Re: [Rd] Interrupting C++ code execution
Peter, On 25/04/11 10:22, schattenpfla...@arcor.de wrote: 1. Calling R_CheckUserInterrupt() interrupts immediately, so I have no possibility to exit my code gracefully. In particular, I suppose that objects created on the heap (e.g., STL containers) are not destructed properly. Sorry not to have seen this thread sooner. You may like to give CXXR a try (http://www.cs.kent.ac.uk/projects/cxxr/). In CXXR the R interpreter is written in C++, and a user interrupt is handled by throwing a C++ exception, so the stack is unwound in an orderly fashion, destructors are invoked, etc. However, it's fair to say that in using CXXR with a multi-threaded program you'll be on the bleeding edge... Andrew __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] median and data frames
This seems trivially fixable using something like
median.data.frame - function(x, na.rm=FALSE) {
sapply(x, function(y, na.rm=FALSE) if(is.factor(y)) NA else
median(y, na.rm=na.rm), na.rm=na.rm)
}
Paul Johnson pauljoh...@gmail.com 28/04/2011 06:20
On Wed, Apr 27, 2011 at 12:44 PM, Patrick Burns
pbu...@pburns.seanet.com wrote:
Here are some data frames:
df3.2 - data.frame(1:3, 7:9)
df4.2 - data.frame(1:4, 7:10)
df3.3 - data.frame(1:3, 7:9, 10:12)
df4.3 - data.frame(1:4, 7:10, 10:13)
df3.4 - data.frame(1:3, 7:9, 10:12, 15:17)
df4.4 - data.frame(1:4, 7:10, 10:13, 15:18)
Now here are some commands and their answers:
median(df4.4)
[1] 8.5 11.5
median(df3.2[c(1,2,3),])
[1] 2 8
median(df3.2[c(1,3,2),])
[1] 2 NA
Warning message:
In mean.default(X[[2L]], ...) :
argument is not numeric or logical: returning NA
The sessionInfo is below, but it looks
to me like the present behavior started
in 2.10.0.
Sometimes it gets the right answer. I'd
be grateful to hear how it does that -- I
can't figure it out.
Hello, Pat.
Nice poetry there! I think I have an actual answer, as opposed to the
usual crap I spew.
I would agree if you said median.data.frame ought to be written to
work columnwise, similar to mean.data.frame.
apply and sapply always give the correct answer
apply(df3.3, 2, median)
X1.3 X7.9 X10.12
2 8 11
apply(df3.2, 2, median)
X1.3 X7.9
28
apply(df3.2[c(1,3,2),], 2, median)
X1.3 X7.9
28
mean.data.frame is now implemented as
mean.data.frame - function(x, ...) sapply(x, mean, ...)
I think we would suggest this for medians:
??
median.data.frame - function(x,...) sapply(x, median, ...)
?
It works, see:
median.data.frame(df3.2[c(1,3,2),])
X1.3 X7.9
28
Would our next step be to enter that somewhere in R bugzilla? (I'm not
joking--I'm that naive).
I think I can explain why the current median works intermittently in
those cases you mention. Give it a small set of pre-sorted data, all
is well. median.default uses a sort function, and it is confused when
it is given a data.frame object rather than just a vector.
I put a browser() at the top of median.default
median(df3.2[c(1,3,2),])
Called from: median.default(df3.2[c(1, 3, 2), ])
Browse[1] n
debug at tmp#4: if (is.factor(x)) stop(need numeric data)
Browse[2] n
debug at tmp#4: NULL
Browse[2] n
debug at tmp#6: if (length(names(x))) names(x) - NULL
Browse[2] n
debug at tmp#6: names(x) - NULL
Browse[2] n
debug at tmp#8: if (na.rm) x - x[!is.na(x)] else if (any(is.na(x)))
return(x[FALSE][NA])
Browse[2] n
debug at tmp#8: if (any(is.na(x))) return(x[FALSE][NA])
Browse[2] n
debug at tmp#8: NULL
Browse[2] n
debug at tmp#12: n - length(x)
Browse[2] n
debug at tmp#13: if (n == 0L) return(x[FALSE][NA])
Browse[2] n
debug at tmp#13: NULL
Browse[2] n
debug at tmp#15: half - (n + 1L)%/%2L
Browse[2] n
debug at tmp#16: if (n%%2L == 1L) sort(x, partial = half)[half] else
mean(sort(x,
partial = half + 0L:1L)[half + 0L:1L])
Browse[2] n
debug at tmp#16: mean(sort(x, partial = half + 0L:1L)[half + 0L:1L])
Browse[2] n
[1] 2 NA
Warning message:
In mean.default(X[[2L]], ...) :
argument is not numeric or logical: returning NA
Note the sort there in step 16. I think that's what is killing us.
If you are lucky, give it a small data frame that is in order, like
df3.2, the sort doesn't produce gibberish. When I get to that point, I
will show you the sort's effect.
First, the case that works. I moved the browser() down, because I
got tired of looking at the same old not-yet-erroneous output.
median(df3.2)
Called from: median.default(df3.2)
Browse[1] n
debug at tmp#15: half - (n + 1L)%/%2L
Browse[2] n
debug at tmp#16: if (n%%2L == 1L) sort(x, partial = half)[half] else
mean(sort(x,
partial = half + 0L:1L)[half + 0L:1L])
Browse[2] n
debug at tmp#16: mean(sort(x, partial = half + 0L:1L)[half + 0L:1L])
Interactively, type
Browse[2] sort(x, partial = half + 0L:1L)
NA NA NA NA NA NA
1 1 7 NULL NULL NULL NULL
2 2 8 NA NA NA NA
3 3 9 NA NA NA NA
Warning message:
In format.data.frame(x, digits = digits, na.encode = FALSE) :
corrupt data frame: columns will be truncated or padded with NAs
But it still gives you a right answer:
Browse[2] n
[1] 2 8
But if you give it data out of order, the second column turns to NA,
and that causes doom.
median(df3.2[c(1,3,2),])
Called from: median.default(df3.2[c(1, 3, 2), ])
Browse[1] n
debug at tmp#15: half - (n + 1L)%/%2L
Browse[2] n
debug at tmp#16: if (n%%2L == 1L) sort(x, partial = half)[half] else
mean(sort(x,
partial = half + 0L:1L)[half + 0L:1L])
Browse[2] n
debug at tmp#16: mean(sort(x, partial = half + 0L:1L)[half + 0L:1L])
Interactively:
Browse[2] sort(x, partial = half + 0L:1L)
NA NA NA NA NA NA
1 1 NULL 7 NULL NULL NULL
3 3 NA 9 NA NA NA
2 2 NA 8 NA NA NA
Warning message:
In format.data.frame(x, digits = digits, na.encode = FALSE) :
corrupt data frame:
[Rd] request for R-exts addition
would it be possible / make sense to copy some of the information in ?news into the R-exts manual, where package writers are most likely (?) to look for it? The information therein seems more appropriate for the extensions manual ... cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] patch about recent cairo device on win32
dear all: now I am happy with cairo on win32, but it depends gtk2 for windows and have CJK problem. so I change a litte bit to avoid this two problem. to apply those two patch, you should build pixman and cairo without gtk2 using mingw from source. Yu Gong__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Interrupting C++ code execution
Andrew, You may like to give CXXR a try (http://www.cs.kent.ac.uk/projects/cxxr/). In CXXR the R interpreter is written in C++, and a user interrupt is handled by throwing a C++ exception, so the stack is unwound in an orderly fashion, destructors are invoked, etc. Thank you for this suggestion. CXXR is a very interesting project! For my current project, however, I aim at distributing the program to other R users on pre-installed cluster nodes. Thus, I have no choice with respect to the underlying R interpreter. Best regards, Peter __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] cairo device on win32 without gtk2
now cairo device work on win32, but it depends gtk2 for windows and have CJK problem. so I change a litte bit to avoid these two problem. to apply these two patch, you should build pixman and cairo without gtk2 using mingw from source. Yu Gong__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] GPLv2-only code in R?
Hello, I'm sending this to R-devel under the guideline that the ensuing discussion would probably be unintelligible to people who aren't programmers. If that's not right, I apologize. http://www.r-project.org/Licenses/ says in part: Some files are licensed under 'GPL (version 2 or later)', which includes GPL-3. See the comments in the files to see if this applies. This implies that there are files in R that do *not* have the or later language, and can only be used under GPLv2. I've done some initial searches for files in the R source code that don't have the or later language, but haven't turned anything up yet. If anybody knows of any off-hand and could point me to them, I'd appreciate it. Thank you, -- Brett Smith License Compliance Engineer, Free Software Foundation Support the FSF by becoming an Associate Member: http://fsf.org/jf __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] GPLv2-only code in R?
On 27/04/2011 12:55 PM, Brett Smith wrote: Hello, I'm sending this to R-devel under the guideline that the ensuing discussion would probably be unintelligible to people who aren't programmers. If that's not right, I apologize. http://www.r-project.org/Licenses/ says in part: Some files are licensed under 'GPL (version 2 or later)', which includes GPL-3. See the comments in the files to see if this applies. This implies that there are files in R that do *not* have the or later language, and can only be used under GPLv2. I've done some initial searches for files in the R source code that don't have the or later language, but haven't turned anything up yet. If anybody knows of any off-hand and could point me to them, I'd appreciate it. Package rpart is GPL-2-only in R 2.13.0, but is more liberally licensed in R-patched and R-devel. The survival package was GPL-2-only until R 2.12.1. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] GPLv2-only code in R?
On Thu, 28 Apr 2011, Duncan Murdoch wrote: On 27/04/2011 12:55 PM, Brett Smith wrote: Hello, I'm sending this to R-devel under the guideline that the ensuing discussion would probably be unintelligible to people who aren't programmers. If that's not right, I apologize. http://www.r-project.org/Licenses/ says in part: Some files are licensed under 'GPL (version 2 or later)', which includes GPL-3. See the comments in the files to see if this applies. This implies that there are files in R that do *not* have the or later language, and can only be used under GPLv2. I've done some initial searches for files in the R source code that don't have the or later language, but haven't turned anything up yet. If anybody knows of any off-hand and could point me to them, I'd appreciate it. Package rpart is GPL-2-only in R 2.13.0, but is more liberally licensed in R-patched and R-devel. The survival package was GPL-2-only until R 2.12.1. And all of this in the COPYRIGHTS file for each version of R. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] MDX package?
Much of our data is stored in an MDX datawarehouse using SQL 2008. I was wondering if there has been any work done on interfacing MDX to 'R'? Kevin Burton rkevinbur...@charter.net [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] problems of new cairo device on win32
yesterday i send two email about these problems, but I found the attached patch is removed, so i post again. issue 1 : the new cairo device depend on gtk2, but gtk for windows is buggy, and cairo can be built without gtk2, so I propose build cairo without gtk2 using MinGW, so we can reduce the depend. issue 2 : the default font Helvetica is not an unicode font, so when plots contain East Asia Char, there will be problem, I saw today svn commit, on win32 now use Arial font but still have CJK problem, I think the best way is using Arial Unicode MS font. below is the patch file, : Index: src/library/grDevices/src/cairo/cairoBM.c === --- src/library/grDevices/src/cairo/cairoBM.c(版本 55681) +++ src/library/grDevices/src/cairo/cairoBM.c(工作副本) @@ -25,7 +25,7 @@ /* This module is only compiled if HAVE_WORKING_CAIRO is true */ #ifdef Win32 -#define HAVE_PANGOCAIRO 1 +#define HAVE_PANGOCAIRO 0 #define HAVE_CAIRO_SVG 1 #define HAVE_CAIRO_PDF 1 #define HAVE_CAIRO_PS 1 Index: src/library/grDevices/src/cairo/cairoBM.h === --- src/library/grDevices/src/cairo/cairoBM.h(版本 55681) +++ src/library/grDevices/src/cairo/cairoBM.h(工作副本) @@ -39,7 +39,9 @@ #include stdio.h - +#ifdef Win32 +#undef HAVE_PANGOCAIRO +#endif #ifdef HAVE_PANGOCAIRO # include pango/pango.h # include pango/pangocairo.h Index: src/library/grDevices/src/cairo/cairoX11.c === --- src/library/grDevices/src/cairo/cairoX11.c(版本 55681) +++ src/library/grDevices/src/cairo/cairoX11.c(工作副本) @@ -465,7 +465,11 @@ return raster; } #endif - + +#ifdef Win32 + #undef HAVE_PANGOCAIRO +#endif + #ifdef HAVE_PANGOCAIRO /* - pangocairo section --- */ @@ -782,7 +786,11 @@ pX11Desc xd = (pX11Desc) dd-deviceSpecific; int face = gc-fontface; double size = gc-cex * gc-ps *fs; -char *family = Helvetica; +#ifdef Win32 + char *family = Arial Unicode MS; +#else + char *family = Helvetica; +#endif int slant = CAIRO_FONT_SLANT_NORMAL, wt = CAIRO_FONT_WEIGHT_NORMAL; #ifdef WIN32 char *times = Times New Roman, *hv = Arial; @@ -792,8 +800,8 @@ char *fm = gc-fontfamily; if(streql(fm, mono)) family = courier; -else if(streql(fm, serif)) family = times -else if(streql(fm, sans)) family = hv +else if(streql(fm, serif)) family = times; +else if(streql(fm, sans)) family = hv; else if(fm[0]) family = fm; if (face 1 || face 5) face = 1; if (face == 5) family = Symbol; Index: src/library/grDevices/src/cairo/Makefile.win === --- src/library/grDevices/src/cairo/Makefile.win(版本 55681) +++ src/library/grDevices/src/cairo/Makefile.win(工作副本) @@ -18,15 +18,11 @@ PKG_CPPFLAGS=-I$(R_HOME)/src/include -I. -I.. -DHAVE_CONFIG_H $(arch_DEFS) -PKG_CPPFLAGS+= -I$(GTK2_HOME)/include/cairo \ - -I$(GTK2_HOME)/include/pango-1.0 \ - -I$(GTK2_HOME)/include/glib-2.0 \ - -I$(GTK2_HOME)/lib/glib-2.0/include \ - -I$(GTK2_HOME)/include +PKG_CPPFLAGS+= -I/MinGW/include/cairo \ -PKG_LIBS=-L$(GTK2_HOME)/lib -lpangocairo-1.0 -lpango-1.0 -lcairo \ - -lglib-2.0 -lgobject-2.0 +PKG_LIBS=-L$(GTK2_HOME)/lib -lcairo + all: winCairo.dll @cp winCairo.dll $(R_HOME)/library/grDevices/libs$(R_ARCH) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wish R Core had a standard format (or generic function) for newdata objects
Another way to see your plots is the TkPredict function in the TeachingDemos package. It will default the variables to their medians for numeric predictors and baseline level for factors, but then you can set all of those to something more meaningful one time using the controls, then cycle through the predictors for the plots. It can also give you a command line version of the commands that you could then run, or loop through to get your plots. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r- project.org] On Behalf Of Paul Johnson Sent: Wednesday, April 27, 2011 10:20 AM To: Duncan Murdoch Cc: R Devel List Subject: Re: [Rd] Wish R Core had a standard format (or generic function) for newdata objects On Tue, Apr 26, 2011 at 7:39 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: If you don't like the way this was done in my three lines above, or by Frank Harrell, or the Zelig group, or John Fox, why don't you do it yourself, and get it right this time? It's pretty rude to complain about things that others have given you for free, and demand they do it better. Duncan Murdoch I offer sincere apology for sounding that way. I'm not attacking anybody. I'm just talking, asking don't you agree this were standardized. And you disagree, and I respect that since you are actually doing the work. From a lowly user's point of view, I wish you experts out there would tell us one way to do this, we could follow your example. When there's a regression model fitted with 20 variables in it, and half of them are numeric, 4 are unordered factors, 3 are ordinal factors, and what not, then this is a hard problem for many of us ordinary users. Or it is tedious. They want keep everything fixed, except one variable that takes on different specified values. And they want to do that for every variable, one at a time. Stata has made this easy for many models, R could as well, if we coalesced on a more-or-less standard way to create newdata objects for predict. But, in the end, I agree with your sentiment. I just have to do this, show you it is handy. I think Zelig's setx has it about right, I'll pursue that strategy. pj -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] error while checking package size during Rcmd check
I am receiving this message during
Rcmd check proto-3.9.2.tar.gz
using R version 2.13.0 Patched (2011-04-25 r55638)
* checking installed package size ...Error in if (total 1024 * 5) { : missing
value where TRUE/FALSE needed
Execution halted
I don't get this under R.2.12.x. The size of the tar.gz file is under
600K. What causes this or if its too hard to tell from the message
how can I investigate it further?
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
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Re: [Rd] error while checking package size during Rcmd check
On Thu, Apr 28, 2011 at 9:01 PM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
I am receiving this message during
Rcmd check proto-3.9.2.tar.gz
using R version 2.13.0 Patched (2011-04-25 r55638)
* checking installed package size ...Error in if (total 1024 * 5) { :
missing
value where TRUE/FALSE needed
Execution halted
I don't get this under R.2.12.x. The size of the tar.gz file is under
600K. What causes this or if its too hard to tell from the message
how can I investigate it further?
Also I am using Windows Vista; however, I just found that by upgrading
to the latest Rtools the problem disappears.
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
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[Rd] R CMD check and Suggests Packages
Hello, In my description file, I have an example data package in Suggests: that I've deleted from my library to test what the user who doesn't have it will experience. However, R CMD check won't even pass my package : * checking package dependencies ... ERROR Package required but not available: RepitoolsExamples Why would it have to be installed, if it's only a data package, that isn't needed in any of my code ? The manual also says In particular, large packages providing “only” data for examples or vignettes should be listed in ‘Suggests’ rather than ‘Depends’ in order to make lean installations possible. -- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
