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Please give a solution of installation on Linux

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Please give a solution of installation on Linux

Postby chenlpu » Fri Jul 22, 2005 18:35

Since most practical machine learning tasks are very resource intensive, can anyone give a clear report of a successful Linux installation ?
In our lab, we have a very powerful Linux server, but until now we can not install orange on it.
In previous thread, author mentioned that the setup.py can do the installation. However, I tried it on newest FC4 but it failed.

3x

My error messages

Postby chenlpu » Fri Jul 22, 2005 18:49

-----------------------------------------------------------------------
Here is the error message from my installation
OS: FC4 Linux with GCC 4.0 Python 2.4
orange: snapshot 07 22
on source, make

Code: Select all
(for MODULE in include orange orangeom orangene corn statc ; \
   do make all -C $MODULE OLD=../..; done)
make[1]: Entering directory `/home/chenl/TOOLS/og-snap/orange/source/include'
g++ -fPIC -fpermissive -w -DLINUX -O3 -c stat.cpp -o obj/stat.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c statexceptions.cpp -o obj/statexceptions.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c strings.cpp -o obj/strings.o
ar -r ../../liborange_include.a obj/c2py.o obj/common.o obj/crc32.o obj/lcomb.o obj/stat.o obj/statexceptions.o obj/strings.oar: creating ../../liborange_include.a
make[1]: Leaving directory `/home/chenl/TOOLS/og-snap/orange/source/include'
make[1]: Entering directory `/home/chenl/TOOLS/og-snap/orange/source/orange'
Makefile:5: makefile.deps: No such file or directory
python ../pyxtract/makedep.py -n ORANGE
externs.px
lib_vectors.px
lib_io.px
cls_orange.px
functions.px
cls_example.px
cls_misc.px
cls_value.px
lib_learner.px
lib_kernel.px
orange.px
initialization.px
lib_components.px
lib_preprocess.px
rm -f ppp/stamp
rm -f px/stamp
make[1]: Leaving directory `/home/chenl/TOOLS/og-snap/orange/source/orange'
make[1]: Entering directory `/home/chenl/TOOLS/og-snap/orange/source/orange'
python ../pyxtract/pyprops.py -q -n ORANGE
python ../pyxtract/pyxtract.py -m -q -n ORANGE lib_vectors.cpp lib_io.cpp cls_orange.cpp functions.cpp cls_example.cpp cls_misc.cpp cls_value.cpp lib_learner.cpp lib_kernel.cpp pythonvars.cpp distancemap.cpp orange.cpp lib_components.cpp callback.cpp lib_preprocess.cpp
g++ -fPIC -fpermissive -w -DLINUX -O3 -c assistant.cpp -o obj/assistant.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c assoc.cpp -o obj/assoc.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c assoc_sparse.cpp -o obj/assoc_sparse.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c basket.cpp -o obj/basket.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c basstat.cpp -o obj/basstat.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c bayes.cpp -o obj/bayes.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c boolcnt.cpp -o obj/boolcnt.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c c4.5.cpp -o obj/c4.5.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c c45inter.cpp -o obj/c45inter.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c calibrate.cpp -o obj/calibrate.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c callback.cpp -o obj/callback.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c cartesian.cpp -o obj/cartesian.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c clas_gen.cpp -o obj/clas_gen.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c classfromvar.cpp -o obj/classfromvar.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c classifier.cpp -o obj/classifier.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c cls_example.cpp -o obj/cls_example.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c cls_misc.cpp -o obj/cls_misc.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c cls_orange.cpp -o obj/cls_orange.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c cls_value.cpp -o obj/cls_value.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c contingency.cpp -o obj/contingency.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c converts.cpp -o obj/converts.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c cost.cpp -o obj/cost.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c costwrapper.cpp -o obj/costwrapper.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c decomposition.cpp -o obj/decomposition.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c dictproxy.cpp -o obj/dictproxy.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c discretize.cpp -o obj/discretize.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c dist_clustering.cpp -o obj/dist_clustering.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c distance.cpp -o obj/distance.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c distance_dtw.cpp -o obj/distance_dtw.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c distancemap.cpp -o obj/distancemap.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c distvars.cpp -o obj/distvars.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c domain.cpp -o obj/domain.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c domaindepot.cpp -o obj/domaindepot.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c errors.cpp -o obj/errors.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c estimateprob.cpp -o obj/estimateprob.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c exampleclustering.cpp -o obj/exampleclustering.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c examplegen.cpp -o obj/examplegen.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c examples.cpp -o obj/examples.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c excel.cpp -o obj/excel.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c filegen.cpp -o obj/filegen.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c filter.cpp -o obj/filter.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c functions.cpp -o obj/functions.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c garbage.cpp -o obj/garbage.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c getarg.cpp -o obj/getarg.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c graph.cpp -o obj/graph.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c gslconversions.cpp -o obj/gslconversions.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c hclust.cpp -o obj/hclust.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c imputation.cpp -o obj/imputation.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c induce.cpp -o obj/induce.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c jit_linker.cpp -o obj/jit_linker.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c knn.cpp -o obj/knn.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c learn.cpp -o obj/learn.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c lib_components.cpp -o obj/lib_components.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c lib_io.cpp -o obj/lib_io.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c lib_kernel.cpp -o obj/lib_kernel.o
python ../pyxtract/jitlink_build.py R.so r_imports.hpp
g++ -fPIC -fpermissive -w -DLINUX -O3 -c lib_learner.cpp -o obj/lib_learner.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c lib_preprocess.cpp -o obj/lib_preprocess.o
lib_preprocess.cpp:376: error: explicit specialization of ‘int MapMethods<PVariableFilterMap, TOrangeMap_KV<PVariable, PValueFilter>, PVariable, PValueFilter>::_setitemlow(TOrangeMap_KV<PVariable, PValueFilter>*, PyObject*, PyObject*)’ must be introduced by ‘template <>’
lib_preprocess.cpp:376: error: template-id ‘_setitemlow<>’ for ‘int MapMethods<PVariableFilterMap, TOrangeMap_KV<PVariable, PValueFilter>, PVariable, PValueFilter>::_setitemlow(TOrangeMap_KV<PVariable, PValueFilter>*, PyObject*, PyObject*)’ does not match any template declaration
lib_preprocess.cpp:376: error: invalid function declaration
lib_preprocess.cpp:384: error: explicit specialization of ‘PyObject* MapMethods<PVariableFilterMap, TOrangeMap_KV<PVariable, PValueFilter>, PVariable, PValueFilter>::_setdefault(TPyOrange*, PyObject*)’ must be introduced by ‘template <>’
lib_preprocess.cpp:384: error: template-id ‘_setdefault<>’ for ‘PyObject* MapMethods<PVariableFilterMap, TOrangeMap_KV<PVariable, PValueFilter>, PVariable, PValueFilter>::_setdefault(TPyOrange*, PyObject*)’ does not match any template declaration
lib_preprocess.cpp:384: error: invalid function declaration
make[1]: *** [obj/lib_preprocess.o] Error 1
make[1]: Leaving directory `/home/chenl/TOOLS/og-snap/orange/source/orange'
make[1]: Entering directory `/home/chenl/TOOLS/og-snap/orange/source/orangeom'
Makefile:5: makefile.deps: No such file or directory
python ../pyxtract/makedep.py -n ORANGEOM
triangulate.px
externs.px
initialization.px
rm -f ppp/stamp
rm -f px/stamp
make[1]: Leaving directory `/home/chenl/TOOLS/og-snap/orange/source/orangeom'
make[1]: Entering directory `/home/chenl/TOOLS/og-snap/orange/source/orangeom'
python ../pyxtract/pyxtract.py -m -q -n ORANGEOM triangulate.cpp optimizeAnchors.cpp orangeom.cpp -l ../orange/px/stamp
g++ -fPIC -fpermissive -w -DLINUX -O3 -c optimizeAnchors.cpp -o obj/optimizeAnchors.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c orangeom.cpp -o obj/orangeom.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c triangulate.cpp -o obj/triangulate.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c wml/WmlDelaunay2a.cpp -o obj/WmlDelaunay2a.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c wml/WmlMath.cpp -o obj/WmlMath.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c wml/WmlSystem.cpp -o obj/WmlSystem.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c wml/WmlVector2.cpp -o obj/WmlVector2.o
gcc obj/optimizeAnchors.o obj/orangeom.o obj/triangulate.o obj/WmlDelaunay2a.o obj/WmlMath.o obj/WmlSystem.o obj/WmlVector2.o -shared -lstdc++ -L../.. -lorange_include -lorange -o ../../orangeom.so
/usr/bin/ld: cannot find -lorange
collect2: ld returned 1 exit status
make[1]: *** [../../orangeom.so] Error 1
make[1]: Leaving directory `/home/chenl/TOOLS/og-snap/orange/source/orangeom'
make[1]: Entering directory `/home/chenl/TOOLS/og-snap/orange/source/orangene'
Makefile:5: makefile.deps: No such file or directory
python ../pyxtract/makedep.py -n ORANGENE
externs.px
initialization.px
orangene.px
rm -f ppp/stamp
rm -f px/stamp
make[1]: Leaving directory `/home/chenl/TOOLS/og-snap/orange/source/orangene'
make[1]: Entering directory `/home/chenl/TOOLS/og-snap/orange/source/orangene'
python ../pyxtract/pyprops.py -q -n ORANGENE -l ../orange/ppp/stamp
Warning: type TIntList, required by THeatmap.exampleIndices not registered
python ../pyxtract/pyxtract.py -m -q -n ORANGENE orangene.cpp heatmap.cpp -l ../orange/px/stamp
g++ -fPIC -fpermissive -w -DLINUX -O3 -c heatmap.cpp -o obj/heatmap.o
g++ -fPIC -fpermissive -w -DLINUX -O3 -c orangene.cpp -o obj/orangene.o
gcc obj/heatmap.o obj/orangene.o -shared -lstdc++ -L../.. -lorange_include -lorange -o ../../orangene.so
/usr/bin/ld: cannot find -lorange
collect2: ld returned 1 exit status
make[1]: *** [../../orangene.so] Error 1
make[1]: Leaving directory `/home/chenl/TOOLS/og-snap/orange/source/orangene'
make[1]: Entering directory `/home/chenl/TOOLS/og-snap/orange/source/corn'
g++ -fPIC -fpermissive -w -DLINUX -O3 -c corn.cpp -o obj/corn.o
gcc obj/corn.o -shared -lstdc++ -L../.. -lorange_include -lorange -o ../../corn.so
/usr/bin/ld: cannot find -lorange
collect2: ld returned 1 exit status
make[1]: *** [../../corn.so] Error 1
make[1]: Leaving directory `/home/chenl/TOOLS/og-snap/orange/source/corn'
make[1]: Entering directory `/home/chenl/TOOLS/og-snap/orange/source/statc'
make[1]: *** No rule to make target `../../liborange.so', needed by `obj/statc.o'.  Stop.
make[1]: Leaving directory `/home/chenl/TOOLS/og-snap/orange/source/statc'
make: *** [all] Error 2


Here is the error message from using "python setup.py install"
Code: Select all
running install
Using default system initialization, checking for privileges...
done
running build
running build_py
package init file '__init__.py' not found (or not a regular file)
package init file 'OrangeCanvas/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Associate/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Classify/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Data/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Evaluate/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Other/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Visualize/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/icons/__init__.py' not found (or not a regular file)
package init file '__init__.py' not found (or not a regular file)
package init file 'OrangeCanvas/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Associate/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Classify/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Data/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Evaluate/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Other/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/Visualize/__init__.py' not found (or not a regular file)
package init file 'OrangeWidgets/icons/__init__.py' not found (or not a regular file)
running install_lib
running install_data
error: can't copy 'orange.so': doesn't exist or not a regular file

Postby jurem » Tue Aug 16, 2005 4:03

Hi,
sorry for late reply.

Problem is, that Orange is not yet ported to the Python 2.4. I hope it will be ready soon.
Installation with setup.py fails, because Orange is not yet compiled.

Regards, Jure

Postby Janez » Tue Aug 16, 2005 8:56

Jure, I believe the problem is not in Python 2.4 but in gcc 4.0. I have built Orange against Python 2.4 (on Windows) without any modifications.

By the compiler's error message I'd say that they have AGAIN played with the templates in gcc 4.0. There's nothing related to Python's headers/libraries in the message. Wait till I come home and we'll have another session of gcc cursing.

Postby biodan » Wed Aug 17, 2005 15:41

It is not only a problem with gcc 4 - it also occurs with the 0.96 source using gcc 3.2.3 with Python 2.4.1 on RH EL (Enterprise Linux).

I copied the pyExtract-0.2.1 into the source folder & renamed it pxtract. There was no makedep.py file in the pyExtract. BTW, Google gave me zero hits for 'pyxtract'.

edit: BTW, i think Orange has great promise. I'd like to thank the developers &contributors on the thoughtful design and look forward to further enhancements.

Here are the compilation errors:
------------------------------
(for MODULE in include orange orangeom orangene corn statc ; \
do make all -C $MODULE OLD=../..; done)
make[1]: Entering directory `/usr/local/orange/source/include'
Makefile:5: makefile.deps: No such file or directory
python ../pyxtract/makedep.py -n INCLUDE
python: can't open file '../pyxtract/makedep.py': [Errno 2] No such file or directory
make[1]: *** [makefile.deps] Error 2
make[1]: Leaving directory `/usr/local/orange/source/include'
make[1]: Entering directory `/usr/local/orange/source/orange'
Makefile:5: makefile.deps: No such file or directory
python ../pyxtract/makedep.py -n ORANGE
python: can't open file '../pyxtract/makedep.py': [Errno 2] No such file or directory
make[1]: *** [makefile.deps] Error 2
make[1]: Leaving directory `/usr/local/orange/source/orange'
make: *** orangeom: No such file or directory. Stop.
make: *** orangene: No such file or directory. Stop.
make[1]: Entering directory `/usr/local/orange/source/corn'
gcc obj/corn.o -shared -lstdc++ -L../.. -lorange_include -lorange -o ../../corn.so
/usr/bin/ld: cannot find -lorange_include
collect2: ld returned 1 exit status
make[1]: *** [../../corn.so] Error 1
make[1]: Leaving directory `/usr/local/orange/source/corn'
make[1]: Entering directory `/usr/local/orange/source/statc'
make[1]: *** No rule to make target `../../liborange.so', needed by `obj/statc.o'. Stop.
make[1]: Leaving directory `/usr/local/orange/source/statc'
make: *** [all] Error 2
--------------------------------------

Janez wrote:Jure, I believe the problem is not in Python 2.4 but in gcc 4.0. I have built Orange against Python 2.4 (on Windows) without any modifications.

By the compiler's error message I'd say that they have AGAIN played with the templates in gcc 4.0. There's nothing related to Python's headers/libraries in the message. Wait till I come home and we'll have another session of gcc cursing.

Postby tomaz » Thu Oct 27, 2005 11:21

For Linux installation please see download page.


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