[miso-users] Installation problem

[Julien Roux]

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)

[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
> 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?
> 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