* CPV: sci-biology/primer3-1.1.4-r1 * REPO: gentoo * USE: elibc_glibc kernel_linux test userland_GNU x86 >>> Unpacking source... >>> Unpacking primer3-1.1.4.tar.gz to /var/tmp/portage/sci-biology/primer3-1.1.4-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/primer3-1.1.4-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/primer3-1.1.4-r1/work/src ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/primer3-1.1.4-r1/work/src ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/primer3-1.1.4-r1/work/src ... make -j14 -e gcc -c -O2 -pipe -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 primer3_main.c gcc -c -O2 -pipe -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 primer3.c gcc -c -O2 -pipe -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o dpal_primer.o dpal.c gcc -c -O2 -pipe -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o format_output.o format_output.c gcc -c -O2 -pipe -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o boulder_input.o boulder_input.c gcc -O2 -pipe -c -o oligotm.o oligotm.c gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -o ntdpal_main.o ntdpal_main.c gcc -c -O2 -pipe -o dpal.o dpal.c ntdpal_main.c: In function ‘main’: ntdpal_main.c:159:5: warning: pointer targets in passing argument 1 of ‘dpal’ differ in signedness dpal.h:148:6: note: expected ‘const unsigned char *’ but argument is of type ‘const char *’ ntdpal_main.c:159:5: warning: pointer targets in passing argument 2 of ‘dpal’ differ in signedness dpal.h:148:6: note: expected ‘const unsigned char *’ but argument is of type ‘const char *’ format_output.c: In function ‘print_seq_lines’: format_output.c:382:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result format_output.c:386:12: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result dpal.c: In function ‘_dpal_long_nopath_maxgap1_local’: dpal.c:784:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:786:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:788:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c: In function ‘_dpal_long_nopath_maxgap1_local’: dpal.c:784:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:786:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:788:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c: In function ‘_dpal_long_nopath_maxgap1_global_end’: dpal.c:874:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:876:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:878:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c: In function ‘_dpal_long_nopath_maxgap1_global_end’: dpal.c:874:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:876:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:878:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c: In function ‘_dpal_long_nopath_maxgap1_local_end’: dpal.c:1094:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:1096:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:1098:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c: In function ‘_dpal_long_nopath_maxgap1_local_end’: dpal.c:1094:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:1096:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:1098:16: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c: In function ‘_dpal_long_nopath_generic’: dpal.c:618:15: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:620:15: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:623:19: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c: In function ‘_dpal_long_nopath_generic’: dpal.c:618:15: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:620:15: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result dpal.c:623:19: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result primer3_main.c: In function ‘align’: primer3_main.c:2445:2: warning: format not a string literal and no format arguments primer3_main.c: In function ‘pr_safe_realloc’: primer3_main.c:2981:20: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result primer3_main.c:2981:20: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result primer3_main.c: In function ‘pr_safe_malloc’: primer3_main.c:2971:20: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result primer3_main.c:2971:20: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result primer3_main.c: In function ‘align’: primer3_main.c:2443:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result primer3_main.c:2443:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result ar rv liboligotm.a oligotm.o gcc -O2 -pipe -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm ar: creating liboligotm.a a - oligotm.o ranlib liboligotm.a gcc -O2 -pipe -o oligotm oligotm_main.c liboligotm.a -lm oligotm_main.c: In function ‘main’: oligotm_main.c:115:6: warning: format not a string literal and no format arguments gcc -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o ntdpal ntdpal_main.o dpal.o gcc -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o primer3_core primer3_main.o primer3.o dpal_primer.o format_output.o boulder_input.o liboligotm.a -lm >>> Source compiled. * Tinderbox QA Notice: 'make' called by src_test make -j14 primer_test cd ../test; make test make[1]: Entering directory `/var/tmp/portage/sci-biology/primer3-1.1.4-r1/work/test' make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. cd ../src; make make[2]: Entering directory `/var/tmp/portage/sci-biology/primer3-1.1.4-r1/work/src' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/primer3-1.1.4-r1/work/src' echo 'Testing Tm calcs'; perl oligotm_test.pl ; Testing Tm calcs Tests nr 1-44: OK echo 'Testing alignment calcs'; perl dpal_test.pl ; Testing alignment calcs Error handling of too-long sequence...OK Default implementations + alignment...OK Default implementations + NO alignment 1...OK Default implementations + NO alignment 2...OK Force _dpal_generic...OK Force _dpal_long_nopath_generic 1...OK Force _dpal_long_nopath_generic 2...OK Force long maxgap1 functions 1...OK Force long maxgap1 functions 2...OK echo 'Testing primer3_core '; perl p3test.pl Testing primer3_core p3test.pl: testing ../src/primer3_core START, Mon Aug 30 11:05:49 2010 testing fatal errors... ./primer_global_err/bad_divalent_dntp_conc_1 ./primer_global_err/bad_divalent_dntp_conc_2 ./primer_global_err/bad_divalent_dntp_conc_3 ./primer_global_err/bad_divalent_dntp_conc_4 ./primer_global_err/bad_dna_conc ./primer_global_err/bad_float_1 ./primer_global_err/bad_float_2 ./primer_global_err/bad_float_3 ./primer_global_err/bad_float_4 ./primer_global_err/bad_gc_1 ./primer_global_err/bad_gc_2 ./primer_global_err/bad_gc_3 ./primer_global_err/bad_gc_int_1 ./primer_global_err/bad_gc_int_2 ./primer_global_err/bad_gc_int_3 ./primer_global_err/bad_num_ns ./primer_global_err/bad_num_ns_int ./primer_global_err/bad_product_sizes_1 ./primer_global_err/bad_product_sizes_2 ./primer_global_err/bad_product_sizes_3 ./primer_global_err/bad_product_sizes_4 ./primer_global_err/bad_salt_conc ./primer_global_err/bad_self_any ./primer_global_err/bad_self_any_int ./primer_global_err/bad_self_end ./primer_global_err/bad_self_end_int ./primer_global_err/empty_1 ./primer_global_err/empty_product_size ./primer_global_err/gc_clamp_min_size ./primer_global_err/incorrect_task ./primer_global_err/io_gc_content_obj_fn ./primer_global_err/io_obj_fn ./primer_global_err/max_min_tm ./primer_global_err/max_min_tm_int ./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_min_product ./primer_global_err/max_size_min_product_int ./primer_global_err/min_opt_tm ./primer_global_err/min_opt_tm_int ./primer_global_err/mishyb_obj_fn ./primer_global_err/mispr_obj_fn ./primer_global_err/no_equal ./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 ./primer_global_err/repeat_lib_err2 ./primer_global_err/repeat_lib_err3 ./primer_global_err/repeat_lib_err4 ./primer_global_err/repeat_lib_err5 ./primer_global_err/repeat_lib_err6 ./primer_global_err/repeat_lib_int_err ./primer_global_err/repeat_lib_int_err1 ./primer_global_err/repeat_lib_int_err2 ./primer_global_err/repeat_lib_int_err3 ./primer_global_err/repeat_lib_int_err4 ./primer_global_err/repeat_lib_int_err5 ./primer_global_err/repeat_lib_int_err6 ./primer_global_err/seq_quality1 ./primer_global_err/seq_quality2 ./primer_global_err/seq_quality3 ./primer_global_err/seq_quality4 ./primer_global_err/too_many_product_sizes ./primer_global_err/zero_min_size ./primer_global_err/zero_num_return [OK] primer_boundary...[OK] primer_internal...[OK] primer_boundary_formatted...[OK] primer_internal_formatted...[OK] primer_start_codon...[OK] primer_boundary1...[OK] primer_internal1...[OK] primer_task...[OK] primer_task_formatted...[OK] primer_boundary1_formatted...[OK] primer_internal1_formatted...[OK] primer_check...[OK] primer_must_use...[OK] primer_must_use_formatted...[OK] primer_syntax...[OK] primer_end_pathology...[OK] primer_num_best...[OK] primer_quality_boundary...[OK] primer_obj_fn...[OK] primer...[OK] primer_list_files [OK] primer1...[OK] primer1_list_files [OK] primer_mispriming...[OK] primer_mispriming_formatted...[OK] primer_mispriming_boundary1...[OK] primer_mispriming_boundary1_formatted...[OK] primer_mispriming_boundary2...[OK] primer_mispriming_boundary2_formatted...[OK] primer_mispriming_long_lib...[OK] primer_rat...[OK] primer_human...[OK] long_seq...[OK] primer_position_penalty...[OK] primer_position_penalty_formatted...[OK] p3-tmpl-mispriming...[OK] primer_tm_lc_masking...[OK] primer_tm_lc_masking_formatted...[OK] primer_lib_amb_codes... NOTE: this test takes _much_ longer than the others (10 to 20 minutes or more). starting primer_lib_amb_codes at Mon Aug 30 11:06:08 2010...[OK] DONE Mon Aug 30 11:12:00 2010 echo 'TESTING ALL:' TESTING ALL: make[1]: Leaving directory `/var/tmp/portage/sci-biology/primer3-1.1.4-r1/work/test' >>> Install primer3-1.1.4-r1 into /var/tmp/portage/sci-biology/primer3-1.1.4-r1/image/ category sci-biology >>> Completed installing primer3-1.1.4-r1 into /var/tmp/portage/sci-biology/primer3-1.1.4-r1/image/ * QA Notice: make jobserver unavailable: * * make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment usr/bin/long_seq_tm_test usr/bin/oligotm usr/bin/ntdpal usr/bin/primer3_core  * QA Notice: Files built without respecting LDFLAGS have been detected * Please include the following list of files in your report: * /usr/bin/long_seq_tm_test * /usr/bin/oligotm  * Gentoo contact information ... herds: sci-biology maintainers: