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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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