y and Rpy2 that could help me to decide what to install.
>
> Thanks,
The two have different APIs, and are not directly interchangeable.
The original rpy v1 is no longer being developed, so unless you need
it for some existing code using rpy (v1), go with rpy2.
Peter
---
(2012-03-30)
> ...
>
> Any help would be greatly appreciated.
That looks like the old problem of the regular expression not
expecting two digits in the minor part of the major.minor.revision
scheme. IIRC that is fixed in the repository - since you are
installing from source it should be e
and R-2.12.1 and both Python 26 and Python 27.
>
> Is there a problem with rpy version?
>
> Marko
I see now you're on Windows - did you have Python 2.7 and
R 2.12.1 installed BEFORE using the rpy-1.0.3.win32-py2.7-R.2.12.1
installed?
Peter
what would be the problem?
>
> Thank you,
> Marko
What does this give at the command line?
R --version
What version of rpy do you have? There was a problem with
the two digit revision number (fixed in SVN).
Peter
---
On Mon, Dec 12, 2011 at 3:18 PM, Marko Limbek wrote:
> Thank you Peter, but with me it doesn't work,
> as you can see from the printscreen in the attachment, that I send you.
> I followed all four steps.
> The warning in the picture says that variable resmca is not used.
>
&
mplex R objects unconverted (because converting them
to Python objects was lossy), especially if doing more
analysis with them within R.
> Anyway I will have to switch to rpy2, because the matching
> problem is apparently unsolvable here.
It probably can be solved, but you would be better o
nary. It
wasn't part of standard Python when rpy
was written.
As I have suggested earlier, it might be
worth looking at rpy2 instead.
Peter
--
Learn Windows Azure Live! Tuesday, Dec 13, 2011
Microsoft is holding a spe
aders/.
> I tried to append it in the include search path. Unfortunately this yields
> other errors.
See http://sourceforge.net/mailarchive/message.php?msg_id=28082544
This is fixed in SVN, but there is one more potential problem blocking
releasing an rpy 1.0.4 maintenance release with findin
On Thu, Dec 8, 2011 at 9:50 AM, Marko Limbek wrote:
>
> Hello Peter,
>
> I enclose R code, Python code (for_peter, nominalise) and data.
> these outputs of 'factanal' in R and PYTHON should be the same,
> but are slightly different.
>
> ...
The last line of
o show this? Ideally
both the R version any your Rpy version.
Also what version of R, Python and RPy are you using?
Peter
--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to se
t,
> Marko
The function sorted(...) is a quick fix for iterating over small dicts.
There are also dictionary subclasses which preserve the order.
Something like that might be more appropriate.
Peter
--
Cloud
On Thu, Nov 3, 2011 at 3:01 PM, remy d1 wrote:
> Hi Peter,
> Thanks for help.
> I downloaded rpy from svn (with svn co ...) and I tried to install rpy with
> it (in trunk/rpy directory, but it is version 1.0.3...), but it did not
> work. I still have the same error
You mean this
3 which has a few issues,
and compile from source. If you get this:
/usr/bin/ld: cannot find -lRlapack
then edit setup,py to replace libraries=['R','Rlapack'] with
libraries=['R','lapack']
I've been meaning to work out when to make that last change
aut
On Tue, Sep 13, 2011 at 7:23 PM, Laurent Gautier wrote:
> On 2011-09-13 18:48, Peter Cock wrote:
>>
>> I then fell over what was a new problem for me (/usr/bin/ld: cannot
>> find -lRlapack), but has been reported for rpy2:
>> http://www.mail-archive.com/rpy-list@lis
setup.py to change the lines:
libraries=['R','Rlapack']
to:
libraries=['R','lapack']
This last change has not yet been made in SVN.
Could that be done and another release be made please?
How can I help?
Peter
-
his last change has not yet been made in SVN.
Could that be done and another release be made please?
How can I help?
Peter
--
BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
Learn about the latest advances in
t know how to fix it. Additionally RPy2 hasn't
> solved the problem yet.
Can you give a self contained example in R, and your attempt in Python?
e.g. Try using one of the many built in example datasets in R.
Peter
-
t have dots,
that is what the SyntaxError is trying to tell you.
The fact you then get an "not all arguments have the same length"
suggests there is a secondary problem in your script. I'm not
familiar with the R package survcomp so I
late it?
> Any help is much appreciated,
Which version of rpy or rpy2 are you using?
Peter
--
Benefiting from Server Virtualization: Beyond Initial Workload
Consolidation -- Increasing the use of server virtualization
thanks laurent,
i just needed to remove the '2.1.0dev' which installed by default when i ran
setup.py after cloning the repository and do the following:
hg update -C
before running setup.py install.
this may be obvious but just in case someone else gets confused...
cheers,
p
ot;, line 2, in
AttributeError: 'module' object has no attribute 'aes_string'
any ideas?
Thanks,
Peter
--
Protect Your Site and Customers from Malware Attacks
Learn about various malware tactics and how
SOLVED
had inadvertently installed rpy previously. probably due to having
downloaded the entire repository (rpy and rpy2 branches). simply
followed the instructions here to remove existing rpy installation and
reinstalled from the rpy repo here:
http://www.bitbucket.org/lgautier/rpy2/
peter
On
Any hints even?
thanks and apologies if this is an obvious question
--
Peter
On Thursday, January 13, 2011 at 5:29 PM, Peter wrote:
> Hi,
>
> Im trying to load the rpy libraries for ggplot 2 and importr. I'm on
> Ubuntu 10.10 x64 with R packages installed using ap
==
FAIL: testCallErrorWhenEndedR
(rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
--
Traceback (most recent call last):
File
"/usr/local/lib/python2.6/dist-packages/rpy2/rinterface/tests/test_EmbeddedR.py
]
>
> Is this the right approach or is there a better way?
>
Depending on how you use the data structure, a Python dict
(dictionary - like a Perl hash) might work (but you lose the order).
As of Python 2.7, there is an ordered-dictionary class included
in the collections module - but I don&#
default to the MSVC compiler, try:
python setup.py build --compiler=mingw32
Or, create/edit the file distutils.cfg to make mingw32 the default
compiler for distutils.
Peter
--
The Next 800 Companies to Lead America'
ller you don't run setup.py ;)
Peter
--
The Next 800 Companies to Lead America's Growth: New Video Whitepaper
David G. Thomson, author of the best-selling book "Blueprint to a
Billion" shares his insights a
e up). Have you tried the Windows
installers instead (most recent looks like rpy 2.0.8)?
Peter
--
The Next 800 Companies to Lead America's Growth: New Video Whitepaper
David G. Thomson, author of the best-selling book &
esult of an earlier attempt to get this working.
> Your fix appears to do the job
>
> Thankyou!
Well spotted - I was just writing a reply to clarify if you'd set R_HOME like
that. I'm glad the fix works - Laurent, can you apply this to the repository?
Peter
--
(R_HOME, 'bin', 'i386', 'R.dll')
as a possible location for the DLL to rinterface\__init__.py
Could you post the full traceback?
Peter
--
Nokia and AT&T present the 2010 Calling All In
On Wed, Oct 27, 2010 at 9:26 PM, Deschamps, Benjamin
wrote:
> Peter,
>
> If you re-read my original post, you can see that that location was
> already included in my path... But I agree, I think that rpy2 is
> expecting the R.dll to be in C:\Program Files\R\R-2.12.0\bin and is n
ram Files\R\R-2.12.0\bin\i386
If that works, then rpy2 might be changed able to look there automatically
based on the RHOME location.
Peter
--
Nokia and AT&T present the 2010 Calling All Innovators-North America conte
/eigenvectors.tiff",type="Float32",driver="GTiff")
> """)
>
I wouldn't try and use both rpy and rpy2 in the same script.
Also you don't seem to be using the os, time, string,
unsucsessful), or on
any version of Windows 7 (again, I found an email where
someone tried and failed).
Note that trying rpy2 is also going to be hard work, since Laurent
doesn't have a Windows machine to develop on.
Peter
-
On Fri, Aug 6, 2010 at 8:59 AM, jul wrote:
>
> Use :
> from rpy import *
> instead of:
> import rpy
You can use "from rpy import *" and then just "r", or
"import rpy" and then "rpy.r".
It looks
below). Does anyone have any idea on what is
>> going on?
>>
>> Thanks,
>>
>> Fong
>> ...
>> Exception: "/home/fong/R-2.11.1/bin/R" CMD config --cppflags
>> returned
What happens i
week :(
Hopefully next week... I hope the mingw32 output will be helpful,
I remember the error messages being noticeably different.
Regards,
Peter
--
___
rpy-list mailing li
in
my emails of 14 April? (Thread title "Windows installer for 2.1rc?").
Peter
--
___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list
of
> `R --version'. Does anyone know how to fix it?
What does running 'R --version' at the Windows command prompt do?
Peter
--
___
rpy-list mailin
ll__
return super(SignatureTranslatedFunction, self).__call__(*args,
**kwargs)
File
"/net/gs/vol1/home/psudmant/local_installations/python-2.6.4/lib/python2.6/site-packages/rpy2/robjects/functions.py",
line 35, in __call__
res = super(Function, self).__call__(*new_ar
velopment toolkit (mingw and some unix tools). Check
> the R FAQ for Windows.
You're right. I'd resolved this, I was missing make. With that installed
via cygwin doing "R CMD config --cppflags" and related calls works fine.
I sent some follow up emails about the next proble
On Wed, Apr 14, 2010 at 5:40 PM, Peter wrote:
> On Wed, Apr 14, 2010 at 5:24 PM, Peter wrote:
>> On Wed, Apr 14, 2010 at 5:14 PM, Peter
>> wrote:
>>>
>>> There is no Rinterface.h file under C:\Program
>>> Files\R\R-2.10.1\include (nor C:\Program Files
On Wed, Apr 14, 2010 at 5:24 PM, Peter wrote:
> On Wed, Apr 14, 2010 at 5:14 PM, Peter wrote:
>>
>> There is no Rinterface.h file under C:\Program
>> Files\R\R-2.10.1\include (nor C:\Program Files\R\R-2.9.2\include or
>> C:\Program Files\R\R-2.8.1\include either).
&
On Wed, Apr 14, 2010 at 5:14 PM, Peter wrote:
>
> There is no Rinterface.h file under C:\Program
> Files\R\R-2.10.1\include (nor C:\Program Files\R\R-2.9.2\include or
> C:\Program Files\R\R-2.8.1\include either).
>
I thought this seemed familiar - Laurent Oget had the same issue
ryfunc) NA_unaryfunc, /* nb_absolute; */
(inquiry) NA_nonzero, /* nb_nonzero; /* Used by PyObject_IsTrue */
(unaryfunc) NA_unaryfunc, /* nb_invert; */
(binaryfunc) NA_binaryfunc, /* nb_lshift; */
Peter
--
Download In
On Mon, Apr 12, 2010 at 7:33 PM, Peter wrote:
>
> Any idea how calling "R CMD config --cppflags" behaved? That seems to
> be the stumbling block at the moment and has nothing to do with Python
> or the compiler for rpy2. It could be something funny on my machine...
>
I
sing in the distributed tarball. Was that an oversight, or is it
> correct?
>
> Thanks.
Oh - something specific for Sean Davis' GEOquery module in BioConductor?
http://www.bioconductor.org/packages/2.6/bioc/html/GEOquery.html
Sounds useful for those doing (re)
On Mon, Apr 12, 2010 at 7:20 PM, Laurent Gautier wrote:
>
> On 4/12/10 7:46 PM, Peter wrote:
>>
>> Hi Laurent,
>>
>> Apologies if this is a bit curt/blunt - I'm running late and just
>> squeezed in an attempt to build rpy2 (from the zip file for 2.1.0rc)
-2.9.2 and
R-2.8.2. Just in case it was the problem, I edited my PATH again to
remove C:\cygwin\bin\;C:\cygwin\usr\bin\; and retried, but R acts the
same way.
However, ignoring that, it claims my R installs were not built as libraries (?).
I wonder if this is a Windows specific bug in the config
ons of R? That was quite a useful feature since R releases
are so frequent that not everyone will be using the same one.
If not, would people just want to use the latest R release?
Peter
--
Download Intel® Parallel Studio Ev
here are online tutorials and
several good books) before trying to use rpy or rpy2.
Peter
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, an
o
What command would you use in R, or are you new to R as well?
Peter
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applicatio
oring a GSoC project combining (Bio)python and
rpy2 for accessing R phylogenetic tools from Python:
http://biopython.org/wiki/Google_Summer_of_Code
Peter
--
Download Intel® Parallel Studio Eval
Try the new software tools
of output,
furthermore it doesn't like you are comparing like with like.
What I was hoping you would show was a short R script
(maybe using one of the many built in datasets), with
its output, and your translation into python with rpy2
and
the numbers changed. They
> are totally different. I wonder whether there is any way to solve my problem
> or it is impossible??
>
> Zahra.
Can you construct a (small) self contained example to show the issue?
Peter
--
;)
> shapiro = robjects.r('shapiro.test')
As noted above, rpy2 does things differently. There are good reasons
for this (e.g. R now allows both dot and underscore in argument names,
while historically it did not allow dots).
Regards,
Peter
On Sat, Feb 6, 2010 at 7:46 AM, Laurent Gautier wrote:
>
> On 2/6/10 12:26 AM, Peter wrote:
>>
>> I recall seeing a bug report and fix to cope with the two digit
>> minor release number (the 10 in 2.10.1), try this:
>>
>> https://sourceforge.net/tracker/
sourceforge.net/tracker/?func=detail&atid=453021&aid=2940558&group_id=48422
These days rpy1 doesn't get so much attention (almost
all work is on rpy2 now), but I think it would be nice to
have another point release to include this fix for supporting
recent versions of R. There a
o do is manually remove these files (rpy.py,
py_wintools.py, rpy_version.py, rpy_tools.py, rpy_io.py, plus the
corresponding *.pyc files, and depending on what version of
Python you have there could also be an rpy-XXX.egg file).
Peter
y 1, and
means you can have both installed at the same time.
Peter
--
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14
2.3, 1.7, 3.7]
...
r.plot(x,y,ylim=(-30,30), xlim=(1,5))
Should this be:
p = [11.3, -0.7, -17.6, -6.7, -3.0, -17.6, -6.2, 24.0, 25.9, -26.3,
-19.3, -4.9, 5.5, -11.6, 6.6, -17.8]
t= [2.2, 2.4, 2.5, 1.7, 2.6, 2.8, 2.0, 2.9, 3.4, 3.7, 3.2, 3.2, 1.8,
2.3, 1.7, 3.7]
...
r.plot(t,p,ylim=(-30,30),
argument names, so this mapping isn't
100% safe.
I expect an rpy2 expert will clarify how you are intended to
do this, otherwise consult the docs.
Peter
--
Let Crystal Reports handle the reporting - Free Crystal Repo
k:
r("results$hclust$labels = seq(1,50)")
or
r("results$hclust$labels <- seq(1,50)")
This assumes the variable "results" existing in the R name space (and
not just in the Python namespace). You may need to assign it first,
rpy.r.assign("results",
gits minor version number (R is now 2.10).
> http://www.mail-archive.com/rpy-list@lists.sourceforge.net/msg02262.html
>
> HTH,
>
> L.
It sounds like it would be a good idea to do another rpy1 point release
h call
> would have). Moreover the caching is safe, as it will throw an exception in
> the function has a signature that cannot be translated safely.
>
> http://rpy.sourceforge.net/rpy2/doc-dev/html/robjects.html#functions
That sounds great :)
Peter
--
I used to just write directly to a PDF or PNG file, which bypasses
the whole dynamic popup windows thing and the complications it brings.
Note in rpy you'll need to use dev_off to access the dev.off function in R.
Peter
---
ample in full - complete examples are very useful
when asking for help :)
Regards,
Peter
--
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year.
On Mon, Oct 5, 2009 at 3:53 PM, Nick Schurch wrote:
>
> Thanks for the answer peter, but I'm still having an issue...
>
> When I try:
>
> result<-r.pvclust(data=data, method_hclust="complete",
> method_dist="correlation", nboot=1, init_ran
/bin
Just a guess, but try spelling out your home directory
in full (not just a tilde).
Peter
--
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this
On Wed, Sep 30, 2009 at 4:59 PM, Laurent Gautier wrote:
>
> Peter wrote:
>>
>> Can you do something like check if example_name is a valid argument
>> for the function at run time, and if not, check example.name instead?
>> Would this impose too high a performance
thing like check if example_name is a valid argument
for the function at run time, and if not, check example.name instead?
Would this impose too high a performance cost?
I agree this won't cover the special case of a function which has
two arguments which differ only in underscore vs dot,
simple, predictable, correct in vastly more cases than doing
> no conversion, and for the occasional weird edge-case you can still
> use rcall just like now (only the weird edge-cases are much rarer).
>
> -- Nathaniel
This is like the simple "." to "_" mapping in rpy1, very s
be
interested to see the benchmarks for the different approaches.
Peter
--
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing
x27;method'") is completely greek to
> me.
In Python, the dot means access a method/property of an object.
In R, a dot is just another character in a variable or function name.
Thus rpy maps "_" to "." to allow simple access to these otherwise
invalid R names from within
ython syntax. Also for calling
functions in Python use round brackets, square brackets (generally)
are for indexing.
Peter
--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify y
d")
>
> The .png file is created but it is empty.
You need to also close the output device, using dev.off() in R. Try:
r.dev_off()
at the end of your script.
Peter
--
Let Crystal Reports handle the reporting -
king a copy of the NumPy array
which should give you a continuous C ordered array which owns its
own memory.
Peter
--
___
rpy-list mailing list
rpy-list@lis
type (e.g. signed versus unsigned, or the precision)
I would try making an explicit copy of x to rule some of these issues.
Peter
--
___
rpy-list mailing list
On Sat, Jul 18, 2009 at 5:35 PM, Milton Cezar
Ribeiro wrote:
> Hi Peter,
>
> Thanks for your help.
> I must confess that I tryed to find the right link (with amd64 on the
> filename) without luck up to now. If anyone know what is the link, please,
> let me know.
There are
> python(2.5) from anywhere.
That installer is for 32 bit Windows (you can tell this from the win32
bit in the filename).
You need a 64bit installer! These have amd64 in the filename instead
(and will work on Intel's 64
his:
import rpy
rpy.set_default_mode(rpy.NO_CONVERSION)
#your code here:
rpy.r.library("Rdbi")
rpy.r.library("RdbiPgSQL")
rpy.r.dbConnect(rpy.r.PgSQL(),host="localhost", dbname="simpop",
user="postgres", password="postgres&q
can call the library function with a string
because R understands that. But, for attach, R does not expect a
string, just a symbol, hence the failure. I think I have learnt a
little more about R today :)
Thank you,
Peter
-
'utils', 'datasets',
'methods', 'base']
>>> rpy.r.attach("birthwt")
Traceback (most recent call last):
File "", line 1, in
rpy.RPy_RException: Error in function (what, pos = 2, name =
deparse(substitute(what)), warn.conflicts = TRUE)
t do what you hoped for.
This is equivalent to:
temp = r.as_matrix(erg)
r.is_matrix(temp)
With the default conversion, temp would be a python object.
Peter
--
OpenSolaris 2009.06 is a cutting edge operating system for enterpr
hich is lossy), and then when you pass them back
to R they are re-converted into something not quite the same (probably
an array for some sort).
See:
http://rpy.sourceforge.net/rpy/doc/rpy_html/Conversion-system.html
Try something like this:
import rpy
rpy.set_default_mode(rpy.NO_CONVERSIO
On 5/16/09, krysta Giles-Hansen wrote:
>
> from rpy import r
> import Numeric
Numeric is obsolete - does numpy work better here? I would expect it
to be more tested in rpy.
Peter
--
Crystal Reports - New Fre
On 4/25/09, Ryan Banerjee-R wrote:
>
> Hi All
>
> Not sure about mailing list etiquette but I thought it would
> good to post a solution for others. Thanks for the quick help!
>
I think posting a working solution is excellent e
ot;) is not TRUE
>
> I any ideas how to get this working?
I suspect the problem is how you are trying to supply the formula (you
just used a string, "ys ~ x1s"). Read this:
http://www.warwick.ac.uk/go/peter_cock/python/lin_reg/#lm which should
help.
Peter
--
py2/doc/html/introduction.html#calling-r-functions
Plus this section doesn't mention R functions whose names are invalid in python:
http://rpy.sourceforge.net/rpy2/doc/html/robjects.html#robjects-functions
Peter
--
Crystal R
en). In my own scripts I just
write the image to a PNG or PDF file and don't bother with the
graphics window.
Peter
--
This SF.net email is sponsored by:
High Quality Requirements in a Collaborative Environment
about:
Q: Now, how to extract data from the resulting objects ?
or,
Q: Now, how do we extract data from the resulting objects ?
and,
A: This depends on the type of R object.
or,
A: It depends on the type of R object.
Peter
k on Windows, they plan a beta release this month and the current
plan is for the release to be in early April 2009. Of course, I don't
know if anyone has tested rpy2 with NumPy 1.3 yet...
Peter
--
Apps built with th
is on the mailing list for some
time, so thank you for the reminder!
It would be great if rpy and rpy2 could "clean up" after themselves.
Peter
--
Open Source Business Conference (OSBC), March 24-25, 2009, San
s part of RPy 1.0.1 to deal with a
similar problem with loading the lapack library. I had a quick look
in SVN but couldn't work out what he actually changed in the code.
Peter
--
Open Source Business Conference (OSBC),
to run R directly, hoping it is on the path.
If you want to use this without changing the code try:
* Defining the RHOME environment variable
* Installing win32 http://starship.python.net/crew/mhammond/win32/ so
the registry can be checked
* Makin
you are talking about the python code, I would follow PEP8 and use
four space for indentation (and no tabs).
http://www.python.org/dev/peps/pep-0008/
For C code, well - I think Laurent it is up to you to set the
standard for
l default to the MS compiler, try:
python setup.py build --compiler=mingw32
Or, create/edit the file distutils.cfg to make mingw32 the default
compiler for distutils.
Peter
--
This SF.net email is sponsored by:
SourcForge Co
Did you install the developer headers etc for lapack and blas? I
don't know how things work on freebsd but on Linux often there will be
an lapack package plus an lapack-dev package which I think
th distutils (bdist_wininst)
might help. I've tried, but so far haven't found anything.
Peter
--
___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists
ll work or not.
Peter
--
___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list
1 - 100 of 162 matches
Mail list logo
