Build log

primer3-1.1.4-r1:20100830-090536.log (text/plain), 12.29 KB, created by Diego Elio Pettenò (RETIRED) on 2010-08-30 11:27:13 UTC

 * 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: