[Rd] Console colors do not stick (PR#13625)
Full_Name: Sean Laverty Version: R version 2.8.1 (2008-12-22) OS: os x 10.5.6 Submission from: (NULL) (155.101.41.13) In the console colors window, colors do not stick when palettes are closed. All custom colors are replaced by blue. I've tried all palettes - crayons, sliders, wheel, spectrum. "R.bug.report" 30L, 582C[2;1H<>[6;1H--please do not edit the information below-- Version: platform = i386-apple-darwin8.11.1 arch = i386 os = darwin8.11.1 system = i386, darwin8.11.1 status = major = 2 minor = 8.1 year = 2008 month = 12 day = 22 svn rev = 47281 language = R version.string = R version 2.8.1 (2008-12-22) GUI:[1;1H __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] savePlot export "strange" eps (PR#13620)
Christophe Genolini wrote:
Sorry for that... I find a strange behavior in "savePlot" ; before
report a bug, I read the posting guide and I try to simplify my exemple
as much as possible. Doing this, I change my code and I remove the "
type='eps' " option... Sorry !
Let's start this again.
When I use savePlot(file="toto.eps",type="eps") and I try to incorporate
"toto.eps" in a LaTeX document, I get a strange behavior:
LaTeX run normaly, so does dvips. But the generated postscript include a
graph that overwirte the line above it.
If my latex is
bonjour bonjour2 bonjour3
\begin{center}
\includegraphics[width=12cm]{toto.eps}
\end{center}
Then "bonjour2 bonjour3" is hidden by the graph.
No so for me, but let me (what you still not did), give a reproducible
example:
I opened some vanilla R-2.8.1 under Windows using
RGui --vanilla
in R:
plot(1:10)
savePlot(file="d:/temp/toto.eps", type="eps")
Then I created a LaTeX document:
\documentclass{article}
\usepackage{graphicx}
\begin{document}
bonjour bonjour2 bonjour3
\begin{center}
\includegraphics[width=12cm]{toto.eps}
\end{center}
\end{document}
and ran LaTeX and dvips.
All is fine. So, *please*, specify a reproducible example or we cannot
help. I presume you have a LaTeX problem. Anyway, a better way to export
your graphs would be to use a proper device directly - independent of
what happens here.
And also, this is still not proved to be a bug, particularly not in R!
Uwe Ligges
Version: 2.8.1
OS: Windows XP
LaTeX : Miktex 2.7
Christophe
cgeno...@u-paris10.fr wrote:
Full_Name: Christophe Genolini
Version: 2.8.1
OS: Windows XP
Submission from: (NULL) (82.225.59.146)
savePlot export "eps" graph that seems to be incorrect.
Looks like you saved an EMF rather than an eps file???
Uwe Ligges
Trying to incorporate them in a LaTeX file, I get :
++
Cannot determine size of graphics in foo.eps (no BoundingBox)
--
Trying to open them with GSview, I get :
++
GSview 4.9 2007-11-18
AFPL Ghostscript 8.54 (2006-05-17)
Copyright (C) 2005 artofcode LLC, Benicia, CA. All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Displaying non DSC file C:/Documents and Settings/Christophe/Mes
documents/Recherche/Trajectoires/kmeal/trajectories/testsDev/toti.eps
Error: /undefined in
Operand stack:
Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval--
--nostringval-- 2 %stopped_push --nostringval--
--nostringval-- false 1 %stopped_push 1 3 %oparray_pop
1 3 %oparray_pop 1 3 %oparray_pop 1 3 %oparray_pop
.runexec2 --nostringval-- --nostringval-- --nostringval-- 2
%stopped_push --nostringval--
Dictionary stack:
--dict:1130/1686(ro)(G)-- --dict:0/20(G)-- --dict:74/200(L)--
Current allocation mode is local
Last OS error: No such file or directory
--- Begin offending input ---
€ L z f C fC EMF $6 7
l � ° €— ° G r a p h A p p
% €%
€% €% €% €% €%
€% €% €% €% €% €K @
0 N N y @ N N y @ %
€% €: _ 8 8 8
% ; l *
6 Z õ < @ f ï ` 0 %
€( % €% €K @ 0
N N y @ N N y @ % €% €:
_ 8 8 8%
; m ñ 6 Z » <
@ g µ ` ÷ %
€( % €% €K @ 0
¡ ¡ ¡ ¡ % €% €:
_ 8 8 8 --- End
offending input ---
file offset = 1024
gsapi_run_string_continue returns -101
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Re: [Rd] typo in sprintf format string segfaults R
Sklyar, Oleg (London) wrote:
> typo as simple as %S instead of %s segfaults R devel:
>
not exactly:
sprintf('%S', 'aa')
# error: unrecognised format at end of string
without a segfault. but with another format specifier behind, it will
cause a segfault.
interestingly, here's again the same problem i have reported recently:
that you are given a number of options for how to leave the session, but
you can type ^c and stay in a semi-working session. (and the next
execution of the above will then cause a segfault with immediate exit.)
vQ
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[Rd] typo in sprintf format string segfaults R
typo as simple as %S instead of %s segfaults R devel:
*** R 2.9.0 (svn -r 47821) [/share/research/R-devel/20090203/lib64/R]
***
> sprintf("%S%d", "aaa", 1)
*** caught segfault ***
address 0x8000, cause 'memory not mapped'
Traceback:
1: sprintf("%S%d", "aaa", 1)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
-
> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-02 r47821)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics utils datasets grDevices methods base
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
**
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The contents of this email are for the named addressees ...{{dropped:19}}
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[Rd] Error message for matrix(1)[[1,,]]
> matrix(1)[[1,]] Error in matrix(1)[[1, ]] : invalid subscript type 'symbol' This is of course an incorrect use of [[, but I think the error message could be more helpful. I will guess that it is interpreting the missing value indicator as a symbol, since I get the same error message for > matrix(1)[[ quote(a=), ]] -s PS quote(a=) seems to be the easiest way to get the missing value indicator as a value. Is it by design that it returns the MVI? Or is it a missing error check? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] get_all_vars fails with matrices (PR#13624)
It's not just lists that are odd... > X <- matrix(1:15,5,3) > z <- 26:30 > model.frame(~z+X) z X.1 X.2 X.3 1 26 1 6 11 2 27 2 7 12 3 28 3 8 13 4 29 4 9 14 5 30 5 10 15 > get_all_vars(~z+X) [1] zX ... which is again a problem when trying to pick up unprocessed versions of the variables used by a modelling function On Wednesday 25 March 2009 18:54, Peter Dalgaard wrote: > s.w...@bath.ac.uk wrote: > > Hi, > > > > According to the help file for model.frame/get_all_vars, the following > > should produce the same output from both functions, but it doesn't... > > > >> dat <- list(X=matrix(1:15,5,3),z=26:30) > >> model.frame(~z+X,dat) > > > >z X.1 X.2 X.3 > > 1 26 1 6 11 > > 2 27 2 7 12 > > 3 28 3 8 13 > > 4 29 4 9 14 > > 5 30 5 10 15 > > > >> get_all_vars(~z+X,dat) > > > > [1] zX > > <0 rows> (or 0-length row.names) > > > > -- the equivalent works ok if there are no matrices involved. > > > > I'm using R version 2.9.0 alpha (2009-03-24 r48212) (Suse linux 10 and > > 11, 64 bit intel). I found the problem while trying to fix a problem in > > an mgcv plotting routine. > > > > best, > > Simon > > This works, though: > > dat <- data.frame(X=I(matrix(1:15,5,3)),z=26:30) > > get_all_vars(~z+X,dat) > > z X.1 X.2 X.3 > 1 26 1 6 11 > 2 27 2 7 12 > 3 28 3 8 13 > 4 29 4 9 14 > 5 30 5 10 15 > > but there is something special with lists: > > dat <- as.data.frame(list(X=I(matrix(1:15,5,3)),z=26:30)) > > get_all_vars(~z+X,dat) > > z X.1 X.2 X.3 > 1 26 1 6 11 > 2 27 2 7 12 > 3 28 3 8 13 > 4 29 4 9 14 > 5 30 5 10 15 > > > dat <- data.frame(list(X=I(matrix(1:15,5,3)),z=26:30)) > > get_all_vars(~z+X,dat) > > z X.1 X.2 X.3 > 1 26 1 6 11 > 2 27 2 7 12 > 3 28 3 8 13 > 4 29 4 9 14 > 5 30 5 10 15 > > > dat <- list(X=I(matrix(1:15,5,3)),z=26:30) > > get_all_vars(~z+X,dat) > > [1] z X > <0 rows> (or 0-length row.names) -- > Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK > +44 1225 386603 www.maths.bath.ac.uk/~sw283 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Building R-alpha with ATLAS libraries?
I'm trying to build R-alpha using the ATLAS libraries as described in the R-admin manual, section A.3.1.1 (BLAS) and A.3.2 (LAPACK). I built ATLAS with LAPACK as described in the ATLAS documentation, and the ATLAS version is the latest, 3.9.10. The platform is openSUSE 11.1 x86_64 with GCC 4.3.2. "configure" is finding the ATLAS BLAS all right, but it is not finding the ATLAS LAPACK. The configure command string is ./configure --enable-threads --disable-R-profiling \ --with-blas="-L/usr/local/atlas/lib -lptf77blas -lpthread -latlas" \ --with-lapack="-L/usr/local/atlas/lib -llapack -lptcblas" \ --with-tcltk --with-cairo --with-libpng --with-jpeglib --with-x \ 2>&1 | tee ../R-alpha-config.log Here's what's in the "R-alpha-config.log" file when it gets to the library check part: checking for dgemm_ in -L/usr/local/atlas/lib -lptf77blas -lpthread -latlas... yes checking whether double complex BLAS can be used... yes checking whether the BLAS is complete... yes checking for zgeev_... no checking for zgeev_ in -L/usr/local/atlas/lib -llapack -lptcblas... no checking for zgeev_ in -llapack... no I looked in "R-alpha/config.log" and it looks like "configure" is not searching the right libraries for "zgeev_": configure:38501: checking for zgeev_ configure:38565: gcc -std=gnu99 -o conftest -O3 -march=native -g -pipe -I/usr/local/include -L/usr/local/lib64 conftest.c -L/usr/local/atlas/lib -lptf77blas -lpthread -latlas -lgfortran -lm -ldl -lm >&5 /tmp/ccETmjPn.o: In function `main': /home/Projects/linux_perf_viz/build-scripts/R-alpha/conftest.c:218: undefined reference to `zgeev_' collect2: ld returned 1 exit status configure:38571: $? = 1 I checked the ATLAS libraries and "zgeev_" is there. Did I miss something in the "configure" parameters? -- M. Edward (Ed) Borasky http://www.linkedin.com/in/edborasky I've never met a happy clam. In fact, most of them were pretty steamed. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] "[.data.frame" and lapply
[moving this from R-help to R-devel]
Hi,
Right, so when you call `[`, the dispatch is made internally :
> d <- data.frame( x = 1:5, y = rnorm(5), z = rnorm(5) )
> trace( `[.data.frame` )
> d[ , 1:2] # ensuring the 1:2 is passed to j and the i is passed as
missing
Tracing `[.data.frame`(d, , 1:2) on entry
x y
1 1 0.98946922
2 2 0.05323895
3 3 -0.21803664
4 4 -0.47607043
5 5 1.23366151
> d[ 1:2] # only on argument, so it goes in i
Tracing `[.data.frame`(d, 1:2) on entry
x y
1 1 0.98946922
2 2 0.05323895
3 3 -0.21803664
4 4 -0.47607043
5 5 1.23366151
But that does not explain why this is hapening:
> d[ i = 1:2]
Tracing `[.data.frame`(d, i = 1:2) on entry
x y
1 1 0.98946922
2 2 0.05323895
3 3 -0.21803664
4 4 -0.47607043
5 5 1.23366151
> d[ j = 1:2]
Tracing `[.data.frame`(d, j = 1:2) on entry
x y z
1 1 0.98946922 -0.5233134
2 2 0.05323895 1.3646683
3 3 -0.21803664 -0.4998344
4 4 -0.47607043 -1.8849618
5 5 1.23366151 0.6723562
Arguments are dispatched to `[.data.frame` with their names, and
`[.data.frame` gets confused. I'm not suggesting allowing named
arguments because it already works, what does not work is how
`[.data.frame` treats them, and that needs to be changed, this is a bug.
Romain
> version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status Under development (unstable)
major 2
minor 9.0
year 2009
month 03
day09
svn rev48093
language R
version.string R version 2.9.0 Under development (unstable) (2009-03-09
r48093)
baptiste auguie wrote:
Hi,
I got an off-line clarification from Martin Morgan which makes me
believe it's not a bug (admittedly, I was close to suggesting it before).
Basically, "[" is a .Primitive, for which the help page says,
The advantage of |.Primitive| over |.Internal
| functions
is the potential efficiency of argument passing. However, this is
done by ignoring argument names and using positional matching of
arguments (unless arranged differently for specific primitives such
as |rep
|),
so this is discouraged for functions of more than one argument.
This explains why in my tests the argument names i and j were
completely ignored and only the number and order of arguments changed
the result.
I've learnt my lesson here, but I wonder what could be done to make
this discovery easier for others:
- add a note in the documentation of each .Primitive function (at
least a link to ?.Primitive)
- add such an example in lapply (all examples are for named arguments)
- echo a warning if trying to pass named arguments to a .Primitive
- allow for named arguments as you suggest
I'm not sure the last two would be possible without some cost in
efficiency.
Many thanks,
baptiste
On 26 Mar 2009, at 07:46, Romain Francois wrote:
Hi,
This is a bug I think. [.data.frame treats its arguments differently
depending on the number of arguments.
d <- data.frame(x = rnorm(5), y = rnorm(5), z = rnorm(5) )
d[, 1:2]
x y
1 0.45141341 0.03943654
2 -0.87954548 1.83690210
3 -0.91083710 0.22758584
4 0.06924279 1.26799176
5 -0.20477052 -0.25873225
base:::`[.data.frame`( d, j=1:2)
x y z
1 0.45141341 0.03943654 -0.8971957
2 -0.87954548 1.83690210 0.9083281
3 -0.91083710 0.22758584 -0.3104906
4 0.06924279 1.26799176 1.2625699
5 -0.20477052 -0.25873225 0.5228342
but also:
d[ j=1:2]
x y z
1 0.45141341 0.03943654 -0.8971957
2 -0.87954548 1.83690210 0.9083281
3 -0.91083710 0.22758584 -0.3104906
4 0.06924279 1.26799176 1.2625699
5 -0.20477052 -0.25873225 0.5228342
`[.data.frame` only is called with two arguments in the second case, so
the following condition is true:
if(Narg < 3L) { # list-like indexing or matrix indexing
And then, the function assumes the argument it has been passed is i, and
eventually calls NextMethod("[") which I think calls
`[.listof`(x,i,...), since i is missing in `[.data.frame` it is not
passed to `[.listof`, so you have something equivalent to as.list(d)[].
I think we can replace the condition with this one:
if(Narg < 3L && !has.j) { # list-like indexing or matrix indexing
or this:
if(Narg < 3L) { # list-like indexing or matrix indexing
if(has.j) i <- j
`[.data.frame`(d, j=1:2)
x y
1 0.45141341 0.03943654
2 -0.87954548 1.83690210
3 -0.91083710 0.22758584
4 0.06924279 1.26799176
5 -0.20477052 -0.25873225
However, we would still have this, which is expected (same as d[1:2] ):
`[.data.frame`(d, i=1:2)
x y
1 0.45141341 0.03943654
2 -0.87954548 1.83690210
3 -0.91083710 0.22758584
4 0.06924279 1.26799176
5 -0.20477052 -0.25873225
Romain
baptiste auguie wrote:
Dear all,
Trying to extract a few rows for each element of a list of
dat
