7-source2source root is source/srcconfigurePhase
3no configure script, doing nothingbuildPhase
4build flags: -j48 SHELL=/nix/store/10dxp0qxqxxsyiljrh2kp0xqhz6arhcx-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 libmasker.a masker.o79ar: creating libmasker.a80a - masker.o81ranlib libmasker.a82ar rv liboligotm.a oligotm.o83cc -g -Wall -O2 -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm84ar: creating liboligotm.a85a - oligotm.o86ranlib liboligotm.a87cc -g -Wall -O2 -o oligotm oligotm_main.c liboligotm.a -lm88ar 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 | ~~~~^~~~~100ar rv libdpal.a dpal_primer.o101ar: creating libdpal.a102a - dpal_primer.o103ranlib libdpal.a104cc -g -o ntdpal ntdpal_main.o dpal.o105cc -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/10dxp0qxqxxsyiljrh2kp0xqhz6arhcx-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 128129130TESTING ALIGNMENT CALCS131132echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl 133make[2]: Entering directory '/build/source/src'134no windows135136137TESTING THERMODYNAMIC ALIGNMENT CALCS138139140141TESTING MASKER142143144145TESTING amplicon3_core146147148149TESTING primer3_core150151make[2]: Nothing to be done for 'all'.152make[2]: Leaving directory '/build/source/src'153154TESTING Tm CALCULATIONS155156Tm tests nr 1-Error handling of too-long sequence...[OK]157Default implementations + alignment...Error handling of too-long sequence...158mkdir: ../test/primer_list_tmp159mkdir: ../test/primer1_list_tmp160mkdir: ../test/primer1_th_list_tmp161mkdir: ../test/th-w-other-tasks_list_tmp162p3test.pl for primer3_core version 2.6.11631................................... [OK]164Default implementations + alignment...165166p3test.pl: testing ../src/primer3_core167168START, Sat Oct 3 12:13:50 2026169a3test.pl for amplicon3_core version 2.5.0170171testing fatal errors...172 ./primer_global_err/annealing_temp_salt173Testing --output and --error flags on174../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.tmp2175Default implementations...176177TESTING command line arguments178179Test 1... 180181a3test.pl: testing ../src/amplicon3_core182183START, Sat Oct 3 12:13:50 2026184plain_WNT9B... ./primer_global_err/bad_divalent_dntp_conc_11850s [OK]186plain_TBX18... ./primer_global_err/bad_divalent_dntp_conc_21870s [OK]188plain_RYK...[OK]189Test 2... 0s [OK]190plain_WNT2... ./primer_global_err/bad_divalent_dntp_conc_31910s [OK]192plain_ROCK2... ./primer_global_err/bad_divalent_dntp_conc_41930s [OK]194plain_SFRP3...[OK]195Test 3... 0s [OK]196plain_IFT20... ./primer_global_err/bad_dna_conc197[OK]198Test 4... 0s [OK]199plain_DVL1... ./primer_global_err/bad_first_base_index2000s [OK]201plain_IFT88...[OK]202Test 5... 0s [OK]203plain_FZD2... ./primer_global_err/bad_float_1204[OK]205Passed all tests - [OK]2062072080s [OK]209plain_GAPDH...0s [OK]210plain_WNT1... ./primer_global_err/bad_float_22110s [OK]212plain_MYH6... ./primer_global_err/bad_float_3213 ./primer_global_err/bad_float_42140s [OK]215plain_on_command_line_WNT9B... ./primer_global_err/bad_gc_12160s [OK]217plain_on_command_line_TBX18...0s [OK]218plain_on_command_line_RYK... ./primer_global_err/bad_gc_22190s [OK]220plain_on_command_line_WNT2... ./primer_global_err/bad_gc_32210s [OK]222plain_on_command_line_ROCK2...0s [OK]223plain_on_command_line_SFRP3... ./primer_global_err/bad_gc_int_12240s [OK]225plain_on_command_line_IFT20... ./primer_global_err/bad_gc_int_22260s [OK]227plain_on_command_line_DVL1...50: [OK]2282292300s [OK]231plain_on_command_line_IFT88...0s [OK]232plain_on_command_line_FZD2... ./primer_global_err/bad_gc_int_32330s [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...0s [OK]244classic_WNT2...0s [OK]245classic_ROCK2... ./primer_global_err/bad_product_sizes_22460s [OK]247classic_SFRP3...0s [OK]248classic_IFT20... ./primer_global_err/bad_product_sizes_32490s [OK]250classic_DVL1...0s [OK]251classic_IFT88... ./primer_global_err/bad_product_sizes_42520s [OK]253classic_FZD2...0s [OK]254classic_GAPDH...0s [OK]255classic_WNT1... ./primer_global_err/bad_salt_conc2560s [OK]257classic_MYH6...0s [OK]258 ./primer_global_err/bad_self_any259heli_WNT9B... ./primer_global_err/bad_self_any_int260 ./primer_global_err/bad_self_end2610s [OK]262heli_TBX18... ./primer_global_err/bad_self_end_int263 ./primer_global_err/bad_settings0264 ./primer_global_err/bad_settings12650s [OK]266heli_RYK... ./primer_global_err/bad_settings2267 ./primer_global_err/bad_settings3268 ./primer_global_err/bad_settings4269 ./primer_global_err/bad_settings52700s [OK]271heli_WNT2... ./primer_global_err/bad_settings6272 ./primer_global_err/empty_1273 ./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_fn279 ./primer_global_err/junction_overlap_max_size2800s [OK]281heli_SFRP3... ./primer_global_err/junction_overlap_min_size282 ./primer_global_err/max_annealing_temp2830s [OK]284heli_IFT20... ./primer_global_err/max_min_bound285 ./primer_global_err/max_min_bound_int286 ./primer_global_err/max_min_tm2870s [OK]288heli_DVL1... ./primer_global_err/max_min_tm_int289 ./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_1308 ./primer_global_err/must_match_length_103090s [OK]310heli_MYH6... ./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_93180s [OK]319long_WNT9B... ./primer_global_err/no_equal3200s [OK]321long_TBX18... ./primer_global_err/no_terminal_equal3220s [OK]323long_RYK... ./primer_global_err/opt_max_size3240s [OK]325long_WNT2...0s [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_mispr333 ./primer_global_err/pr_gc_content_obj_fn3340s [OK]335long_IFT88...0s [OK]336long_FZD2... ./primer_global_err/product_size_obj_fn3370s [OK]338long_GAPDH... ./primer_global_err/product_tm_obj_fn3390s [OK]340long_WNT1... ./primer_global_err/repeat_lib_err3410s [OK]342long_MYH6... ./primer_global_err/repeat_lib_err13430s [OK]344optimal_WNT9B... ./primer_global_err/repeat_lib_err23450s [OK]346optimal_TBX18... ./primer_global_err/repeat_lib_err33470s [OK]348optimal_RYK... ./primer_global_err/repeat_lib_err4349 ./primer_global_err/repeat_lib_err53500s [OK]351optimal_WNT2... ./primer_global_err/repeat_lib_err63520s [OK]353optimal_ROCK2... ./primer_global_err/repeat_lib_int_err3540s [OK]355optimal_SFRP3...0s [OK]356optimal_IFT20... ./primer_global_err/repeat_lib_int_err13571s [OK]358optimal_DVL1... ./primer_global_err/repeat_lib_int_err23590s [OK]360optimal_IFT88... ./primer_global_err/repeat_lib_int_err33610s [OK]362optimal_FZD2... ./primer_global_err/repeat_lib_int_err43630s [OK]364optimal_GAPDH... ./primer_global_err/repeat_lib_int_err53650s [OK]366optimal_WNT1... ./primer_global_err/repeat_lib_int_err63670s [OK]368optimal_MYH6... ./primer_global_err/seq_quality13690s [OK]370only_mv_WNT9B... ./primer_global_err/seq_quality23710s [OK]372only_mv_TBX18... ./primer_global_err/seq_quality33730s [OK]374only_mv_RYK... ./primer_global_err/seq_quality43750s [OK]376only_mv_WNT2...0s [OK]377only_mv_ROCK2... ./primer_global_err/too_many_product_sizes3780s [OK]379only_mv_SFRP3... ./primer_global_err/zero_min_size3800s [OK]381only_mv_IFT20... ./primer_global_err/zero_num_return3820s [OK]383only_mv_DVL1...0s [OK]384only_mv_IFT88...[OK]385primer_must_use_th...0s [OK]386only_mv_FZD2...0s [OK]387only_mv_GAPDH...0s [OK]388only_mv_WNT1...0s [OK]389only_mv_MYH6...0s [OK]390no_dmso_WNT9B...0s [OK]391no_dmso_TBX18...0s [OK]392no_dmso_RYK...0s [OK]393primer_sec_struct_dpal...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...0s [OK]403no_dmso_MYH6...0s [OK]404405Tests in a3test.pl ran for 1 s (0.0166666666666667 min)406407DONE Sat Oct 3 12:13:51 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...0s [OK]418primer_thal_max_seq_error...[OK]419Default implementations + NO alignment 2...1s [OK]420primer_first_base_index...0s [OK]421primer_must_match...0s [OK]422test_compl_error...[OK]423Force _dpal_long_nopath_generic 1...0s [OK]424test_left_to_right_of_right...0s [OK]425dv_conc_vs_dntp_conc...0s [OK]426primer_boundary...0s [OK]427primer_boundary1...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...[OK]439Default implementations + NO alignment 1 (interactive)...0s [OK]440primer_internal...0s [OK]441primer_internal1...0s [OK]442primer_internal_formatted...0s [OK]443primer_internal1_formatted...0s [OK]444primer_ok_regions...0s [OK]445primer_ok_regions_formatted...0s [OK]446primer_ok_regions2...[OK]447Default implementations + NO alignment 2 (interactive)...[OK]448Default implementations + alignment (interactive batch inputs)...[OK]449Default implementations + alignment + HAIRPIN (interactive batch inputs)...[OK]4503s [OK]451primer_tm_lc_masking...0s [OK]452primer_tm_lc_masking_formatted...0s [OK]453primer_start_codon...1s [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...0s [OK]461primer_annealing_temp...0s [OK]462primer_windows_newlines...1s [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...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...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...1s [OK]498primer_masker_formatted...2s [OK]499primer_overhang...0s [OK]500primer_overhang_th...9s [OK]501primer_mispriming_th...16s [OK]502th-w-other-tasks...19s [OK]503th-w-other-tasks_list_files...[OK]504primer_new_tasks_th...13s [OK]505primer_sec_struct_thal...8s [OK]506primer_thermod_align...26s [OK]507primer_thermod_align_formatted...23s [OK]508primer1_th...64s [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 Oct 3 12:17:05 2026...64s [OK]513514Tests in p3test.pl ran for 259 s (4.31666666666667 min)515516DONE Sat Oct 3 12:18:09 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/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1528shrinking /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1/bin/amplicon3_core529shrinking /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1/bin/long_seq_tm_test530shrinking /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1/bin/ntdpal531shrinking /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1/bin/ntthal532shrinking /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1/bin/oligotm533shrinking /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1/bin/primer3_core534shrinking /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1/bin/primer3_masker535checking for references to /build/ in /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1...536patching script interpreter paths in /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1537stripping (with command strip and flags -S -p) in /nix/store/5242frxi8inryn416gc15r8y22h4s9qm-primer3-2.6.1/bin