[BioPython] problem installing mxTextTools

Nick Matzke matzke at berkeley.edu
Fri Jul 25 05:27:55 UTC 2008 

Hi all,

I am trying to install biopython and am carefully following the 
directions at:

http://biopython.org/DIST/docs/install/Installation.html

...as instructed, here are the steps I took:


1. I start by successfully installing Python2.4.4 on my Mac OSX 10.4.  I 
set the environment variable so that Python2.4.4 is the default version 
of Python at the terminal.

2. Then, as instructed I try to install mxTextTools.  Downloaded:
egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt

...from here:
http://www.egenix.com/products/python/mxBase/


3. However, none of these (the official instructions, or several 
alternatives proposed in various online fora) work for installing 
mxTextTools.  Here are the results:

3a. instructions here:
http://biopython.org/DIST/docs/install/Installation.html#htoc9

======================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
root# python -V
Python 2.4.4

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
root# python setup.py build
running build
running mx_autoconf
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
-L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
macros to define: [('HAVE_STRPTIME', '1')]
macros to undefine: []
running build_ext

building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
building 'mx.DateTime.mxDateTime.mxDateTime' extension
creating build/temp.macosx-10.3-fat-2.4_ucs2
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
-DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
mx/DateTime/mxDateTime/mxDateTime.c -o 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o
i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
i686-apple-darwin8-gcc-4.0.1: no input files
powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
powerpc-apple-darwin8-gcc-4.0.1: no input files
lipo: can't figure out the architecture type of: /var/tmp//cch9pAof.out
error: command 'gcc' failed with exit status 1

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
root#
======================


3b. Instructions here:
http://www.egenix.com/products/python/mxBase/

sudo python setup.py install

==================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ python -V
Python 2.4.4

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py install
running install
running build
running mx_autoconf
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
-L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
macros to define: [('HAVE_STRPTIME', '1')]
macros to undefine: []
running build_ext

building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
building 'mx.DateTime.mxDateTime.mxDateTime' extension
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
-DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
mx/DateTime/mxDateTime/mxDateTime.c -o 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o
i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
i686-apple-darwin8-gcc-4.0.1: no input files
powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
powerpc-apple-darwin8-gcc-4.0.1: no input files
lipo: can't figure out the architecture type of: /var/tmp//ccGUEnk3.out
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

==================




3c. Instructions here:
http://www.egenix.com/mailman-archives/egenix-users/2007-October/114291.html

sudo python setup.py build --skip install
================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ python -V
Python 2.4.4
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py build --skip install
running build
skipping the build process and reusing the existing build files and data
error: build/build-macosx-10.3-fat-py2.4_ucs2.pck: No such file or directory
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ ls
COPYRIGHT               PKG-INFO                build 
installer.bmp           mxSetup.pyc             wininst.bat
LICENSE                 README                  egenix_mx_base.py 
mx                      setup.cfg
MANIFEST                bdist_zope.bat          egenix_mx_base.pyc 
mxSetup.py              setup.py
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ ls ./build
build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
temp.darwin-8.11.1-i386-2.3_ucs2
lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 
temp.macosx-10.3-fat-2.4_ucs2
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$
================


4. Give up and email the biopython list.  Help!!  Please!!


5. Ask existential questions about why, oh why, all useful software 
comes with dependencies that you have to compile yourself and which 
never, ever compile correctly when the instructions are followed even on 
utterly standard systems like Mac OSX 10.4.


Thanks very very much,
Nick







-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab website: http://ib.berkeley.edu/people/lab_detail.php?lab=54
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: 
http://fisher.berkeley.edu/~edna/lab_test/members/matzke.html
Lab phone: 510-643-6299
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Office hours for Bio1B: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================

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