In data venerdì 23 agosto 2019 12:51:06 CEST, Laurent Gautier ha scritto:
Hello,
> Atlassian has announced the end of support for Mercurial repositories, so
> rpy2 will have to find a new home for its main source repository:
You might want to look at sourcehut.org.
--
Luca Beltrame
In data giovedì 27 febbraio 2014 17:22:57, Luca Beltrame ha scritto:
> There are several others like this, same error string.
I fixed it by setting proper CFLAGS (CFLAGS=-std=c99), so perhaps it may have
been a local issue.
--
Luca Beltrame, Ph.D.
Translational Genomics Unit, Department
:3: error: ISO C90 forbids
mixed declarations and code [-Werror=declaration-after-statement]
PyObject *key = PyLong_FromVoidPtr((void *)object);
^
There are several others like this, same error string.
--
Luca Beltrame, Ph.D.
Translational Genomics Unit, Department of Oncology
IRCCS
of which is more "comfortable" for a given community.
--
Luca Beltrame, Ph.D.
Translational Genomics Unit, Department of Oncology
IRCCS Istituto di Ricerche Farmacologiche "Mario Negri"
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In data venerdì 27 settembre 2013 14:13:24, Laurent Gautier ha scritto:
> I am sure I can have the time to work on this over the week-end. In case
> I don't, please make sure there is an entry about the issue in bitbucket
> (so it is not forgotten).
Done, issue #150.
--
Luca
In data venerdì 27 settembre 2013 11:10:13, Luca Beltrame ha scritto:
> R --version
> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> Platform: x86_64-suse-linux-gnu (64-bit)
Reverting to R 3.0.1 fixes the
In data venerdì 27 settembre 2013 11:13:08, Luca Beltrame ha scritto:
> FYI, the rpy2 version is the latest available (2.3.7).
Minimal testing case that shows the problem:
import rpy2.rinterface as rinterface
rinterface.initr()
rinterface.baseenv.get("file")
--
Luca B
In data venerdì 27 settembre 2013 11:10:13, Luca Beltrame ha scritto:
> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
FYI, the rpy2 version is the latest available (2.3.7).
--
Luca Beltrame, Ph.D.
Translational Genomics Unit, Department of Oncology
IRCCS Istituto di Ricerche F
;s a bug or just
a local error)?
--
Luca Beltrame, Ph.D.
Translational Genomics Unit, Department of Oncology
IRCCS Istituto di Ricerche Farmacologiche "Mario Negri"
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ssue to use .ro (I do in several other places for selection).
–
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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This occurs with the latest 2.3. Example case:
robjects.IntVector([0,1,2]) + 1
This is what it returns
[ 0,1,2,1]
While I'd expect, like in R
> c(0,1,2) + 1
[1] 1 2 3
Is this a bug, or do I have to do things differently?
--
Luca Beltra
kegg_env = graphite.__rdata__.fetch("kegg (pathways)")
> kegg = kegg_env['kegg']
I did something similar using wherefrom(), in fact.
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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attr(graphite, "kegg")
Out[6]: True
In [8]: rpy2.__version__
Out[8]: '2.2.5'
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Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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In data martedì 12 marzo 2013 17:03:26, Luca Beltrame ha scritto:
> This package provides a series of classes, in this case I wanted to access
> the "kegg" class.
Just as a small correction, it's a R "list" containing classes. It's present
in the package e
ovides a series of classes, in this case I wanted to access the
"kegg" class.
With 2.2.x, this
graphite.kegg
worked while in 2.3.x causes AttributeError.
Where I can start digging to find the problem?
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negr
ne I wrote. Laurent, if you make a release containing that converter soon,
I'll make a PR to pandas to use that code path. This will mean of course that
newer pandas will have to require that specific version of rpy2.
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department
On Thu, 10 Jan 2013 20:00:44 +0100 (CET), Samuel Lampa wrote:
> Ah, many thanks! :)
A comment: if you're using R just to do a hypergeometric test, probably
the R-Python overhead is not worth the effort. Scipy has the exact same
function, with the advantage that you don't have to go through
96 self._parent.__sexp__ = res.__sexp__
RRuntimeError: Error in [[<-.data.frame`(list(src = c(NA, NA, NA, NA, NA, NA,
NA, NA, : argument "values" is missing, with no default
It looks like a limitation on rpy2's part, as both approaches work in pure R.
--
Luc
"3", "4", : argument "value" is missing, with no default
Anything I'm doing wrong? Or is there a more efficient way? (For reference,
I'm trying to *avoid* creating taggedlists and so on because they involve
intermediates, and with large objects that
(I
assume that similarly, "as_matrix" would work).
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Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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return res
At least on my applications, which make use of importr() quite a lot, I notice
that there is a significant (but unscientifically observed) delay when using
importr(). If the code is already using it somewhere else in the same module,
then it would not matter, however (at least IMO).
Matrix, this
messes up the column order (rows become columns).
To be precise, the code I *tried* to use:
kv = [(k, v) for k, v in tlist.iteritems()]
kv = tuple(kv)
df = baseenv_ri.get("data.frame").rcall(kv, globalenv_ri)
super(DataFrame, self).__init__(df)
which doesn't rea
have a separate parameter to
construct an instance from a Matrix.
- it is preferable using a class/static method to create a DataFrame from a
matrix (e.g. DataFrame.from_matrix)
Opinions?
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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In data venerdì 25 novembre 2011 09:59:13, Luca Beltrame ha scritto:
> Weird. For reference, I have python 2.7 (distro-supplied), R 2.14 (packaged,
> but self compiled) and rpy 2.2.4 (self compiled).
I'm happy to report that it was a local installation issue: recompiling rpy2
fixed i
ame):
def __init__(self, tlist=None, matrix=None):
then going on. If this is a sensible design, I can try cooking up something
and doing a pull request on bitbucket later on.
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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Des
rtualenv (checking both the 2.2 and the
unstable version) to see if I can replicate the issue. If I do, I'll start
debugging the loop that collects the method names to see why it's generating
an empty vector.
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mar
ll_methods.do_slot("names"), all_methods):
Further debugging has shown that all_methods is empty.
Should I file a bug, or is it likely a local install problem?
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Ins
n Python 2.7 w/rpy2 2.2 (the latest available verison),
self compiled, and R 2.14.
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Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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("base") and then use the functions
defined there.
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Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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In data venerdì 14 ottobre 2011 04:07:36, William T. Martin ha scritto:
> How do I access/capture the month headers?
What kind of object is it? if it's a named vector, or similar (list, etc.),
you can use the "names" attribute to get a vector of the names.
--
L
In data lunedì 12 settembre 2011 11:45:32, Luca Beltrame ha scritto:
> I forgot to add that I had to change the code to use list comprehensions
> instead of generators, because otherwise I'd get a ValueError with "The
> object does not have a length." (on rpy 2.2.x).
In data lunedì 12 settembre 2011 11:07:42, Luca Beltrame ha scritto:
> Thanks Laurent, that did it.
I forgot to add that I had to change the code to use list comprehensions
instead of generators, because otherwise I'd get a ValueError with "The object
does not have a length.&q
In data lunedì 12 settembre 2011 10:55:33, Laurent Gautier ha scritto:
> from rpy2.robjects.vector import BoolVector
> select_b = BoolVector(x in differential for x in source.rx2('gene'))
> mysubset = source.rx(select_b, True)
Thanks Laurent, that did it.
--
Luca Beltrame, Ph
Hello,
in R I'm using something like this expression:
mysubset <- source[source$gene %in% differential, ]
where "differential" is a vector and "source" a dataframe.
How can I replicate the use of %in% in rpy2?
Thanks.
--
Luca Beltrame, Ph.D. - Translational Genom
bug or am I doing something wrong?
Thanks.
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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In data mercoledì 25 maggio 2011 18:18:17, hai scritto:
> $ R RHOME
> $ echo R_HOME
Found the issue, and it's unrelated to rpy2. In Ubuntu (and possibly Debian),
"R" is a shell wrapper, and sets R_DOC_DIR as /usr/share/R/doc on startup.
Sorry for the noise.
-
usr/share/R/doc"
(correct)
I suspect some changes on Ubuntu packages, as on my main openSUSE system (self
packaged R) the first output (Python) is correct.
How can that be possible?
(rpy2.2 RC)
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri
_function('%s$specified_column_name" % data_table)) #
> This is no good. Doesn't work properly
You should use "importr" and call the functions directly from Python. See the
rpy2 documentation for more details.
Hope this helps.
--
Luca Beltrame, P
Hello,
while working with Matrix instances (rpy 2.1.9) I noticed that the rownames
attribute is read-only and can't be set (unlike the corresponding attribute of
DataFrame). Was it by design, or just a slip?
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department,
In data giovedì 7 aprile 2011 07:23:41, Laurent ha scritto:
> rpy2-2.2.x is believed to be more convenient to use. I can only
> encourage to already use it instead of 2.1.9.
Are there any API incompatibilities with 2.1.x or is it a drop-in replacement?
--
Luca Beltrame, Ph.D. - Transla
In data martedì 5 aprile 2011 12:11:09, Moritz Beber ha scritto:
> I'm almost convinced there must be a better way but I haven't found one yet.
According to what I found in the documentation, it is possible in rpy 2.2 but
not in 2.1.x. Laurent, am I correct?
--
Luca B
ks in advance.
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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Xperia(TM) PLAY
It's a major breakthr
(lists, for example). The former is
important to me because I will be able to reduce the number of kludges in my
code.
--
Luca Beltrame, Ph.D. - Translational Genomics Unit
Oncology Department, Mario Negri Institute
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In data domenica 27 marzo 2011 22:54:31, Laurent ha scritto:
> The next tag will be rpy2-2.2.0beta and will already become the default
> package on Pypi.
How does 2.2 fare in terms of stability? The new features it has make it a
worthwhile candidate for some projects I'm starting just now, hence
nother.value")
in Python I would use:
my_list = robjects.StrVector(["some.value", "another.value"])
my_list.names = ["a", "b"]
Is this the right approach or is there a better way?
--
Luca Beltrame, Ph.D. - luca.beltr...@unifi.it
Post-doctoral rese
Speaking of "issues" (which I consider minor) in 2.1.x I found at the moment,
it is not possible to pass format parameters when saving a DataFrame object
(i.e. the R equivalents "sep, row.names, quote" and so on). Should I file a
bug report (on which tracker?) so that it doesn't get lost?
sign
In data venerdì 16 aprile 2010 07:37:45, hai scritto:
> I pushed a version 0.2.1 to Pypi that fixes that.
I just downloaded the 0.2.1 tarball from PyPI and apparently geoquery.py (or
equivalent) is not present.
It is present in the repository now, though, so I'll fetch it from there.
In data venerdì 9 aprile 2010 16:19:19, Laurent ha scritto:
> Thanks. Glad to read this seems somehow useful.
One question on that: the documentation mentions a "bioc.geoquery" module, but
this is missing in the distributed tarball. Was that an oversight, or is it
correct?
Than
In data venerdì 2 aprile 2010 22:03:57, Laurent ha scritto:
Hello,
> There is documentation at:
> http://packages.python.org/rpy2-bioconductor-extensions/
This really rocks. Thanks for creating it.
--
Luca Beltrame, Ph.D. - luca.beltr...@unifi.it
Post-doctoral research fellow -
parameter = {"length.out":2}
sequence = list(base.seq(-10, 0, **parameter))
len(sequence)
Result: 2 # Correct
Is this a bug? If so, where should I report it?
--
Luca Beltrame, Ph.D. - luca.beltr...@unifi.it
Post-doctoral research fellow - Duccio Cavalieri group
Department of Pharmacology, U
unless I do:
importr("base")
base.is_null(test_list.rx2("c"))
True
Is there another way to go around this problem or should I stick with this
solution for now?
Thanks.
--
Luca Beltrame, Ph.D. - luca.beltr...@unifi.it
Post-doctoral research fellow - Duccio Cavalieri group
De
d I handle such a case?
Thanks!
--
Luca Beltrame, Ph.D.
Post-doctoral research fellow - Duccio Cavalieri group
Department of Pharmacology, University of Firenze
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ame") and get the actual value.
.rx is equivalent to [value]
.rx2 is equivalent to [[value]]
--
Luca Beltrame, Ph.D.
Post-doctoral research fellow - Duccio Cavalieri group
Department of Pharmacology, University of Firenze
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cause it's part of the base R, but I
was actually referring to "dendrapply", a variant (in stats) that is used to
do the same on dendrograms (I use it to color them). As the result is a R
object (a dendrogram) I guess I'll keep using the "r" instance for that fo
e, 1, my_function)
Or is there a better way?
Thanks!
--
Luca Beltrame, Ph.D. - luca.beltr...@unifi.it
Post-doctoral research fellow - Duccio Cavalieri group
Department of Pharmacology, University of Firenze
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constructing a DataFrame now only
sets the numeric progression in the rownames attribute and thus causes
problems.
Are there technical reasons for this, and how to work it around?
--
Luca Beltrame, Ph.D
Post-doctoral research fellow - Duccio Cavalieri group
Department of Pharmacology, Univer
e useful for other people as well.
--
Luca Beltrame, Ph.D.
Post-doctoral research fellow - Duccio Cavalieri group
Department of Pharmacology, University of Firenze
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in R):
length(which(keys == mydata$label))
(mydata is a R list - hence I would be able to use the .rx2 accessor)
Has anyone got a hint on how to translate this using rpy 2.1.x?
Thanks!
--
Luca Beltrame, Ph.D.
Post-doctoral research fellow - Duccio Cavalieri group
Department of Pharmacolog
x27;m running a local copy of rpy2 2.1 as I still have a system-
wide 2.0.x needed for some projects.
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Luca Beltrame, Ph.D.
Post-doctoral research fellow - Duccio Cavalieri group
Department of Pharmacology, University of Firenze
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