[miso-users] Installation problem

Wed Dec 14 14:58:28 EST 2011

Sounds good, I'll wait for the official release of the R interface then!
Thanks for answering so quickly
Julien

On 12/14/11 1:45 PM, Yarden Katz wrote:
> Hi Julien,
>
> See replies below:
>
> On Dec 14, 2011, at 2:34 PM, Julien Roux wrote:
>
>> Dear Yarden and Gabor,
>> Thanks a lot for your quick answers. I am answering both your emails below:
>>> Could you please send us what version of make and gcc you are using, and on what operating system?
>> [jroux at bigmem01 MISO]$ gcc -v
>> Using built-in specs.
>> Target: x86_64-redhat-linux
>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
>> Thread model: posix
>> gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)
> I'm using gcc 4.4.3
>
>> [jroux at bigmem01 MISO]$ make -v
>> GNU Make 3.81
>> Copyright (C) 2006  Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions.
>> There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
>> PARTICULAR PURPOSE.
>> This program built for x86_64-redhat-linux-gnu
> ..And same version of make as you.  I did notice that some users who got the error you got upgraded make/gcc and it then worked, but in this case it doesn't look like a "make" difference.
>
>>> Also, did you download fastmiso from github?
>> Yes
>>> If so, can you confirm that you are indeed on the "fastmiso" branch, by typing:
>>>
>>> $ git branch
>>>
>>> It should output a "*" next to "fastmiso"
>> Yes this is what I get
>>> if you only need the Python version and not the R, then instead of
>>> 'make' you can run 'make Pythonpackage' and this should solve your
>>> error. (Which seems to come from some autotools version mismatch.)
>> That works indeed. Is it still fastMISO? BTW I was not aware that a R version exists. Do you have a documentation on this somewhere?
>
> It's still fastmiso.  Just to clarify: fastmiso is a fast C engine that does probabilistic inference under the hood, but it is wrapped by an interface (which is made to be identical to the pure Python of MISO).  This interface is written in Python, so that's what the "Pythonpackage" refers to.  There's also another interface to fastmiso, written in R, and we're working on documenting that.  When it's ready we'll post it on the website in addition to the current Python interface.
>
> best, --Yarden
>
>
>>> If you want to build both by just typing "make", I do believe the error will go away if you upgrade your version of the make program/autotools...
>> Mmm this is a cluster and I don't have administration rights... I can still talk to the administrator
>> Thanks again for your help!
>> Julien
>>>
>>>
>>>
>>> On Dec 14, 2011, at 12:49 PM, Julien Roux wrote:
>>>
>>>> Dear MISO developers,
>>>>
>>>> I am trying to install fastMISO but I encountered some errors when
>>>> running the "make" command (see below)
>>>> Any idea how to fix this?
>>>> Thanks a lot
>>>> Julien
>>>>
>>>> --------------------------------
>>>> [jroux at bigmem01 MISO]$ make
>>>> cp src/assignment.c splicing/src/assignment.c
>>>> cp src/complexity.c splicing/src/complexity.c
>>>> cp src/convert.c splicing/src/convert.c
>>>> cp src/error.c splicing/src/error.c
>>>> cp src/fortran_stuff.c splicing/src/fortran_stuff.c
>>>> cp src/gff.c splicing/src/gff.c
>>>> cp src/ident.c splicing/src/ident.c
>>>> cp src/lapack.c splicing/src/lapack.c
>>>> cp src/lawson_hanson_nnls.c splicing/src/lawson_hanson_nnls.c
>>>> cp src/matrix.c splicing/src/matrix.c
>>>> cp src/memory.c splicing/src/memory.c
>>>> cp src/miso.c splicing/src/miso.c
>>>> cp src/miso_paired.c splicing/src/miso_paired.c
>>>> cp src/nnls.c splicing/src/nnls.c
>>>> cp src/qsort.c splicing/src/qsort.c
>>>> cp src/qsort_r.c splicing/src/qsort_r.c
>>>> cp src/random.c splicing/src/random.c
>>>> cp src/simulator.c splicing/src/simulator.c
>>>> cp src/solve.c splicing/src/solve.c
>>>> cp src/strvector.c splicing/src/strvector.c
>>>> cp src/util.c splicing/src/util.c
>>>> cp src/vector.c splicing/src/vector.c
>>>> cp src/f2c.h splicing/src/f2c.h
>>>> cp src/splicing_error.h splicing/src/splicing_error.h
>>>> cp src/splicing.h splicing/src/splicing.h
>>>> cp src/splicing_lapack.h splicing/src/splicing_lapack.h
>>>> cp src/splicing_matrix.h splicing/src/splicing_matrix.h
>>>> cp src/splicing_matrix_pmt.h splicing/src/splicing_matrix_pmt.h
>>>> cp src/splicing_memory.h splicing/src/splicing_memory.h
>>>> cp src/splicing_pmt.h splicing/src/splicing_pmt.h
>>>> cp src/splicing_pmt_off.h splicing/src/splicing_pmt_off.h
>>>> cp src/splicing_random.h splicing/src/splicing_random.h
>>>> cp src/splicing_vector.h splicing/src/splicing_vector.h
>>>> cp src/splicing_vector_pmt.h splicing/src/splicing_vector_pmt.h
>>>> cp src/matrix.pmt splicing/src/matrix.pmt
>>>> cp src/vector.pmt splicing/src/vector.pmt
>>>> cd splicing&&   autoconf&&   autoheader
>>>> Use of inherited AUTOLOAD for non-method Autom4te::XFile::msg() is
>>>> deprecated at /usr/share/autoconf/Autom4te/XFile.pm line 238.
>>>> Can't locate auto/Autom4te/XFile/msg.al in @INC (@INC contains:
>>>> /usr/share/autoconf
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .)
>>>> at /usr/share/autoconf/Autom4te/XFile.pm line 238
>>>> make: *** [splicing_0.1.tar.gz] Error 1
>>>>
>>>> -- 
>>>> Julien Roux, PhD
>>>> Gilad lab, Department of Human Genetics, University of Chicago
>>>> http://giladlab.uchicago.edu/
>>>> 920 East 58th Street, CLSC 317, Chicago, IL 60637, USA
>>>> tel: +1-773-834-1984   fax: +1-773-834-8470
>>>>
>>>> _______________________________________________
>>>> miso-users mailing list
>>>> miso-users at mit.edu
>>>> http://mailman.mit.edu/mailman/listinfo/miso-users
>> -- 
>> Julien Roux, PhD
>> Gilad lab, Department of Human Genetics, University of Chicago
>> http://giladlab.uchicago.edu/
>> 920 East 58th Street, CLSC 317, Chicago, IL 60637, USA
>> tel: +1-773-834-1984   fax: +1-773-834-8470
>>

-- 
Julien Roux, PhD
Gilad lab, Department of Human Genetics, University of Chicago
http://giladlab.uchicago.edu/
920 East 58th Street, CLSC 317, Chicago, IL 60637, USA
tel: +1-773-834-1984   fax: +1-773-834-8470