Created
August 14, 2009 00:14
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pyrimidine1:HMM cjfields$ perl Makefile.PL | |
Writing Makefile for Bio::Ext::HMM | |
pyrimidine1:HMM cjfields$ make | |
cp HMM.pm blib/lib/Bio/Ext/HMM.pm | |
/opt/perl/bin/perl /opt/perl/lib/5.10.0/ExtUtils/xsubpp -typemap /opt/perl/lib/5.10.0/ExtUtils/typemap -typemap typemap HMM.xs > HMM.xsc && mv HMM.xsc HMM.c | |
Please specify prototyping behavior for HMM.xs (see perlxs manual) | |
cc -c -fno-common -DPERL_DARWIN -no-cpp-precomp -nostdinc -B/Developer/SDKs/MacOSX10.5.sdk/usr/include/gcc -B/Developer/SDKs/MacOSX10.5.sdk/usr/lib/gcc -isystem/Developer/SDKs/MacOSX10.5.sdk/usr/include -F/Developer/SDKs/MacOSX10.5.sdk/System/Library/Frameworks -fno-strict-aliasing -pipe -I/opt/local/include -O3 -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" "-I/opt/perl/lib/5.10.0/darwin-64int-ld-2level/CORE" HMM.c | |
HMM.c: In function ‘XS_Bio__Ext__HMM_HMM_statistical_training’: | |
HMM.c:44: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM_HMM_likelihood’: | |
HMM.c:101: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM_HMM_baum_welch_training’: | |
HMM.c:133: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM_HMM_viterbi’: | |
HMM.c:180: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM__HMM_get_init_entry’: | |
HMM.c:247: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM__HMM_set_init_entry’: | |
HMM.c:273: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM__HMM_get_a_entry’: | |
HMM.c:297: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM__HMM_set_a_entry’: | |
HMM.c:324: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM__HMM_get_e_entry’: | |
HMM.c:349: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM__HMM_set_e_entry’: | |
HMM.c:376: warning: cast to pointer from integer of different size | |
HMM.c: In function ‘XS_Bio__Ext__HMM__HMM_DESTROY’: | |
HMM.c:402: warning: cast to pointer from integer of different size | |
cc -c -fno-common -DPERL_DARWIN -no-cpp-precomp -nostdinc -B/Developer/SDKs/MacOSX10.5.sdk/usr/include/gcc -B/Developer/SDKs/MacOSX10.5.sdk/usr/lib/gcc -isystem/Developer/SDKs/MacOSX10.5.sdk/usr/include -F/Developer/SDKs/MacOSX10.5.sdk/System/Library/Frameworks -fno-strict-aliasing -pipe -I/opt/local/include -O3 -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" "-I/opt/perl/lib/5.10.0/darwin-64int-ld-2level/CORE" hmmlib.c | |
Running Mkbootstrap for Bio::Ext::HMM () | |
chmod 644 HMM.bs | |
rm -f blib/arch/auto/Bio/Ext/HMM/HMM.bundle | |
env MACOSX_DEPLOYMENT_TARGET=10.3 cc -bundle -undefined dynamic_lookup -L/opt/local/lib HMM.o hmmlib.o -o blib/arch/auto/Bio/Ext/HMM/HMM.bundle \ | |
-lm \ | |
chmod 755 blib/arch/auto/Bio/Ext/HMM/HMM.bundle | |
cp HMM.bs blib/arch/auto/Bio/Ext/HMM/HMM.bs | |
chmod 644 blib/arch/auto/Bio/Ext/HMM/HMM.bs | |
pyrimidine1:HMM cjfields$ make test | |
PERL_DL_NONLAZY=1 /opt/perl/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl | |
Baum-Welch Training | |
=================== | |
Initial Probability Array: | |
0.499997 0.500003 | |
Transition Probability Matrix: | |
0.499997 0.500003 | |
0.499997 0.500003 | |
Emission Probability Matrix: | |
0.133333 0.143333 0.163333 0.123333 0.143333 0.293333 | |
0.133333 0.143333 0.163333 0.123333 0.143333 0.293333 | |
Log Probability of sequence 1: -521.808 | |
Log Probability of sequence 2: -426.057 | |
Statistical Training | |
==================== | |
Initial Probability Array: | |
1 0 | |
Transition Probability Matrix: | |
------------- EXCEPTION ------------- | |
MSG: Sum of probabilities for each from-state must be 1.0! | |
STACK Bio::Tools::HMM::transition_prob /Users/cjfields/bioperl/bioperl-live/Bio/Tools/HMM.pm:499 | |
STACK toplevel test.pl:82 | |
------------------------------------- | |
make: *** [test_dynamic] Error 255 | |
pyrimidine1:HMM cjfields$ make test | |
PERL_DL_NONLAZY=1 /opt/perl/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl | |
Baum-Welch Training | |
=================== | |
S should be monotonic increasing! | |
make: *** [test_dynamic] Error 255 | |
pyrimidine1:HMM cjfields$ make test | |
PERL_DL_NONLAZY=1 /opt/perl/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl | |
Baum-Welch Training | |
=================== | |
Initial Probability Array: | |
0.499997 0.500003 | |
Transition Probability Matrix: | |
0.499997 0.500003 | |
0.499997 0.500003 | |
Emission Probability Matrix: | |
0.133333 0.143333 0.163333 0.123333 0.143333 0.293333 | |
0.133333 0.143333 0.163333 0.123333 0.143333 0.293333 | |
Log Probability of sequence 1: -521.808 | |
Log Probability of sequence 2: -426.057 | |
Statistical Training | |
==================== | |
Initial Probability Array: | |
1 0 | |
Transition Probability Matrix: | |
------------- EXCEPTION ------------- | |
MSG: Sum of probabilities for each from-state must be 1.0! | |
STACK Bio::Tools::HMM::transition_prob /Users/cjfields/bioperl/bioperl-live/Bio/Tools/HMM.pm:499 | |
STACK toplevel test.pl:82 | |
------------------------------------- | |
make: *** [test_dynamic] Error 255 | |
pyrimidine1:HMM cjfields$ |
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