Re: [Rpy] Arguments to high-level plotting commands

2008-02-14 Thread Peter
r.image(x,y,f,axes=FALSE) > NameError: name 'FALSE' is not defined > > rpy.r.image(x,y,z) does only work without additional arguments. Does > anyone know how I can code that in Python? The problem is much simpler, FALSE is not defined in python (it is in R). You just need to

Re: [Rpy] Arguments to high-level plotting commands

2008-02-14 Thread Peter
> By the way, > > k = rpy.r.terrain.colors(100) > > fails. Is there trick to get access to the terrain.colors or to other R > functions which have a dot (I don't know if there are many)? Yes, as the rpy documentation explains, use an underscore instead: k = rpy.r.ter

Re: [Rpy] Code adds space when 'paste' is used

2008-02-15 Thread Peter
e as a python variable] > Of course this works in R directly and a search of RPY info sources > for paste func() with sep doesn't turn up anything useful. It certainly looks like there is a bug here somewhere... Peter --

Re: [Rpy] Wiki for RPy Documentation?

2008-03-31 Thread Peter
ch could be merged in... >From experience in other projects, a wiki worthwhile if you can get a good sized group of people involved. Otherwise it can just get spammed and cause more work. Peter - Check out the new SourceF

Re: [Rpy] read csv in python, and pass it on to R?

2008-04-01 Thread Peter
d for read.table() by experimenting in an R session, and then try the same from rpy. This assumes you do not need the actual data in python too. I don't know if you can pass the file pointer (handle) from python to R. I would be interested to know if this is possible. Peter On Tue, Apr 1, 2008

[Rpy] Updated homepage

2008-04-24 Thread Peter
mer 2007, which gives a bad impression for first time visitors. Peter - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Us

Re: [Rpy] Updated homepage

2008-04-24 Thread Peter
t know how the release process works, but it would make sense to add a news entry when ever uploading a new release. > I'd also like to point that "summer 2007" is not even one year old. > That's not too bad. Yeah - but it is close to a year old. The 1.0 release was p

Re: [Rpy] filled.contour

2008-05-15 Thread Peter
See http://www.warwick.ac.uk/go/peter_cock/r/ramachandran/ for a similar example and also http://www.warwick.ac.uk/go/peter_cock/python/ramachandran/drawing/ for a neat way to do this from python with rpy. Peter - This SF.net email i

Re: [Rpy] SF.net SVN: rpy: [558] branches/rpy_nextgen/setup.py

2008-06-09 Thread Peter
is now 1.0a0 (one-zero-alpha-zero). Doesn't this risk confusion with the current rpy 1.x series? Wouldn't it be a lot clearer if the version number of next_gen rpy aka rpy2 started with a 2? Peter - Check out the ne

[Rpy] RPy news pages

2008-06-09 Thread Peter
from the Sourceforge pages, and has only four entries, covering the release of rpy 1.0.3, 0.4.6, 0.4.5 and 0.4.4. I would disable the sourceforge news page (point it at the website if possible) and and the release of rpy 1.0.3 to the main news page.

Re: [Rpy] [Numpy-discussion] working with matrix....

2008-06-27 Thread Peter
y simple statistics, then python should be fine. You may find the numpy and scipy libraries helpful - they do include some statistical code. Peter - Check out the new SourceForge.net Marketplace. It's the best place to

Re: [Rpy] Ask two simple questions

2008-07-26 Thread Peter
r.library("gplot") > > the error comes:"there is no package for gplot" > > How can I get the package? As you are using windows, the easiest way would be to run the R GUI, and install the gplot package via the menus. You can also go this from the R command lin

Re: [Rpy] How to create logic vectors

2008-07-26 Thread Peter
pure python, which might be easier depending on why you want to do this. a = [1,2,3,4] b = [x<3 for x in a] Or using numpy, a = numpy.array([1,2,3,4], numpy.int) b = a < 3 Peter - This SF.Net email is sponsored by the Mobl

Re: [Rpy] rpy2: alpha2 released

2008-08-07 Thread Peter
t; CMD config --ldflags returned -F/Library/Frameworks/R.framework/.. -framework R I have Python 2.5.2 and R version 2.7.0 (plus a working installation of rpy 1.0.3). Peter - This SF.Net email is sponsored by the Moblin Your M

Re: [Rpy] rpy2: alpha2 released

2008-08-07 Thread Peter
ing -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --ta

Re: [Rpy] problems using step with Rpy

2008-10-04 Thread Peter
"foreign") > r.library("stats") > dat = r.read_dbf("D:/rTesting/myDataFile.dbf") > #FIXME: can't get as_is =" FALSE" to work In python, FALSE isn't defined as python uses False instead. Try: dat = r.read_dbf("D:/rTesting/myDataFile.d

Re: [Rpy] Plotting in RPy v2.0.0.3a

2008-10-09 Thread Peter
x27;dev.off']() is what you are looking for. Does the rpy v1 style r.dev_off() still work in rpy v2? Personally I much prefer this to r['dev.off']() for readability. Peter - This SF.Net email is sponsored

Re: [Rpy] rpy2-beta...

2008-10-13 Thread Peter
t;>> dir(rpy2) ['__builtins__', '__doc__', '__file__', '__name__', '__path__'] Thanks Peter - This SF.Net email is sponsored by the Moblin Your Move Developer'

Re: [Rpy] Plotting in RPy v2.0.0.3a

2008-10-13 Thread Peter
Peter wrote: >> Does the rpy v1 style r.dev_off() still work in rpy v2? Laurent replied: > Not directly. I have a sketchy attempt at making it possible (will be > there for the 2.0 release, still scheduled for November), but it will > not be the default. > >> Personally I

Re: [Rpy] Plotting in RPy v2.0.0.3a

2008-10-14 Thread Peter
ent, could you show us how you would write this trivial plot example (at the start of this thread) using rpy2.rpy_classic? Thanks Peter - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Buil

Re: [Rpy] Plotting in RPy v2.0.0.3a

2008-10-14 Thread Peter
y what you mean by "The aim of rpy_classic is to have rpy code running without (much) modification." Do you mean old rpy1 code, or something different? I was making an assumption based on the name that the rpy_classic module would provide "classic" (i.e. "old fashioned&qu

Re: [Rpy] build an R DataFrame from a python dictionary in Rpy2

2008-10-17 Thread Peter
taf = ro.r['data.frame'](**d) Hi Laurent, You mentioned using rpy2.rlike.container.TaggedList and rpy2.robjects.RDataFrame (new in rpy2) as a "safer" approach. Could you show us how this example would work that way? Given how important dataframes are in R, this discuss

[Rpy] rpy and rpy2 debian/ubuntu packages

2008-10-20 Thread Peter
right - simply switching existing debian/ubuntu packages from rpy 1.x to rpy 2.x would be bad. As with other libraries etc, just add new packages with rpy2 in the name for rpy 2.x instead, as both can be installed together without pro

Re: [Rpy] List index out of range

2008-11-12 Thread Peter
recently discussed on the mailing list and fixed. Basically rpy2 is having trouble locating R. If you make sure the folder where R.exe was installed is on the windows PATH environment variable (via control panel, system, advanced, environment variables), or setup th

Re: [Rpy] List index out of range

2008-11-12 Thread Peter
recently discussed on the mailing list and fixed. Basically rpy2 is having trouble locating R. If you make sure the folder where R.exe was installed is on the windows PATH environment variable (control panel/system/advanced/environment variables), or setup th

[Rpy] rpy2 on windows doesn't use the registry

2008-11-12 Thread Peter
e rpy/rpy_tools.py for how to do this. I contributed this code 3 years ago which is why I thought to check for rpy2 as well (see rpy.py revision 186). Peter - This SF.Net email is sponsored by the Moblin Your Move Develo

Re: [Rpy] rpy2 on windows doesn't use the registry

2008-11-12 Thread Peter
of R installed). If I can find the time this week I'll try and test this out on my Windows machine - but no promises. From memory the registry gives the base folder, and you have to add the "bin" directory to get the full path for the DLL. Peter P.S. I would change this error mes

Re: [Rpy] Postscript and PDF with errors --> do not open

2008-11-13 Thread Peter
imple R plotting example to make a PS and PDF file, and see if those files work. That should tell us if its an rpy problem or not. Peter - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Bui

Re: [Rpy] [PATCH] passing numpy arrays to rpy2 functions

2008-11-20 Thread Peter
-wise (Fortran style) arrays. Perhaps any numpy arrays using the Fortran convention could be passed to/from R more efficiently? Peter - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Buil

Re: [Rpy] Could I be taken of the list please?

2008-11-20 Thread Peter
nt via the list is a URL, https://lists.sourceforge.net/lists/listinfo/rpy-list Go to this page, at the bottom is a form to unsubscribe. Peter - This SF.Net email is sponsored by the Moblin Your Move Developer's chal

Re: [Rpy] future of rpy 1.0

2008-12-01 Thread Peter
tware) for any version of python. Peter - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip

Re: [Rpy] RPy2 fails on Windows and R-2.8.0

2008-12-01 Thread Peter
at is happening? It looks like R_HOME has been detected as "C" rather than something like "C:\Program Files\". This could be bug as there have been some changes to this code recently. A few relevant questions: Did you setup an R_HOME environment variable? Is R on

Re: [Rpy] future of rpy 1.0

2008-12-02 Thread Peter
ompilers... and I'm not >> that good at this stuff: I am mostly a pure Python programmer :) > > I don't think that R for win32 is (was ?) compiled with MSVC, but with > mingw32. You may end up with R, python and your extensions compi

Re: [Rpy] RPy2 fails on Windows and R-2.8.0

2008-12-02 Thread Peter
rompt, try "import win32api". If this works, it is installed. If you get an ImportError, it is not. This module comes as part of Mark Hammond's pywin32 package, see http://sourceforge.net/projects/pywin32/ Peter ---

Re: [Rpy] RPy2 fails on Windows and R-2.8.0

2008-12-02 Thread Peter
s" % R_HOME) > RuntimeError: Unable to locate R.dll within C This is the same error as before - which to me suggests a bug in how rpy2 is using R_HOME. I suspect its something along the lines of a bit of code expecting a list of all the R installations found (there could be more than one) and

Re: [Rpy] Problem with R's hist() function

2008-12-17 Thread Peter
our graphs as a result. You will need to explicitly set the graph captions, and then everything is fine. Peter -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't

Re: [Rpy] rpy2 windows binary install

2008-12-19 Thread Peter
ll work or not. Peter -- ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list

Re: [Rpy] rpy2 windows binary install

2008-12-19 Thread Peter
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

Re: [Rpy] build rpy2 on FreeBSD failed

2008-12-31 Thread Peter
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

Re: [Rpy] compiling rpy2 on windows R-2.8.1

2009-01-12 Thread Peter
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

Re: [Rpy] [patch] R 2.7 compatibility fix for rpy_device.c

2009-02-09 Thread Peter
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

Re: [Rpy] Using rpy in a python-com Object from Excel

2009-02-16 Thread Peter
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

Re: [Rpy] Problem loading library

2009-02-24 Thread Peter
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),

Re: [Rpy] Rtmp* file in /tmp

2009-03-06 Thread Peter
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

Re: [Rpy] rpy2 install problem

2009-03-12 Thread 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

Re: [Rpy] Anova example

2009-04-10 Thread Peter
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

Re: [Rpy] Plot window closes immediately

2009-04-14 Thread Peter
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

Re: [Rpy] r.pdf() question

2009-04-25 Thread 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

Re: [Rpy] Rpy, using R plm package

2009-04-25 Thread Peter
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 --

Re: [Rpy] --SPAM-- MID: Re: Rpy, using R plm package 32.1455

2009-04-25 Thread Peter
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

Re: [Rpy] Barplot Error: rpy.RPy_RException: Error in -0.01 * height : non-numeric argument to binary operator

2009-05-16 Thread Peter
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

Re: [Rpy] matrix problem with rpy 1.0.3

2009-06-03 Thread Peter
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

Re: [Rpy] matrix problem with rpy 1.0.3

2009-06-03 Thread Peter
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

Re: [Rpy] help with loading library

2009-06-15 Thread 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)

Re: [Rpy] help with loading library

2009-06-15 Thread Peter
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 -

Re: [Rpy] Python and RPY to manipulate R and Rdbi , R and GRASS

2009-06-25 Thread Peter
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

Re: [Rpy] win32api error under Vista 64b

2009-07-18 Thread Peter
> 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

Re: [Rpy] win32api error under Vista 64b

2009-07-18 Thread Peter
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

Re: [Rpy] Still accepting RPy Bugs?

2009-07-23 Thread Peter
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

Re: [Rpy] Still accepting RPy Bugs?

2009-07-23 Thread Peter
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

Re: [Rpy] Unable to plot

2009-08-07 Thread Peter
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 -

Re: [Rpy] read_table on RPy2

2009-08-14 Thread Peter
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

Re: [Rpy] rpy syntax error...

2009-09-11 Thread Peter
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

Re: [Rpy] Making dataframes ... fast

2009-09-29 Thread Peter
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

Re: [Rpy] na.action?

2009-09-30 Thread Peter
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

Re: [Rpy] na.action?

2009-09-30 Thread Peter
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,

Re: [Rpy] na.action?

2009-09-30 Thread Peter
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

Re: [Rpy] Building rpy in the home directory

2009-10-05 Thread Peter
/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

Re: [Rpy] rpy syntax error...

2009-10-05 Thread Peter
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

Re: [Rpy] printing object with rpy

2009-10-13 Thread 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.

Re: [Rpy] printing object with rpy

2009-10-13 Thread 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 ---

Re: [Rpy] na.action?

2009-10-18 Thread Peter
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 --

Re: [Rpy] rpy-list Digest, Vol 42, Issue 2

2009-11-12 Thread Peter
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

Re: [Rpy] accessing data within a dataframe

2009-11-12 Thread Peter
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",

Re: [Rpy] Error using phyper with rpy2

2009-11-23 Thread Peter
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

Re: [Rpy] object not found

2009-12-09 Thread Peter
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),

Re: [Rpy] rpy in Windows, how to get started?

2010-01-04 Thread 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

Re: [Rpy] Remove compiled version

2010-01-08 Thread Peter
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

Re: [Rpy] Startup pains, getting the simple examples to work!

2010-02-05 Thread Peter
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

Re: [Rpy] Startup pains, getting the simple examples to work!

2010-02-06 Thread 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/

Re: [Rpy] Followup on startup pains.

2010-02-08 Thread 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

Re: [Rpy] mclust package of R

2010-03-02 Thread Peter
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 --

Re: [Rpy] mclust package of R

2010-03-02 Thread Peter
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

Re: [Rpy] Google SoC 2010

2010-03-10 Thread Peter
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

Re: [Rpy] Fisher's exact test

2010-03-16 Thread Peter
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

Re: [Rpy] Fisher's exact test

2010-03-16 Thread Peter
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

Re: [Rpy] Windows installer for 2.1rc?

2010-04-10 Thread Peter
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

Re: [Rpy] Windows installer for 2.1rc?

2010-04-12 Thread Peter
-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

Re: [Rpy] Windows installer for 2.1rc?

2010-04-12 Thread Peter
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)

Re: [Rpy] rpy2 and bioconductor

2010-04-14 Thread Peter
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)

Re: [Rpy] Windows installer for 2.1rc?

2010-04-14 Thread Peter
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

[Rpy] warning: "/*" within comments in na_values.c

2010-04-14 Thread Peter
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

Re: [Rpy] Windows installer for 2.1rc?

2010-04-14 Thread Peter
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

Re: [Rpy] Windows installer for 2.1rc?

2010-04-14 Thread Peter
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). &

Re: [Rpy] Windows installer for 2.1rc?

2010-04-14 Thread Peter
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

Re: [Rpy] Windows installer for 2.1rc?

2010-04-19 Thread Peter
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

Re: [Rpy] Bug:Couldn't obtain version number from output of `R --version'

2010-04-21 Thread Peter
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

Re: [Rpy] problems with clean WINXP RPy2.10 and R2.11.0

2010-04-30 Thread Peter
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

Re: [Rpy] Windows installer for 2.1rc?

2010-04-30 Thread Peter
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

Re: [Rpy] Error when installing Rpy2

2010-07-06 Thread Peter
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

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