GHMM Library
 

I would like to use the General Hidden Markov Model (GHMM) library as part of my PhD project in bioinformatics.
But the current version of this package (0.6.0) as well as a CVS download won't compile on any of the machines I tried. I tried SuSe 9 (amd64), Fedora Cora 3 (x86), Gentoo (amd64) and Mac OSX.
I get this errror:
Why does it require itself to be installed to get compiled? How can I fix this absurd problem?
Anybody successfully compiled this library?

Or does someone know an other hidden markov model library?

also unable to install GHMM
 

Hello,

I have also been trying to install GHMM and have been unsuccessful.

RAN: ./configure
ERROR: config.status: error: cannot find input file: ghmmwrapper/Makefile.in
COPIED: Makefile.in to ghmmwrapper
RAN: make
ERROR: make[2]: *** No rule to make target `configure.in', needed by `../aclocal.m4'. Stop.
COPIED: configure.in to ghmmmwrapper
RAN: make
ERROR: make[2]: *** No rule to make target `acinclude.m4', needed by `../aclocal.m4'. Stop.
COPIED: acinclude.m4 to ghmmwrapper
RAN: make
ERROR: /home/edkirton/ghmm-0.6.0/missing: line 46: automake-1.7: command not found
INSTALLED: automake-1.7 (even though automake-1.9 was previously installed)
RAN: make
ERROR: aclocal: configure.in: 91: macro `AM_PROG_LIBTOOL' not found in library

Can any linux gurus out there help us?

Ed

I wrote an email to the author (Alexander Schliep) and my bug was fixed by using the newst version from CVS:
(no space beween the -d: and pserver, but I had to make one there or it would display a smiley from -d:p)

Hope this helps with your bug too...

ghmm installation problem
 

Hi

I want to use GHMM as part of my PhD ptoject but i've a lot of problems during installation. Many of required dependencies are referring to very old libraries (in particular i'm not able to compile xmlio on my distros, UBUNTU 6.06 and SUSE 10.1).

During the configuration stage of compilation i get the following error:

...
checking for pow in -lm... yes
configure: "not using gsl"
checking for cos in -lm... yes
checking libxml2 version... Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found

configure: error: Failed: please install atleast libxml-2.6.0

It is strange because libxml 2 seems to ve properly installed on the system (as i've just verifyed):

mtbi0@ublinxbox:/$ find -name 'libxml*'
./var/lib/dpkg/info/libxml2-utils.list
./var/lib/dpkg/info/libxml2-utils.md5sums
./var/lib/dpkg/info/libxml2.list
./var/lib/dpkg/info/libxml2.md5sums
./var/lib/dpkg/info/libxml2.postinst
./var/lib/dpkg/info/libxml2.postrm
./var/lib/dpkg/info/libxml2.shlibs
./var/lib/dpkg/info/libxmlsec1-nss.list
./var/lib/dpkg/info/libxmlsec1-nss.md5sums
./var/lib/dpkg/info/libxmlsec1-nss.postinst
./var/lib/dpkg/info/libxmlsec1-nss.postrm
./var/lib/dpkg/info/libxmlsec1-nss.shlibs
./var/lib/dpkg/info/libxmlsec1-openssl.list
./var/lib/dpkg/info/libxmlsec1-openssl.md5sums
./var/lib/dpkg/info/libxmlsec1-openssl.postinst
./var/lib/dpkg/info/libxmlsec1-openssl.postrm
./var/lib/dpkg/info/libxmlsec1-openssl.shlibs
./var/lib/dpkg/info/libxmlsec1.list
./var/lib/dpkg/info/libxmlsec1.md5sums
./var/lib/dpkg/info/libxmlsec1.postinst
./var/lib/dpkg/info/libxmlsec1.postrm
./var/lib/dpkg/info/libxmlsec1.shlibs

(Well ... to be more precise i hope that this is indicating the library is correctly installed ... but a run of apt-get install libxml2 results in a message like this:"libxml2 is already at the most recent version" and so i'm confident in the presence of libxml2).

There is anyone who tryed to install ghmm on Ubuntu? On SUSE 10.1 i was able to compile the library but not the python wrapper and the editor HMMed (it looks very well in the screenshots...) but after the just performed migration to Ubuntu (because a lot of problems in the YAST update system of SUSE 10.1) i can't compile neither the library and the wrapper/editor.

Sorry for the long and probably boring post ... (also i'm not completely sure if this is, in effect, an off topic) and for oddities in my english.
Any help would be greatly appreciated ... many tanks in advance.

PS:
Despite a lot of searches in the Internet for an alternative HMM library suitable for bioinformatics pourposes i've not found a valid alternative.

What version of libxml2 specifically do you have installed? Just because it is the most recent in the apt repository doesn't mean it's the most recent version on the Internet. If it is the required version or higher, file a bug report.

Hi

Tanks for your answer sonicbhoc. The installed libxml2 version (i've get this information using apt-cache show libxml2) is the following:

Package: libxml2
Priority: optional
Section: libs
Installed-Size: 1344
Maintainer: Debian XML/SGML Group <debian-xml-sgml-pkgs@lists.alioth.debian.org>
Architecture: i386
Version: 2.6.24.dfsg-1ubuntu1
...


As i writed im my previous post the configuraton error ends with a request of installing "atleast libxml-2.6.0" but the installed library seems to be matching the requirements.

I'm worried about the problem may be originated by some specific system setting (i'm new to ububtu and, in general, debian like linux distributions) because the

"Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable"

contained in the error message. A simple echo $PKG_CONFIG_PATH allowed me to verify that this variable seems to be not setted. Another (i think most serious) problem is that, using the find command, i was not able to find the required file (libxml-2.0.pc) on my system.

I'm very confused ...

I just tried to install it again on my gentoo laptop and it worked perfectly.
All I did was:
I have this version of libXML installed:
On distris like ubuntu you have to make sure that really all parts of the build toolchain are installed. My PKG_CONFIG_PATH contains only /usr/qt/3/lib/pkgconfig, so it doesn't seem relevant here. Does building other stuff work?

problem with pkgconfig, not libxml2
 

mtbi0,

i had similar problems, installing ghmm on
an OSX machine (10.3). i'd been using fink to
grab all the necessary bits, but then ran into
the same complaint you mention regarding the version
of libxml-2, even after i had built the
most recent version (2.6,26-1 as of this
writing) from source.

it turns out that the problem was that the config
script generating this error assumes the use of pkgconfig:

if $PKGCONFIG --atleast-version=2.6 libxml-2.0; then
echo "... ok"
else
echo `$PKGCONFIG --modversion libxml-2.0`
{ { echo "$as_me:$LINENO: error: Failed: please install at least libxml-2.6.0" >&5
echo "$as_me: error: Failed: please install at least libxml-2.6.0" >&2;}
{ (exit 1); exit 1; }; }
fi

(note, this test of libxml-2 is the ONLY place pkgconfig
seems to be invoked!) installing pkgconfig
allows the $PKGCONFIG shell variable to be bound correctly,
and made it work for me.

Try installing libxml2-dev
 

I had the same problem installing ghmm on Ubuntu. I solved it by installing libxml2-dev. You should be able to do this by running:
sudo apt-get install libxml2-dev

-S

ghmm python wrapper error
 

Friends

I tried to install ghmmwraper (python) in my Fedora 8 .
But it shows the following error
ghmmwrapper_wrap.c: In function ‘double_2d_array’:
ghmmwrapper_wrap.c:3215: warning: implicit declaration of function ‘matrix_d_alloc’
ghmmwrapper_wrap.c:3215: warning: return makes pointer from integer without a cast
ghmmwrapper_wrap.c: In function ‘free_2darrayd’:
ghmmwrapper_wrap.c:3255: warning: implicit declaration of function ‘matrix_d_free’
ghmmwrapper_wrap.c: In function ‘free_2darrayint’:
ghmmwrapper_wrap.c:3286: warning: implicit declaration of function ‘matrix_i_free’
ghmmwrapper_wrap.c: In function ‘_wrap_matrix_d_alloc_copy’:
ghmmwrapper_wrap.c:3427: warning: implicit declaration of function ‘matrix_d_alloc_copy’
ghmmwrapper_wrap.c: In function ‘_wrap_matrix_i_alloc’:
ghmmwrapper_wrap.c:3489: warning: implicit declaration of function ‘matrix_i_alloc’
ghmmwrapper_wrap.c: In function ‘_wrap_matrix_d_print’:
ghmmwrapper_wrap.c:3598: warning: implicit declaration of function ‘matrix_d_print’
ghmmwrapper_wrap.c: In function ‘_wrap_viterbi’:
ghmmwrapper_wrap.c:8769: warning: implicit declaration of function ‘viterbi’
ghmmwrapper_wrap.c: In function ‘_wrap_viterbi_logp’:
ghmmwrapper_wrap.c:8823: warning: implicit declaration of function ‘viterbi_logp’
ghmmwrapper_wrap.c: In function ‘_wrap_discriminative’:
ghmmwrapper_wrap.c:8891: warning: implicit declaration of function ‘discriminative’
ghmmwrapper_wrap.c: In function ‘_wrap_discrime_compute_performance’:
ghmmwrapper_wrap.c:8941: warning: implicit declaration of function ‘discrime_compute_performance’
ghmmwrapper_wrap.c: In function ‘_wrap_sdmodel_get_class_set’:
ghmmwrapper_wrap.c:10898: warning: assignment from incompatible pointer type
ghmmwrapper_wrap.c: In function ‘_wrap_sfoba_forward’:
ghmmwrapper_wrap.c:13037: warning: implicit declaration of function ‘sfoba_forward’
ghmmwrapper_wrap.c: In function ‘_wrap_sfoba_backward’:
ghmmwrapper_wrap.c:13109: warning: implicit declaration of function ‘sfoba_backward’
ghmmwrapper_wrap.c: In function ‘_wrap_sfoba_logp’:
ghmmwrapper_wrap.c:13163: warning: implicit declaration of function ‘sfoba_logp’
ghmmwrapper_wrap.c: In function ‘_wrap_smodel_alloc_fill’:
ghmmwrapper_wrap.c:13221: warning: implicit declaration of function ‘smodel_alloc_fill’
ghmmwrapper_wrap.c: In function ‘_wrap_smodel_set_pivector’:
ghmmwrapper_wrap.c:13265: warning: implicit declaration of function ‘smodel_set_pivector’
ghmmwrapper_wrap.c: In function ‘_wrap_smodel_set_fixvector’:
ghmmwrapper_wrap.c:13309: warning: implicit declaration of function ‘smodel_set_fixvector’
ghmmwrapper_wrap.c: In function ‘_wrap_smodel_set_transition’:
ghmmwrapper_wrap.c:13371: warning: implicit declaration of function ‘smodel_set_transition’
ghmmwrapper_wrap.c: In function ‘_wrap_smodel_get_transition’:
ghmmwrapper_wrap.c:13425: warning: implicit declaration of function ‘smodel_get_transition’
ghmmwrapper_wrap.c: In function ‘_wrap_smodel_set_mean’:
ghmmwrapper_wrap.c:13469: warning: implicit declaration of function ‘smodel_set_mean’
ghmmwrapper_wrap.c: In function ‘_wrap_smodel_set_variance’:
ghmmwrapper_wrap.c:13513: warning: implicit declaration of function ‘smodel_set_variance’
ghmmwrapper_wrap.c: In function ‘_wrap_smodel_sorted_individual_likelihoods’:
ghmmwrapper_wrap.c:13622: warning: implicit declaration of function ‘smodel_sorted_individual_likelihoods’
ghmmwrapper_wrap.c: In function ‘_wrap_sviterbi’:
ghmmwrapper_wrap.c:13676: warning: implicit declaration of function ‘sviterbi’
ghmmwrapper_wrap.c: In function ‘_wrap_setPythonCallback’:
ghmmwrapper_wrap.c:13889: warning: implicit declaration of function ‘setPythonCallback’
ghmmwrapper_wrap.c: In function ‘_wrap_executePythonCallback’:
ghmmwrapper_wrap.c:13943: warning: implicit declaration of function ‘executePythonCallback’
gcc -pthread -shared build/temp.linux-i686-2.5/sclass_change.o build/temp.linux-i686-2.5/pclasschange.o build/temp.linux-i686-2.5/gql.o build/temp.linux-i686-2.5/ghmmwrapper_wrap.o -L/usr/local/lib -L/usr/local/share/swig -L/usr/lib -lstdc++ -lm -lghmm -lswigpy -lpython2.5 -o build/lib.linux-i686-2.5/_ghmmwrapper.so
/usr/bin/ld: cannot find -lswigpy
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit statu

Swig is available in the system



Jaganadh G

Hi all,

I have exactly the same problem. I really need to get ghmmwrapper to work, but I'm stumped. Plus, the ghmm 'support' mailing list on sourceforge seems to be decomissioned... anyone figured a way around this glitch?

Cheers,

HM

Hi everyone,
tried to install the ghmm; and all was good until had to instal the ghmm wrapper. Any solutions? (The errors are as below)

Thanks!!

ubuntu@ubuntu:~/ghmm/ghmmwrapper$ swig -python -nodefaultctor ghmmwrapper.i
ubuntu@ubuntu:~/ghmm/ghmmwrapper$ python setup.py build
running build
running build_py
copying ghmmwrapper.py -> build/lib.linux-i686-2.6
running build_ext
building '_ghmmwrapper' extension
swigging ghmmwrapper.i to ghmmwrapper_wrap.c
swig -python -o ghmmwrapper_wrap.c ghmmwrapper.i
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I.. -I/usr/include/python2.6 -c sclass_change.c -o build/temp.linux-i686-2.6/sclass_change.o -O2 -pipe -Wall
sclass_change.c:40:20: error: Python.h: No such file or directory
sclass_change.c: In function ‘python_class_change’:
sclass_change.c:87: error: ‘PyObject’ undeclared (first use in this function)
sclass_change.c:87: error: (Each undeclared identifier is reported only once
sclass_change.c:87: error: for each function it appears in.)
sclass_change.c:87: error: ‘pName’ undeclared (first use in this function)
sclass_change.c:87: error: ‘pDict’ undeclared (first use in this function)
sclass_change.c:87: warning: left-hand operand of comma expression has no effect
sclass_change.c:87: error: ‘pArgs’ undeclared (first use in this function)
sclass_change.c:87: warning: left-hand operand of comma expression has no effect
sclass_change.c:87: error: ‘pValue’ undeclared (first use in this function)
sclass_change.c:87: warning: left-hand operand of comma expression has no effect
sclass_change.c:87: error: ‘pList’ undeclared (first use in this function)
sclass_change.c:87: warning: left-hand operand of comma expression has no effect
sclass_change.c:90: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
sclass_change.c:90: error: ‘pModule’ undeclared (first use in this function)
sclass_change.c:91: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
sclass_change.c:91: error: ‘pFunc’ undeclared (first use in this function)
sclass_change.c:98: warning: implicit declaration of function ‘PyString_FromString’
sclass_change.c:100: warning: implicit declaration of function ‘PyImport_Import’
sclass_change.c:106: warning: implicit declaration of function ‘PyModule_GetDict’
sclass_change.c:115: warning: implicit declaration of function ‘PyDict_GetItemString’
sclass_change.c:120: warning: implicit declaration of function ‘Py_DECREF’
sclass_change.c:124: warning: implicit declaration of function ‘PyTuple_New’
sclass_change.c:126: warning: implicit declaration of function ‘PyList_New’
sclass_change.c:128: warning: implicit declaration of function ‘PyFloat_FromDouble’
sclass_change.c:129: warning: implicit declaration of function ‘PyList_SetItem’
sclass_change.c:131: warning: implicit declaration of function ‘PyTuple_SetItem’
sclass_change.c:133: warning: implicit declaration of function ‘PyInt_FromLong’
sclass_change.c:139: warning: implicit declaration of function ‘PyObject_CallObject’
sclass_change.c:142: warning: implicit declaration of function ‘PyInt_AsLong’
sclass_change.c: At top level:
sclass_change.c:186: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
sclass_change.c: In function ‘executePythonCallback’:
sclass_change.c:203: error: ‘PyObject’ undeclared (first use in this function)
sclass_change.c:203: error: ‘pArgs’ undeclared (first use in this function)
sclass_change.c:203: error: ‘pValue’ undeclared (first use in this function)
sclass_change.c:203: warning: left-hand operand of comma expression has no effect
sclass_change.c:203: error: ‘pList’ undeclared (first use in this function)
sclass_change.c:203: warning: left-hand operand of comma expression has no effect
sclass_change.c:220: error: ‘pyCallback’ undeclared (first use in this function)
sclass_change.c: At top level:
sclass_change.c:245: error: expected declaration specifiers or ‘...’ before ‘PyObject’
sclass_change.c: In function ‘setPythonCallback’:
sclass_change.c:246: error: ‘pyCallback’ undeclared (first use in this function)
sclass_change.c:246: error: ‘py_cb’ undeclared (first use in this function)
error: command 'gcc' failed with exit status 1

Have python-dev installed then everything should be good.

This is the top hit on Google when you search for "ghmm libxml". The libxml version issue was a problem for me, too, when I tried to install GHMM on Ubuntu. Here are the steps that worked for me, just in case anyone else is stuck:

And I was also using the ghmmwrapper, which required that I add the line "/usr/local/lib" to /etc/ld.so.conf and then run .

That got everything working for me on Ubuntu 12.10.