Re: [Rd] fortran 90 underscore error
We have no position about Fortran 90. We provide the means to specify an F90 compiler and note that its use is not portable as not all platforms have one. (A very few are still using gcc3 with g77.) This simply is not an R issue, and seems specific to your unstated platform (*PLEASE* do follow the posting guide). On Mon, 14 Mar 2011, jgar...@ija.csic.es wrote: Hi there, I am preparing a package based on Fortran 90 code. I've put the main code is a MODULE, and I'm having several error messages with the linker: R CMD SHLIB --output=mylib.so nrtype.f90 topbalmod.f90 runmodels.f90 The several error messages are related with the addition of an underscore to function names (no problem with subroutine names). E.g.: topbalmod.o:topbalmod.f90:.text+0x357f: undefined reference to 'runga_' After some googling, AFAIK, it seems the addition of underscores (I'm using gfortran) may be avoided by the option -fno-underscoring, but its use is not recomended as it is not of general use by all compilers. I'm just wondering if R developers just recommend not to use user defined fortran functions at all to avoid this problem, or alternatively if you could provided with some example about how to circumvent it (perhaps to convert all fortran 90 functions into subroutines?). Thanks and best regards. Javier --- -- 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] Feature request: txtProgressBar with ability to write to arbitrary stream
Hi all, I use txtProgressBar to monitor progress of large computations. What I miss is the ability to redirect the progress bar to a stream other than stdout, specifically to the message stream. This would be useful for running Sweave scripts: When redirected to stderr, the bar could be visible even though console output is diverted to the output file (and there would be no cluttering of the generated latex). I'd suggest the following changes to txtProgressBar: - a new argument 'file' (compare to 'cat') which defaults to stderr() (there might be reasons to use stdout(), but I believe a progress bar is mostly intended as a diagnostic tool and not for console output, which is printed or saved in some cases). - the calls to 'cat' that update the progress bar get 'file = file' as additional argument so that output is redirected as desired. In case anyone from the core team is willing to incorparate this idea, I attached the patch file for the necessary changes below. Best regards, Andreas 3c3 width = NA, title, label, style = 1) --- width = NA, title, label, style = 1, file=stderr()) 23c23 cat(paste(rep.int(char, nb-.nb), collapse=)) --- cat(paste(rep.int(char, nb-.nb), collapse=), file = file) 27c27 \r, paste(rep.int(char, nb), collapse=), sep = ) --- \r, paste(rep.int(char, nb), collapse=), sep = , file = file) 38c38 cat(\r, paste(rep.int(char, nb), collapse=), sep = ) --- cat(\r, paste(rep.int(char, nb), collapse=), sep = , file = file) 42c42 \r, paste(rep.int(char, nb), collapse=), sep = ) --- \r, paste(rep.int(char, nb), collapse=), sep = , file = file) 54c54 cat(paste(c(\r |, rep.int( , nw*width+6)), collapse=)) --- cat(paste(c(\r |, rep.int( , nw*width+6)), collapse=), file = file) 59c59 ), collapse=)) --- ), collapse=), file = file) 68c68 cat(\n) --- cat(\n, file = file) -- Andreas Borg Medizinische Informatik UNIVERSITÄTSMEDIZIN der Johannes Gutenberg-Universität Institut für Medizinische Biometrie, Epidemiologie und Informatik Obere Zahlbacher Straße 69, 55131 Mainz www.imbei.uni-mainz.de Telefon +49 (0) 6131 175062 E-Mail: b...@imbei.uni-mainz.de Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und löschen Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail und der darin enthaltenen Informationen ist nicht gestattet. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Standardized Pearson residuals
Peter Dalgaard: It would also be nice for teaching purposes if glm or
summary.glm had a
pearsonchisq component and a corresponding extractor function, but I
can imagine that there might be arguments against it that haven't
occured to me. Plus, I doubt that anyone wants to touch glm unless it's
to repair a bug. If I'm wrong about all that though, ...
This would remedy what I have long judged a deficiency in summary.glm().
The information is important for diagnostic purposes. One should not have
to fit a model with a quasi error, or suss out how to calculate the Pearson
chi square from the glm model object, to discover that the information in the
model object is inconsistent with simple binomial or poisson assumptions.
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
http://www.maths.anu.edu.au/~johnm
On 15/03/2011, at 10:00 PM, r-devel-requ...@r-project.org wrote:
From: Brett Presnell presn...@stat.ufl.edu
Date: 15 March 2011 2:40:29 PM AEDT
To: peter dalgaard pda...@gmail.com
Cc: r-devel@r-project.org
Subject: Re: [Rd] Standardized Pearson residuals
Thanks Peter. I have just a couple of minor comments, and another
possible feature request, although it's one that I don't think will be
implemented.
peter dalgaard pda...@gmail.com writes:
On Mar 14, 2011, at 22:25 , Brett Presnell wrote:
Is there any reason that rstandard.glm doesn't have a pearson option?
And if not, can it be added?
Probably... I have been wondering about that too. I'm even puzzled why
it isn't the default. Deviance residuals don't have quite the
properties that one might expect, e.g. in this situation, the absolute
residuals sum pairwise to zero, so you'd expect that the standardized
residuals be identical in absolute value
y - 1:4
r - c(0,0,1,1)
c - c(0,1,0,1)
rstandard(glm(y~r+c,poisson))
1 2 3 4
-0.2901432 0.2767287 0.2784603 -0.2839995
in comparison,
i - influence(glm(y~r+c,poisson))
i$pear.res/sqrt(1-i$hat)
1 2 3 4
-0.2817181 0.2817181 0.2817181 -0.2817181
The only thing is that I'm always wary of tampering with this stuff,
for fear of finding out the hard way why thing are the way they
are
I'm sure that's wise, but it would be nice to get it in as an option,
even if it's not the default
Background: I'm currently teaching an undergrad/grad-service course from
Agresti's Introduction to Categorical Data Analysis (2nd edn) and
deviance residuals are not used in the text. For now I'll just provide
the students with a simple function to use, but I prefer to use R's
native capabilities whenever possible.
Incidentally, chisq.test will have a stdres component in 2.13.0 for
much the same reason.
Thank you. That's one more thing I won't have to provide code for
anymore. Coincidentally, Agresti mentioned this to me a week or two ago
as something that he felt was missing, so that's at least two people who
will be happy to see this added.
It would also be nice for teaching purposes if glm or summary.glm had a
pearsonchisq component and a corresponding extractor function, but I
can imagine that there might be arguments against it that haven't
occured to me. Plus, I doubt that anyone wants to touch glm unless it's
to repair a bug. If I'm wrong about all that though, ...
BTW, as I go along I'm trying to collect a lot of the datasets from the
examples and exercises in the text into an R package (icda). It's far
from complete and what is there needed tidying up, but I hope to
eventually to round it into shape and put it on CRAN, assuming that
Agresti approves and that there are no copyright issues.
I think something along the following lines should do it:
rstandard.glm -
function(model,
infl=influence(model, do.coef=FALSE),
type=c(deviance, pearson), ...)
{
type - match.arg(type)
res - switch(type, pearson = infl$pear.res, infl$dev.res)
res - res/sqrt(1-infl$hat)
res[is.infinite(res)] - NaN
res
}
[[alternative HTML version deleted]]
__
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Re: [Rd] Standardized Pearson residuals
On 15/03/11 13:17 PM, peter dalgaard pda...@gmail.com wrote: On Mar 15, 2011, at 04:40 , Brett Presnell wrote: Background: I'm currently teaching an undergrad/grad-service course from Agresti's Introduction to Categorical Data Analysis (2nd edn) and deviance residuals are not used in the text. For now I'll just provide the students with a simple function to use, but I prefer to use R's native capabilities whenever possible. Incidentally, chisq.test will have a stdres component in 2.13.0 for much the same reason. Thank you. That's one more thing I won't have to provide code for anymore. Coincidentally, Agresti mentioned this to me a week or two ago as something that he felt was missing, so that's at least two people who will be happy to see this added. And of course, I was teaching a course based on Agresti Franklin: Statistics, The Art and Science of Learning from Data, when I realized that R was missing standardized residuals. So nobody uses McCullagh Nelder: Generalized Linear Models in teaching, since they don't realize that R is missing Anscombe residuals, too? Cheers, Jari Oksanen __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Feature request: txtProgressBar with ability to write to arbitrary stream
Here's a temporary fix; reassign 'cat' in the environment of 'txtProgressBar': tpbEnv - new.env() assign(cat, function(...) cat(file=stderr(),...), tpbEnv) environment(txtProgressBar) - tpbEnv Best, Matt On 03/15/2011 05:37 AM, Andreas Borg wrote: Hi all, I use txtProgressBar to monitor progress of large computations. What I miss is the ability to redirect the progress bar to a stream other than stdout, specifically to the message stream. This would be useful for running Sweave scripts: When redirected to stderr, the bar could be visible even though console output is diverted to the output file (and there would be no cluttering of the generated latex). I'd suggest the following changes to txtProgressBar: - a new argument 'file' (compare to 'cat') which defaults to stderr() (there might be reasons to use stdout(), but I believe a progress bar is mostly intended as a diagnostic tool and not for console output, which is printed or saved in some cases). - the calls to 'cat' that update the progress bar get 'file = file' as additional argument so that output is redirected as desired. In case anyone from the core team is willing to incorparate this idea, I attached the patch file for the necessary changes below. Best regards, Andreas 3c3 width = NA, title, label, style = 1) --- width = NA, title, label, style = 1, file=stderr()) 23c23 cat(paste(rep.int(char, nb-.nb), collapse=)) --- cat(paste(rep.int(char, nb-.nb), collapse=), file = file) 27c27 \r, paste(rep.int(char, nb), collapse=), sep = ) --- \r, paste(rep.int(char, nb), collapse=), sep = , file = file) 38c38 cat(\r, paste(rep.int(char, nb), collapse=), sep = ) --- cat(\r, paste(rep.int(char, nb), collapse=), sep = , file = file) 42c42 \r, paste(rep.int(char, nb), collapse=), sep = ) --- \r, paste(rep.int(char, nb), collapse=), sep = , file = file) 54c54 cat(paste(c(\r |, rep.int( , nw*width+6)), collapse=)) --- cat(paste(c(\r |, rep.int( , nw*width+6)), collapse=), file = file) 59c59 ), collapse=)) --- ), collapse=), file = file) 68c68 cat(\n) --- cat(\n, file = file) -- Matthew S Shotwell Assistant Professor School of Medicine Department of Biostatistics Vanderbilt University __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Standardized Pearson residuals
On Mar 15, 2011, at 13:42 , John Maindonald wrote:
Peter Dalgaard: It would also be nice for teaching purposes if glm or
summary.glm had a
pearsonchisq component and a corresponding extractor function, but I
can imagine that there might be arguments against it that haven't
occured to me. Plus, I doubt that anyone wants to touch glm unless it's
to repair a bug. If I'm wrong about all that though, ...
Umm, that was Brett, actually.
This would remedy what I have long judged a deficiency in summary.glm().
The information is important for diagnostic purposes. One should not have
to fit a model with a quasi error, or suss out how to calculate the Pearson
chi square from the glm model object, to discover that the information in the
model object is inconsistent with simple binomial or poisson assumptions.
It could be somewhere between useless and misleading in cases like binary
logistic regression though. (Same thing goes for the test against the saturated
model: Sometimes it makes sense and sometimes not.)
John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax : +61 2(6125)5549
Centre for Mathematics Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
http://www.maths.anu.edu.au/~johnm
On 15/03/2011, at 10:00 PM, r-devel-requ...@r-project.org wrote:
From: Brett Presnell presn...@stat.ufl.edu
Date: 15 March 2011 2:40:29 PM AEDT
To: peter dalgaard pda...@gmail.com
Cc: r-devel@r-project.org
Subject: Re: [Rd] Standardized Pearson residuals
Thanks Peter. I have just a couple of minor comments, and another
possible feature request, although it's one that I don't think will be
implemented.
peter dalgaard pda...@gmail.com writes:
On Mar 14, 2011, at 22:25 , Brett Presnell wrote:
Is there any reason that rstandard.glm doesn't have a pearson option?
And if not, can it be added?
Probably... I have been wondering about that too. I'm even puzzled why
it isn't the default. Deviance residuals don't have quite the
properties that one might expect, e.g. in this situation, the absolute
residuals sum pairwise to zero, so you'd expect that the standardized
residuals be identical in absolute value
y - 1:4
r - c(0,0,1,1)
c - c(0,1,0,1)
rstandard(glm(y~r+c,poisson))
1 2 3 4
-0.2901432 0.2767287 0.2784603 -0.2839995
in comparison,
i - influence(glm(y~r+c,poisson))
i$pear.res/sqrt(1-i$hat)
1 2 3 4
-0.2817181 0.2817181 0.2817181 -0.2817181
The only thing is that I'm always wary of tampering with this stuff,
for fear of finding out the hard way why thing are the way they
are
I'm sure that's wise, but it would be nice to get it in as an option,
even if it's not the default
Background: I'm currently teaching an undergrad/grad-service course from
Agresti's Introduction to Categorical Data Analysis (2nd edn) and
deviance residuals are not used in the text. For now I'll just provide
the students with a simple function to use, but I prefer to use R's
native capabilities whenever possible.
Incidentally, chisq.test will have a stdres component in 2.13.0 for
much the same reason.
Thank you. That's one more thing I won't have to provide code for
anymore. Coincidentally, Agresti mentioned this to me a week or two ago
as something that he felt was missing, so that's at least two people who
will be happy to see this added.
It would also be nice for teaching purposes if glm or summary.glm had a
pearsonchisq component and a corresponding extractor function, but I
can imagine that there might be arguments against it that haven't
occured to me. Plus, I doubt that anyone wants to touch glm unless it's
to repair a bug. If I'm wrong about all that though, ...
BTW, as I go along I'm trying to collect a lot of the datasets from the
examples and exercises in the text into an R package (icda). It's far
from complete and what is there needed tidying up, but I hope to
eventually to round it into shape and put it on CRAN, assuming that
Agresti approves and that there are no copyright issues.
I think something along the following lines should do it:
rstandard.glm -
function(model,
infl=influence(model, do.coef=FALSE),
type=c(deviance, pearson), ...)
{
type - match.arg(type)
res - switch(type, pearson = infl$pear.res, infl$dev.res)
res - res/sqrt(1-infl$hat)
res[is.infinite(res)] - NaN
res
}
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
__
Re: [Rd] Standardized Pearson residuals
On Mar 15, 2011, at 14:22 , Jari Oksanen wrote: On 15/03/11 13:17 PM, peter dalgaard pda...@gmail.com wrote: On Mar 15, 2011, at 04:40 , Brett Presnell wrote: Background: I'm currently teaching an undergrad/grad-service course from Agresti's Introduction to Categorical Data Analysis (2nd edn) and deviance residuals are not used in the text. For now I'll just provide the students with a simple function to use, but I prefer to use R's native capabilities whenever possible. Incidentally, chisq.test will have a stdres component in 2.13.0 for much the same reason. Thank you. That's one more thing I won't have to provide code for anymore. Coincidentally, Agresti mentioned this to me a week or two ago as something that he felt was missing, so that's at least two people who will be happy to see this added. And of course, I was teaching a course based on Agresti Franklin: Statistics, The Art and Science of Learning from Data, when I realized that R was missing standardized residuals. So nobody uses McCullagh Nelder: Generalized Linear Models in teaching, since they don't realize that R is missing Anscombe residuals, too? Cheers, Jari Oksanen Well, if you can read the book, you can probably write the code... The other books are for beginners who may need the convenience (and persuasion power) of standard software. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Feature request: txtProgressBar with ability to write to arbitrary stream
On 15/03/2011 8:46 AM, Matt Shotwell wrote: Here's a temporary fix; reassign 'cat' in the environment of 'txtProgressBar': tpbEnv- new.env() assign(cat, function(...) cat(file=stderr(),...), tpbEnv) environment(txtProgressBar)- tpbEnv I would suggest renaming the function as well. What's done above creates a new function called txtProgressBar, it doesn't modify the original one, so depending on scoping issues it may appear to only work sometimes. But if you did stderrProgressBar - txtProgressBar environment(stderrProgressBar) - tpbEnv you'll get clear messages if it is out of scope when you try to use it. Duncan Murdoch Best, Matt On 03/15/2011 05:37 AM, Andreas Borg wrote: Hi all, I use txtProgressBar to monitor progress of large computations. What I miss is the ability to redirect the progress bar to a stream other than stdout, specifically to the message stream. This would be useful for running Sweave scripts: When redirected to stderr, the bar could be visible even though console output is diverted to the output file (and there would be no cluttering of the generated latex). I'd suggest the following changes to txtProgressBar: - a new argument 'file' (compare to 'cat') which defaults to stderr() (there might be reasons to use stdout(), but I believe a progress bar is mostly intended as a diagnostic tool and not for console output, which is printed or saved in some cases). - the calls to 'cat' that update the progress bar get 'file = file' as additional argument so that output is redirected as desired. In case anyone from the core team is willing to incorparate this idea, I attached the patch file for the necessary changes below. Best regards, Andreas 3c3 width = NA, title, label, style = 1) --- width = NA, title, label, style = 1, file=stderr()) 23c23 cat(paste(rep.int(char, nb-.nb), collapse=)) --- cat(paste(rep.int(char, nb-.nb), collapse=), file = file) 27c27 \r, paste(rep.int(char, nb), collapse=), sep = ) --- \r, paste(rep.int(char, nb), collapse=), sep = , file = file) 38c38 cat(\r, paste(rep.int(char, nb), collapse=), sep = ) --- cat(\r, paste(rep.int(char, nb), collapse=), sep = , file = file) 42c42 \r, paste(rep.int(char, nb), collapse=), sep = ) --- \r, paste(rep.int(char, nb), collapse=), sep = , file = file) 54c54 cat(paste(c(\r |, rep.int( , nw*width+6)), collapse=)) --- cat(paste(c(\r |, rep.int( , nw*width+6)), collapse=), file = file) 59c59 ), collapse=)) --- ), collapse=), file = file) 68c68 cat(\n) --- cat(\n, file = file) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Feature request: txtProgressBar with ability to write to arbitrary stream
You could use winProgressBar (windows only) or TkProgressBar (tcltk package required) instead, then nothing is output to the console/standard out but you still have a visual of your progress. -- 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 Andreas Borg Sent: Tuesday, March 15, 2011 4:37 AM To: R-devel@r-project.org Subject: [Rd] Feature request: txtProgressBar with ability to write to arbitrary stream Hi all, I use txtProgressBar to monitor progress of large computations. What I miss is the ability to redirect the progress bar to a stream other than stdout, specifically to the message stream. This would be useful for running Sweave scripts: When redirected to stderr, the bar could be visible even though console output is diverted to the output file (and there would be no cluttering of the generated latex). I'd suggest the following changes to txtProgressBar: - a new argument 'file' (compare to 'cat') which defaults to stderr() (there might be reasons to use stdout(), but I believe a progress bar is mostly intended as a diagnostic tool and not for console output, which is printed or saved in some cases). - the calls to 'cat' that update the progress bar get 'file = file' as additional argument so that output is redirected as desired. In case anyone from the core team is willing to incorparate this idea, I attached the patch file for the necessary changes below. Best regards, Andreas 3c3 width = NA, title, label, style = 1) --- width = NA, title, label, style = 1, file=stderr()) 23c23 cat(paste(rep.int(char, nb-.nb), collapse=)) --- cat(paste(rep.int(char, nb-.nb), collapse=), file = file) 27c27 \r, paste(rep.int(char, nb), collapse=), sep = ) --- \r, paste(rep.int(char, nb), collapse=), sep = , file = file) 38c38 cat(\r, paste(rep.int(char, nb), collapse=), sep = ) --- cat(\r, paste(rep.int(char, nb), collapse=), sep = , file = file) 42c42 \r, paste(rep.int(char, nb), collapse=), sep = ) --- \r, paste(rep.int(char, nb), collapse=), sep = , file = file) 54c54 cat(paste(c(\r |, rep.int( , nw*width+6)), collapse=)) --- cat(paste(c(\r |, rep.int( , nw*width+6)), collapse=), file = file) 59c59 ), collapse=)) --- ), collapse=), file = file) 68c68 cat(\n) --- cat(\n, file = file) -- Andreas Borg Medizinische Informatik UNIVERSITÄTSMEDIZIN der Johannes Gutenberg-Universität Institut für Medizinische Biometrie, Epidemiologie und Informatik Obere Zahlbacher Straße 69, 55131 Mainz www.imbei.uni-mainz.de Telefon +49 (0) 6131 175062 E-Mail: b...@imbei.uni-mainz.de Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und löschen Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail und der darin enthaltenen Informationen ist nicht gestattet. __ 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] object not found whilst loading namespace
I've been updating a package and, when installing a local devel version, I get an error object 'confusionMatrix' not found whilst loading namespace. Looking around online, it appears that this might be related to loading a specific RData file, but it doesn't seem to be the case AFAICT. I've installed the devel version in the last week without issues and the confusionMatrix code has been touched in a while. Thanks, Max sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] caret_4.71 reshape_0.8.3 plyr_1.2.1 lattice_0.18-8 loaded via a namespace (and not attached): [1] grid_2.11.1 pkg_kuhna03$ R CMD INSTALL caret * installing to library ‘/Library/Frameworks/R.framework/Resources/library’ * installing *source* package ‘caret’ ... ** libs *** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include-fPIC -g -O2 -c caret.c -o caret.o gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o caret.so caret.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Resources/library/caret/libs/i386 *** arch - x86_64 gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include-fPIC -g -O2 -c caret.c -o caret.o gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o caret.so caret.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Resources/library/caret/libs/x86_64 ** R ** data ** inst ** preparing package for lazy loading Loading required package: plyr Attaching package: 'reshape' The following object(s) are masked from 'package:plyr': round_any ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error : object 'confusionMatrix' not found whilst loading namespace 'caret' ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Resources/library/caret’ * restoring previous ‘/Library/Frameworks/R.framework/Resources/library/caret’ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] object not found whilst loading namespace
Please disregard the last email... The issue was a syntactical error in a file that, alphabetically, comes before confusionMatrix.R in the package. The odd thing was that the problem in this file did not throw and error (or I would have easily found it). I decided to source the R files one by one to see if there were any issues and that showed the problem: source(~/Code/caret/pkg/caret/R/classLevels.R) Error in source(~/Code/caret/pkg/caret/R/classLevels.R) : ~/Code/caret/pkg/caret/R/classLevels.R:150:0: unexpected end of input Thanks anyway, Max On Tue, Mar 15, 2011 at 9:48 PM, Max Kuhn mxk...@gmail.com wrote: I've been updating a package and, when installing a local devel version, I get an error object 'confusionMatrix' not found whilst loading namespace. Looking around online, it appears that this might be related to loading a specific RData file, but it doesn't seem to be the case AFAICT. I've installed the devel version in the last week without issues and the confusionMatrix code has been touched in a while. Thanks, Max sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] caret_4.71 reshape_0.8.3 plyr_1.2.1 lattice_0.18-8 loaded via a namespace (and not attached): [1] grid_2.11.1 pkg_kuhna03$ R CMD INSTALL caret * installing to library ‘/Library/Frameworks/R.framework/Resources/library’ * installing *source* package ‘caret’ ... ** libs *** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c caret.c -o caret.o gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o caret.so caret.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Resources/library/caret/libs/i386 *** arch - x86_64 gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -c caret.c -o caret.o gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o caret.so caret.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Resources/library/caret/libs/x86_64 ** R ** data ** inst ** preparing package for lazy loading Loading required package: plyr Attaching package: 'reshape' The following object(s) are masked from 'package:plyr': round_any ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error : object 'confusionMatrix' not found whilst loading namespace 'caret' ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Resources/library/caret’ * restoring previous ‘/Library/Frameworks/R.framework/Resources/library/caret’ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] object not found whilst loading namespace
On 11-03-15 9:59 PM, Max Kuhn wrote: Please disregard the last email... The issue was a syntactical error in a file that, alphabetically, comes before confusionMatrix.R in the package. The odd thing was that the problem in this file did not throw and error (or I would have easily found it). I decided to source the R files one by one to see if there were any issues and that showed the problem: source(~/Code/caret/pkg/caret/R/classLevels.R) Error in source(~/Code/caret/pkg/caret/R/classLevels.R) : ~/Code/caret/pkg/caret/R/classLevels.R:150:0: unexpected end of input The files are concatenated into one big file which is sourced. You've got an unclosed parenthesis/brace/bracket in this file, but some later file closed it -- so that file probably has an extra closing one. Duncan Murdoch Thanks anyway, Max On Tue, Mar 15, 2011 at 9:48 PM, Max Kuhnmxk...@gmail.com wrote: I've been updating a package and, when installing a local devel version, I get an error object 'confusionMatrix' not found whilst loading namespace. Looking around online, it appears that this might be related to loading a specific RData file, but it doesn't seem to be the case AFAICT. I've installed the devel version in the last week without issues and the confusionMatrix code has been touched in a while. Thanks, Max sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] caret_4.71 reshape_0.8.3 plyr_1.2.1 lattice_0.18-8 loaded via a namespace (and not attached): [1] grid_2.11.1 pkg_kuhna03$ R CMD INSTALL caret * installing to library ‘/Library/Frameworks/R.framework/Resources/library’ * installing *source* package ‘caret’ ... ** libs *** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include-fPIC -g -O2 -c caret.c -o caret.o gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o caret.so caret.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Resources/library/caret/libs/i386 *** arch - x86_64 gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include-fPIC -g -O2 -c caret.c -o caret.o gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o caret.so caret.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Resources/library/caret/libs/x86_64 ** R ** data ** inst ** preparing package for lazy loading Loading required package: plyr Attaching package: 'reshape' The following object(s) are masked from 'package:plyr': round_any ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error : object 'confusionMatrix' not found whilst loading namespace 'caret' ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Resources/library/caret’ * restoring previous ‘/Library/Frameworks/R.framework/Resources/library/caret’ __ 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] .libPaths() on Windows may return duplicated paths
In R v2.12.2 patched (2011-03-13 r54787) and also in R v2.13.0 devel
(2011-03-15 r54806), .libPaths() may return the multiple paths
referring to the same normalized path name. Here is an example from
Rterm --vanilla using R v2.12.2 patched:
paths - .libPaths(c(C:/, C:\\))
paths
[1] C:/
[2] C:\\
[3] C:/PROGRA~1/R/R-2.13.0dev/library
The reason is that .libPaths() does not detect paths[1] and paths[2]
to be equal;
.libPaths
function (new)
{
if (!missing(new)) {
new - Sys.glob(path.expand(new))
paths - unique(path.expand(c(new, .Library.site, .Library)))
.lib.loc - paths[file.info(paths)$isdir %in% TRUE]
}
else .lib.loc
}
One solution would be to replace:
paths - unique(path.expand(c(new, .Library.site, .Library)))
with
paths - path.expand(c(new, .Library.site, .Library))
paths - utils::normalizePath(paths)
paths - unique(paths)
This would obviously not work because this would make .libPaths()
depend on the utils package as standing. Migrating normalizePath() to
the 'base' package would be one solution.
Finally, this causes update.packages() to try to download and install
the same package multiple times, e.g.
.libPaths()
[1] C:\\Users\\hb/R/win-library/2.12
[2] C:/PROGRA~1/R/R-2.12.2patched/library
[3] C:\\Users\\hb\\R\\win-library\\2.12
update.packages()
digest :
Version 0.4.1 installed in C:\Users\hb/R/win-library/2.12
Version 0.4.2 available at http://cran.stat.ucla.edu
Update (y/N/c)? y
digest :
Version 0.4.1 installed in C:\Users\hb\R\win-library\2.12
Version 0.4.2 available at http://cran.stat.ucla.edu
Update (y/N/c)? y
...
Obviously, I know how to fix/avoid this myself, but I figured it is
more generic if .libPaths() does it for everyone.
/Henrik
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