Re: [Rpy] rpy2 install on redhat 6.7

[Larry Martell]

I also tried building rpy2 from source and that failed with:

gcc -pthread -shared
build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o
-L/usr/local/lib64/R/lib -Lbuild/temp.linux-x86_64-2.7
-Wl,-R/usr/local/lib64/R/lib -lRblas -lgfortran -lm -lreadline -lpcre
-llzma -lbz2 -lz -lrt -ldl -lm -lr_utils -o
build/lib.linux-x86_64-2.7/rpy2/rinterface/_rinterface.so
-Wl,--export-dynamic -fopenmp -Wl,--whole-archive
/usr/local/lib64/R/lib/libR.a -Wl,--no-whole-archive

/usr/bin/ld: cannot find -lr_utils

But I could not find how to get libr_utils.

On Sun, Jul 16, 2017 at 10:33 AM, Larry Martell  wrote:
> I upgraded to R 3.3.3 and now the rpy2 install fails with this:
>
> Collecting rpy2
>
>   Using cached rpy2-2.8.6.tar.gz
>
> Requirement already satisfied (use --upgrade to upgrade): six in
> /usr/local/lib/python2.7/site-packages (from rpy2)
>
> Requirement already satisfied (use --upgrade to upgrade):
> singledispatch in /usr/local/lib/python2.7/site-packages (from rpy2)
>
> Installing collected packages: rpy2
>
>   Running setup.py install for rpy2 ... error
>
> Complete output from command /usr/local/bin/python2.7 -u -c
> "import setuptools,
> tokenize;__file__='/tmp/pip-build-eFwk3n/rpy2/setup.py';exec(compile(getattr(tokenize,
> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
> 'exec'))" install --record /tmp/pip-w5v7yg-record/install-record.txt
> --single-version-externally-managed --compile:
>
> R version 3.3.3 (2017-03-06) -- "Another Canoe"
>
> /usr/local/lib64/R/bin/R CMD config --ldflags
>
> /usr/local/lib64/R/bin/R CMD config --cppflags
>
>
>
> Compilation parameters for rpy2's C components:
>
> include_dirs= ['/usr/local/lib64/R/include']
>
> library_dirs= ['/usr/local/lib64/R/lib']
>
> libraries   = ['Rblas', 'gfortran', 'm', 'readline',
> 'pcre', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm']
>
> extra_link_args = ['-Wl,--export-dynamic', '-fopenmp',
> '-Wl,--whole-archive', '/usr/local/lib64/R/lib/libR.a',
> '-Wl,--no-whole-archive']
>
>
>
> running install
>
> running build
>
> running build_py
>
> creating build
>
> creating build/lib.linux-x86_64-2.7
>
> creating build/lib.linux-x86_64-2.7/rpy2
>
> copying ./rpy/__init__.py -> build/lib.linux-x86_64-2.7/rpy2
>
> copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
>
> copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
>
> copying ./rpy/tests.py -> build/lib.linux-x86_64-2.7/rpy2
>
> creating build/lib.linux-x86_64-2.7/rpy2/rlike
>
> copying ./rpy/rlike/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
>
> copying ./rpy/rlike/indexing.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
>
> copying ./rpy/rlike/container.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
>
> copying ./rpy/rlike/functional.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
>
> creating build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> copying ./rpy/rlike/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> copying ./rpy/rlike/tests/test_indexing.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> copying ./rpy/rlike/tests/test_functional.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> copying ./rpy/rlike/tests/test_container.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>
> creating build/lib.linux-x86_64-2.7/rpy2/rinterface
>
> copying ./rpy/rinterface/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface
>
> creating build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpSymbol.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpVector.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_Sexp.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpExtPtr.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpEnvironment.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_EmbeddedR.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_SexpClosure.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> copying ./rpy/rinterface/tests/test_Device.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>
> creating build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> copying ./rpy/robjects/functions.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
>
> 

Re: [Rpy] rpy2 install on redhat 6.7

[Larry Martell]

Yes, I see that warning, but I have R version 3.1.0 and the rpy2 docs
say it works with 3.1+

How do I fix the 'R headers cannot be found' issue? I do have R-devel installed.

On Mon, Jul 10, 2017 at 6:34 PM, Laurent Gautier  wrote:
> R headers cannot be found.
>
> Note that there is a warning about the R version being too old for support
> with that version of rpy2 ( maybe it will work, maybe it won't).
>
> On Mon, Jul 10, 2017, 11:18 AM Larry Martell 
> wrote:
>>
>> Trying to install rpy2 on redhat 6.7. I have R version 3.1.0:
>>
>> $ R --version
>>
>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>>
>> Here is what I get from pip2.7 install rpy2:
>>
>> $ pip install rpy2
>>
>> Collecting rpy2
>>   Downloading rpy2-2.8.6.tar.gz (191kB)
>> 100% || 194kB 1.3MB/s
>> Requirement already satisfied (use --upgrade to upgrade): six in
>> /usr/local/lib/python2.7/site-packages (from rpy2)
>> Collecting singledispatch (from rpy2)
>>   Downloading singledispatch-3.4.0.3-py2.py3-none-any.whl
>> Installing collected packages: singledispatch, rpy2
>>   Running setup.py install for rpy2 ... error
>> Complete output from command /usr/local/bin/python2.7 -u -c
>> "import setuptools,
>>
>> tokenize;__file__='/tmp/pip-build-cM5dhd/rpy2/setup.py';exec(compile(getattr(tokenize,
>> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
>> 'exec'))" install --record /tmp/pip-zyalf5-record/install-record.txt
>> --single-version-externally-managed --compile:
>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>> /tmp/pip-build-cM5dhd/rpy2/setup.py:236: UserWarning: R did not
>> seem to have the minimum required version number
>>   warnings.warn("R did not seem to have the minimum required
>> version number")
>> /usr/local/lib64/R/bin/R CMD config --ldflags
>> R was not built as a library
>> /usr/local/lib64/R/bin/R CMD config --cppflags
>> R was not built as a library
>> /tmp/pip-build-cM5dhd/rpy2/setup.py:251: UserWarning: No include
>> specified
>>   warnings.warn('No include specified')
>> /tmp/pip-build-cM5dhd/rpy2/setup.py:262: UserWarning: No libraries
>> as -l arguments to the compiler.
>>   warnings.warn('No libraries as -l arguments to the compiler.')
>>
>> Compilation parameters for rpy2's C components:
>> include_dirs= []
>> library_dirs= []
>> libraries   = []
>> extra_link_args = []
>>
>> running install
>> running build
>> running build_py
>> creating build
>> creating build/lib.linux-x86_64-2.7
>> creating build/lib.linux-x86_64-2.7/rpy2
>> copying ./rpy/__init__.py -> build/lib.linux-x86_64-2.7/rpy2
>> copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy
>> copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
>> copying ./rpy/tests.py -> build/lib.linux-x86_64-2.7/rpy2
>> creating build/lib.linux-x86_64-2.7/rpy2/rlike
>> copying ./rpy/rlike/__init__.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rlike
>> copying ./rpy/rlike/indexing.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rlike
>> copying ./rpy/rlike/container.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rlike
>> copying ./rpy/rlike/functional.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rlike
>> creating build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>> copying ./rpy/rlike/tests/__init__.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>> copying ./rpy/rlike/tests/test_indexing.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>> copying ./rpy/rlike/tests/test_functional.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>> copying ./rpy/rlike/tests/test_container.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
>> creating build/lib.linux-x86_64-2.7/rpy2/rinterface
>> copying ./rpy/rinterface/__init__.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rinterface
>> creating build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>> copying ./rpy/rinterface/tests/test_SexpSymbol.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>> copying ./rpy/rinterface/tests/__init__.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>> copying ./rpy/rinterface/tests/test_SexpVector.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>> copying ./rpy/rinterface/tests/test_Sexp.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>> copying ./rpy/rinterface/tests/test_SexpExtPtr.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>> copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>> copying ./rpy/rinterface/tests/test_SexpEnvironment.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>> copying ./rpy/rinterface/tests/test_EmbeddedR.py ->
>> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
>> copying ./rpy/rinterface/tests/test_SexpClosure.py 

Re: [Rpy] rpy2 install on redhat 6.7

[Laurent Gautier]

R headers cannot be found.

Note that there is a warning about the R version being too old for support
with that version of rpy2 ( maybe it will work, maybe it won't).

On Mon, Jul 10, 2017, 11:18 AM Larry Martell 
wrote:

> Trying to install rpy2 on redhat 6.7. I have R version 3.1.0:
>
> $ R --version
>
> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>
> Here is what I get from pip2.7 install rpy2:
>
> $ pip install rpy2
>
> Collecting rpy2
>   Downloading rpy2-2.8.6.tar.gz (191kB)
> 100% || 194kB 1.3MB/s
> Requirement already satisfied (use --upgrade to upgrade): six in
> /usr/local/lib/python2.7/site-packages (from rpy2)
> Collecting singledispatch (from rpy2)
>   Downloading singledispatch-3.4.0.3-py2.py3-none-any.whl
> Installing collected packages: singledispatch, rpy2
>   Running setup.py install for rpy2 ... error
> Complete output from command /usr/local/bin/python2.7 -u -c
> "import setuptools,
>
> tokenize;__file__='/tmp/pip-build-cM5dhd/rpy2/setup.py';exec(compile(getattr(tokenize,
> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
> 'exec'))" install --record /tmp/pip-zyalf5-record/install-record.txt
> --single-version-externally-managed --compile:
> R version 3.1.0 (2014-04-10) -- "Spring Dance"
> /tmp/pip-build-cM5dhd/rpy2/setup.py:236: UserWarning: R did not
> seem to have the minimum required version number
>   warnings.warn("R did not seem to have the minimum required
> version number")
> /usr/local/lib64/R/bin/R CMD config --ldflags
> R was not built as a library
> /usr/local/lib64/R/bin/R CMD config --cppflags
> R was not built as a library
> /tmp/pip-build-cM5dhd/rpy2/setup.py:251: UserWarning: No include
> specified
>   warnings.warn('No include specified')
> /tmp/pip-build-cM5dhd/rpy2/setup.py:262: UserWarning: No libraries
> as -l arguments to the compiler.
>   warnings.warn('No libraries as -l arguments to the compiler.')
>
> Compilation parameters for rpy2's C components:
> include_dirs= []
> library_dirs= []
> libraries   = []
> extra_link_args = []
>
> running install
> running build
> running build_py
> creating build
> creating build/lib.linux-x86_64-2.7
> creating build/lib.linux-x86_64-2.7/rpy2
> copying ./rpy/__init__.py -> build/lib.linux-x86_64-2.7/rpy2
> copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy
> copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
> copying ./rpy/tests.py -> build/lib.linux-x86_64-2.7/rpy2
> creating build/lib.linux-x86_64-2.7/rpy2/rlike
> copying ./rpy/rlike/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike
> copying ./rpy/rlike/indexing.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike
> copying ./rpy/rlike/container.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike
> copying ./rpy/rlike/functional.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike
> creating build/lib.linux-x86_64-2.7/rpy2/rlike/tests
> copying ./rpy/rlike/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
> copying ./rpy/rlike/tests/test_indexing.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
> copying ./rpy/rlike/tests/test_functional.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
> copying ./rpy/rlike/tests/test_container.py ->
> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
> creating build/lib.linux-x86_64-2.7/rpy2/rinterface
> copying ./rpy/rinterface/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface
> creating build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/test_SexpSymbol.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/test_SexpVector.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/test_Sexp.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/test_SexpExtPtr.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/test_SexpEnvironment.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/test_EmbeddedR.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/test_SexpClosure.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> copying ./rpy/rinterface/tests/test_Device.py ->
> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
> creating build/lib.linux-x86_64-2.7/rpy2/robjects
> copying ./rpy/robjects/__init__.py ->
> build/lib.linux-x86_64-2.7/rpy2/robjects
> copying ./rpy/robjects/functions.py ->
>