[Rd] Surprising length() of POSIXlt vector (PR#14073)

2009-11-19 Thread mark
str(dates) # POSIXlt[1:9], format: "2009-01-01" "2009-01-02" "2009-01-03" "2009-01-04" ... print(dates[20]) # [1] "2009-01-20" print(length(dates[20])) # [1] 9 I've since realised that POSIXct makes date vectors easier, but could w

Re: [Rd] Surprising length() of POSIXlt vector (PR#14073)

2009-11-20 Thread mark
n the end, "[" sees a different length to "[[" and "$" here, so a length.POSIXlt() just shuffles the issue around. Anyhow, I somehow missed there have been other PRs on this, including discussion on r-devel of "[" and logical vs physical length() under PR#10507. I'm sorry for being repetitive. Mark <>< __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] load, environment[[, and attr<-/attributes<- (PR#8457)

2006-01-02 Thread mark . bravington
Full_Name: Mark Bravington Version: 2.2.1 OS: Windows XP Submission from: (NULL) (203.132.243.69) # [EMAIL PROTECTED] There is a bug to do with 'load', environment access via '[[', and 'attr<-' or 'attributes<-'. Modifying the attributes of

[Rd] Warning from Sys.junction when using network drive.

2018-02-07 Thread MARK BANGHART
(mkjunction(fr, link)) did not produce an error. I would appreciate any help you can provide on this issue. Thanks, Mark [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] undefined symbol errors when compiling package using ALTREP API

2019-06-04 Thread Mark Klik
#x27; is defined as: SEXP attribute_hidden ALTVEC_EXTRACT_SUBSET(SEXP x, SEXP indx, SEXP call) My question is why these differences between Windows / OSX and Linux exist and if they are intentional? Do I need special build parameters to make sure my package builds correctly on Linux? thanks f

Re: [Rd] [External] undefined symbol errors when compiling package using ALTREP API

2019-06-04 Thread Mark Klik
hanks for your time & best, Mark On Tue, Jun 4, 2019 at 6:52 PM Tierney, Luke wrote: > On Tue, 4 Jun 2019, Mark Klik wrote: > > > Hello, > > > > I'm developing a package (lazyvec) that makes full use of the ALTREP > > framework (R >= 3.6.0). > >

Re: [Rd] [External] undefined symbol errors when compiling package using ALTREP API

2019-06-04 Thread Mark Klik
panded vector and can take a lot of RAM for large datasets. So being able to make use of the internal representation of (a few of the) base ALTREP vectors can be very interesting for (non-R) serialization schemes. thanks for your time! Mark On Tue, Jun 4, 2019 at 11:50 PM Gabriel Becker wrote:

Re: [Rd] [External] undefined symbol errors when compiling package using ALTREP API

2019-06-05 Thread Mark Klik
thanks Luke, I can work with that and will watch out for changes and new developments in the ALTREP code with great interest. all the best, Mark On Wed, Jun 5, 2019 at 6:02 PM Tierney, Luke wrote: > For now you can use > > R_altrep_inherits(x, R_compact_intseq_class) > &g

Re: [Rd] Help useRs to use R's own Time/Date objects more efficiently

2020-04-05 Thread Mark Leeds
Hi All: I've been following this thread and just want to add one pointer. For those who aren't interested in using new packages that try to make dates-times easier but also find the base R tools confusing, below is link to an extremely well written document from over 15 years ago. It's probably al

Re: [Rd] [External] Re: Help useRs to use R's own Time/Date objects more efficiently

2020-04-05 Thread Mark Leeds
gt; > I couldn't find a discussion of POSIXct/POSIXlt objects in the R > > manuals (unless I missed it somewhere), so perhaps "An Introduction to > > R" could be updated to include this subject, and then the help files > > could reference that? > > > &g

Re: [Rd] Trying to understand the search path and namespaces

2010-11-15 Thread Mark Leeds
Hi Duncan: Luke's article is in the June, 2003 edition of R-news On Mon, Nov 15, 2010 at 8:43 PM, Duncan Murdoch wrote: > Hadley Wickham wrote: > >> Hi all, >> >> I'm trying to understand how the search path and namespaces interact. >> For example, take the devtools package which suggests the te

[Rd] how to store package options over sessions?

2010-11-20 Thread Mark Heckmann
package load. Is that possible and if yes, is the standard way to implement this? Thanks, Mark ––– Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Celler Straße 27 28205 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com

[Rd] R crashes if "toFile" given "~/" in Linux envirnonment

2011-05-16 Thread Mark Kimpel
h. Is this expected behavior? See my output below and sessionInfo(). Also, not shown, but 'setwd("~/Desktop")' works just fine. Thanks, Mark # sample code from Rgraphviz clusterData help page library(graph) library(Rgraphviz) g1_gz <- gzfile(system.file("GXL/graphExa

Re: [Rd] R crashes if "toFile" given "~/" in Linux envirnonment

2011-05-16 Thread Mark Kimpel
Thanks Simon. There was no help page for "toFile" (the first thing I tried) so I didn't realize it was an Rgraphviz function. I'll contact the maintainers. Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter

[Rd] Graphical option to update.packages in development version (build of the 2011-07-31 r56569) for Windows not working properly

2011-08-04 Thread Mark Difford
es: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.14.0 - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in conte

Re: [Rd] Graphical option to update.packages in development version (build of the 2011-07-31 r56569) for Windows not working properly

2011-08-21 Thread Mark Difford
Thanks for the feedback, Uwe. Will try the most recent development version. Best, Mark Difford. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com

[Rd] suppressing stderr output from system() calls

2011-10-05 Thread Mark Cowley
hit with a 'job failed' status, when all that might have happened is an R package got installed, or a file got downloaded via FTP. Any ideas? Can system() and .Internal() output be redirected to stdout? cheers, Mark sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-apple-darw

[Rd] Fresh build from source of R-3.2.5 failing "make check" under 64-bit Ubuntu

2016-04-20 Thread Mark Dalphin
ot; > stopifnot(identical(res[,"Package"], setNames(,sort(c(p.lis, "myTst", + res[,"LibPath"] == "myLib") Error: identical(res[, "Package"], setNames(, sort(c(p.lis, "myTst" is not TRUE Execution halted > ls myLib exNSS4

Re: [Rd] Fresh build from source of R-3.2.5 failing "make check" under 64-bit Ubuntu [SOLVED]

2016-04-21 Thread Mark Dalphin
ence:/mnt/home/opt/apps on /opt/apps type nfs (rw,soft,bg,nfsvers=3,addr=XXX.XXX.XXX.XXX) Just the NFS, I guess. This is not good, but not an R-Devel problem. Thanks for the help. Cheers, Mark Dalphin PhD Director of Bioinformatics mark.dalp...@pacificedge.co.nz Ph: +64 3 479 4690 Cell

[Rd] A bug in the R Mersenne Twister (RNG) code?

2016-08-30 Thread Mark Roberts
I apologize for having wasted your time. If you (collectively) can't do that, then R is very likely using incorrectly implemented MT code. And if this latter possibility is true, it seems to me that this is something that should be fixed. Mark Roberts, Ph.D.

Re: [Rd] optim(…, method=‘L-BFGS-B’) stops with an error message while violating the lower bound

2016-10-08 Thread Mark Leeds
Hi Spencer: See the link below about L-BFGS-B below because I had problems with it a good while back (and I think the link description is the cause but I can't prove it ) so eventually I moved to the Rvmmin(b) package. It's a package but really an algorithm. Rvmmin(b) uses a variable-metric alg

Re: [Rd] optim(…, method=‘L-BFGS-B’) stops with an error message while violating the lower bound

2016-10-08 Thread Mark Leeds
tly rather than in optimx. I did a lot of optimizations ( hundreds ) at one point and I never saw it return NA ?? 2) I wasn't sure about 2) either so I figured it was safer to get away from L-BFGS-B. On Sat, Oct 8, 2016 at 7:03 PM, Spencer Graves wrote: > Hi, Mark et al.: > &

Re: [Rd] getGraphicsEvent() alternative for cairo graphics device?

2016-11-15 Thread Mark O'Connell
Hi Paul, No problem. Is it best if I post examples to the bug report 16951? Kind regards, Mark -- Mark O'Connell, PhD student Department of Mathematics & Statistics 231 Top Logic National University of Ireland, Maynooth - Paul Murrell wrote: > > Thanks Frederick. > &

Re: [Rd] Wrongly converging glm()

2017-07-20 Thread Mark Leeds
Hi Harm-Jan. I've been following this thread to some degree and just want to add that this issue is not specific to the GLM. It's a problem with optimization of functions in general. I was using use Rvmmin with constraints which is an extremely solid optimization package written by John Nash ( use

Re: [Rd] Wrongly converging glm()

2017-07-21 Thread Mark Leeds
about this for a long time and only happened to notice it when playing around with the likelihood by fixing the offending parameter to various values and optimizing over the non-offending parameter. Thanks for eloquent explanation. Mark On Fri, Jul 21, 2017 at 9:

Re: [Rd] Wrongly converging glm()

2017-07-21 Thread Mark Leeds
objective function seemed independent of one of the parameters. On Fri, Jul 21, 2017 at 4:36 PM, Ravi Varadhan wrote: > “So, what I learned the hard way was termination due to reasonable > stopping criteria DOES NOT NECESSARILY EQUAL OPTIMAL.” > > > > Yes, I agree, Mark

Re: [Rd] suppressing stderr output from system() calls

2011-10-05 Thread Mark Cowley
install.package & all code which has embedded install.packages calls, are there any other ways? @Brian, thanks for the pointer to the news article on connections - I did learn something there cheers, Mark On 06/10/2011, at 3:59 AM, Martin Morgan wrote: > On 10/05/2011 02:36 AM, Mark Co

[Rd] R CMD INSTALL writes to stderr

2011-10-10 Thread Mark Cowley
sages that are produced by install.packages() when R libraries are being installed. So, will it be possible for R CMD INSTALL output be written to stdout in the future? kind regards, Mark - Mark Cowley, PhD Pancreatic Cancer Program | Peter

Re: [Rd] R CMD INSTALL writes to stderr

2011-10-10 Thread Mark Cowley
. Code available if anyone's interested cheers, Mark On 11/10/2011, at 12:23 PM, Simon Urbanek wrote: > > On Oct 10, 2011, at 8:48 PM, Mark Cowley wrote: > >> Dear list, >> (this is a follow up from a previous query) >> >> Why does R CMD INSTALL write most o

[Rd] R fails when converting units using Hershey-Fonts

2011-10-25 Thread Mark Heckmann
"dimension", "y", "dimension", valueOnly = valueOnly) 4: convertHeight(stringHeight(label), unitTo = "mm") Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace System: MacOS 10.6

[Rd] cygwin R-2.14.0 build fail

2011-11-12 Thread Mark Carter
I tried to build R-2.14.0 on cygwin using the commands: ./configure --with-x=no make I started to get a whole lot of errors starting with: /cygdrive/c/Users/mcarter/src/R-2.14.0/src/modules/internet/Rhttpd.c:275: undefined reference to `_R_InputHandlers' which I have pasted at http://pastebin.c

[Rd] Unable to reload Rdoc

2012-01-27 Thread Mark Cowley
this & continue within the same R session? cheers, Mark # 1) using Hadley's devtools > library(devtools) > library(updateR) # my package under development > install("~/src/R/updateR") > install("~/src/R/updateR") Installing updateR * checking for file ‘/Users/

Re: [Rd] Unable to reload Rdoc

2012-01-29 Thread Mark Cowley
Gentlemen, Thanks for your insights, all 3 hints are very useful. Mark On 28/01/2012, at 8:29 AM, Henrik Bengtsson wrote: > Related: To simplify reloading a help page after restarting R, I do > have the following in my ~/.Rprofile: > > # Always only the HTML help on the same

Re: [Rd] Higher Resolution Icons for Windows / Mac

2012-04-10 Thread Mark Lang
-formatted icon files. Again, the files were created using your previously posted logos, so I give them to you under the Creative Commons Attribution ShareAlike license. Thank you, Mark Lang School of Marine and Atmospheric Sciences Stony Brook University 133 Endeavour Hall mark.l...@stonybrook.edu

Re: [Rd] The constant part of the log-likelihood in StructTS

2012-05-02 Thread Mark Leeds
those also. My point is that, if you're comparing likelihoods of different models, if possible, it's best to use ONE package/function so that you don't use different likelihoods by accident. Mark Also, not sure why this is on R-dev ? M

[Rd] R-2.15.1 CMD CHECK output: "Call Sequence"

2012-10-20 Thread Mark Cowley
nything like this before. This is on a pretty fresh OSX 10.8 Mountain Lion installation, where I installed R from CRAN via pkg. Is this a problem unique to me? cheers, Mark heres' a snippet from testing one of my packages under development: * checking for unstated dependencies in R code ... WAR

Re: [Rd] R-2.15.1 CMD CHECK output: "Call Sequence"

2012-10-21 Thread Mark Cowley
guilty of not looking beyond the spotlight of the current package. kind regards, Mark On 21/10/2012, at 1:50 AM, Prof Brian Ripley wrote: > On Sat, 20 Oct 2012, Mark Cowley wrote: > >> Hi guRus, > >> i'm running R-2.15.1 and the R CMD CHECK output appears to have

[Rd] Getting ordered factor levels from C

2012-10-24 Thread Mark Lilback
en','red'), ordered=TRUE) When I get the "levels" attribute in C, I get back the the first vector, not the second. If I run attr(lvls,"levels") in R, I get back the second vector. There are no attributes besides class and levels, so how do I get the list o

Re: [Rd] Getting ordered factor levels from C

2012-10-24 Thread Mark Lilback
t 2:14 PM, Mark Lilback wrote: > >> I'm working on an R package in C and can't seem to get the same level >> information about a factor that the R console displays. >> >> If I define a factor as: >> >> lvls <- factor(c('red',&#x

Re: [Rd] Recommended way to call/import functions from a Suggested package

2013-02-22 Thread Mark Leeds
Hi David: According to the description on cran, lattice imports grid. I don't know if you've seen it but www.obeautifulcode.com has a very nice topic in its archives called "How R Searches and Finds Stuff" which is relatde to your question that I found it to be really helpful. A lot of people on

Re: [Rd] Recommended way to call/import functions from a Suggested package

2013-02-22 Thread Mark Leeds
ld be installed from cran. On Fri, Feb 22, 2013 at 10:07 PM, Mark Leeds wrote: > Hi David: According to the description on cran, lattice imports grid. > > I don't know if you've seen it but www.obeautifulcode.com has a very nice > topic in its archives called "How R Se

Re: [Rd] install.packages now intentionally references .Rprofile?

2009-05-21 Thread Mark Kimpel
when it was working, hence my desire for a fix for my code. Thanks, Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work

[Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny

2009-07-15 Thread Mark Kimpel
. Thanks, Mark mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: su root Password: mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include# /home/mkimpel/R_HOME/R-2.9.1/R-build/bin/R WARNING: ignoring environment value of R_HOME R version 2.9.1 (2009-06-26) Copyright (C) 2009 The R Foundation for

Re: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny

2009-07-15 Thread Mark Kimpel
debian-xps /usr/lib/jvm/java-6-sun/include: printenv PATH /home/mkimpel/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/lib/jvm/ mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: On Wed, Jul 15, 2009 at 2:46 PM, Mark Kimpel wrote: &g

Re: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny

2009-07-15 Thread Mark Kimpel
Well, guess what, rJava also compiles on R-devel (soon to be R-2.10.0). I'll stick with that for my purposes. Thanks for your suggestion. Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University Scho

[Rd] What changed in the R Windows interface from v2.6.2 to v2.7.0?

2009-07-30 Thread Mark Thyer
help on this matter is greatly appreciated. The ability to launch R from a Fortran application is important for the usability of the RFortran software library (www.rfortran.org <http://www.rfortran.org/> ) that we are developing. Cheers, Mark ___

[Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze

2009-09-16 Thread Mark Kimpel
;d like to get R-devel up and running if possible. I am sure there is more info I can provide, but before deluging the list with unnecessary output, I thought I would ask first what would be helpfu. Mark #Make R cd ~/R_HOME wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz tar -xzf R-devel

Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze

2009-09-16 Thread Mark Kimpel
pace in my R_HOME or any of its subdirectories. Will report back on what I get with gcc 4.3 just as soon as I read the R-admin manual and figure out how to get configure configured Mark mkimpel-XPS ~/sshfs: R --vanilla R version 2.10.0 Under development (unstable) (2009-09-15 r49711) Copy

Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze

2009-09-16 Thread Mark Kimpel
.omegahat.org/R";, ask = FALSE) last.update <- current.time local(save(last.update, file = ".Rupdate.date")) print("packages updated") } else {print("packages do not need updated")} setwd(old.wd) } ###

Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze

2009-09-16 Thread Mark Kimpel
R is loaded, the function loads into R just fine and in facts runs as intended. So, perhaps there is something in the way R is sourcing the file or with the source command itself? Thanks for helping me to figure this out, let me know if there is anything specific you want me to try.

Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze

2009-09-16 Thread Mark Kimpel
Thanks, no problem for me to wait for the fix. It's just nice to know that I was able to help improve R in a small way by using R-devel. Usually, it is ME making the error! Thanks again for all your development efforts. Cheers, Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psych

Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze

2009-09-21 Thread Mark Kimpel
Just downloaded and installed "R version 2.10.0 Under development (unstable) (2009-09-21 r49771)" and am happy to report that my .Rprofile loads appropriately with no segfaults. Thanks Duncan! Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School o

Re: [Rd] Surprising length() of POSIXlt vector (PR#14073)

2009-11-20 Thread Mark White
n the end, "[" sees a different length to "[[" and "$" here, so a length.POSIXlt() just shuffles the issue around. Anyhow, I somehow missed there have been other PRs on this, including discussion on r-devel of "[" and logical vs physical length() under PR#10507. I'm sorry for being repetitive. Mark <>< __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] question about differences in behavior with NA subscripts in matrix vs. data.frame

2009-12-03 Thread Mark Kimpel
ation of the behavior, but the rationale for its existence. Could someone explain to me why the difference is logical and useful? This seems more of a devel than a help issue, my apologies if I've posted to the incorrect list. Mark # a.vec <- c("A", "", "B

Re: [Rd] Rcpp: Clarifying the meaning of GPL?

2009-12-22 Thread Mark Kimpel
ue is important, that good communication is important, and that there are some basic principals that seem reasonable to uphold should we wish the R community to continue to be developer friendly. Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicin

Re: [Rd] Best style to organize code, namespaces

2010-02-23 Thread Mark Kimpel
r Duncan's wish of single stepping through multiple levels (if I am interpreting him correctly). It's not very fancy, but it has gotten the job done for me. Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfi

Re: [Rd] Windows Vista Issues

2007-09-06 Thread Mark Difford
hough it's not necessary anymore (to have a truly smooth R). You really don't need it switched on if you have decent anti-virus stuff &c. Regards, Mark Difford. Dominick Samperi-2 wrote: > > Uwe Ligges wrote: >> There is not a single R-Vista issue here (and no R issue

[Rd] Regression test failed when building on an "older" Linux cluster

2007-10-19 Thread Dalphin, Mark
ing the regression tests work in the absence of documentation, along with the rest of R seems reasonable. We are now using R on the compute cluster. This email's purpose is to suggest that R may at times be built in an environment without documentation tools and it would be nice if the regres

Re: [Rd] Regression test failed when building on an "older" Linux cluster

2007-10-24 Thread Dalphin, Mark
ly once where I had noted the failure. I probably should have grepped for "example(" before concluding that. I'll see if we can install an upgraded Perl on a shared location and build R against that. I that solves the problem, I'll report back. Thank you for your time. Reg

[Rd] Problem compiling R 3.6.1 on POWER 570 system

2007-12-19 Thread Mark Komarinski
mpiling the code in 32 bit mode (which is why it's skipping libgcc_s_64.o I guess my questions are: has anyone compiled this for this system? And if so, how did you do it? -Mark -- Mark Komarinski [EMAIL PROTECTED] Sr. Research Systems Architect htt

Re: [Rd] Problem compiling R 2.6.1 on POWER 570 system

2007-12-20 Thread Mark Komarinski
Cookies all around for the rapid and accurate help! I wound up using a variation of the below (the non-quoted part is what I changed): On 12/19/2007 04:15 PM, Andrew Ferris wrote: > Hello Mark, > > Here's the full configure that I used to get 2.4.1 to work on 64bit SL

[Rd] regexp with [:upper:] (PR#11032)

2008-03-24 Thread mark . bravington
Full_Name: Mark Bravington Version: 2.6.2 patched OS: Windows XP Pro Submission from: (NULL) (140.79.22.104) > grep( '[:upper:]', letters, val=T) # shurely shouldn't match anything ?? [1] "e" "p" "r" "u" The converse ( '[:lo

[Rd] error with R-patched (2008-05-02 r45591)

2008-05-03 Thread Mark Kimpel
hat R-patched includes the latest bug fixes. Mark mkimpel-m90 ~/R_HOME/R-patched/R-build/bin: ./R R version 2.7.0 Patched (2008-05-02 r45591) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welco

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-03 Thread Mark Kimpel
e. Anyway, that's the issue, R-patched doesn't like "(R)". Mark On Sat, May 3, 2008 at 4:20 PM, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > On Sat, 3 May 2008, Mark Kimpel wrote: > > Just installed the latest R-patched and get the error seen at the end of >

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-04 Thread Mark Kimpel
Thanks guys. For the benefit of anyone following up on this in the future, I solved my problem in my offending file with: iconv -f LATIN1 -t UTF-8 methods.output.func.R >> methods.output.func.R Mark On Sun, May 4, 2008 at 4:13 AM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > Pr

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-04 Thread Mark Kimpel
You're correct, bad form on my part. In reality, I did it in two steps as you suggested, just condensed for purposes of a brief communication. mark On Mon, May 5, 2008 at 1:52 AM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > Mark Kimpel wrote: > > > Thanks guys. Fo

[Rd] problem building R packages on RHEL 4 Linux with Intel compilers

2008-05-29 Thread Mark Kimpel
c; gmake; gmake install ### checking for gcc... gcc checking for C compiler default output file name... configure: error: C compiler cannot create executables See `config.log' for more details. -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indi

Re: [Rd] problem building R packages on RHEL 4 Linux with Intel compilers

2008-05-29 Thread Mark Kimpel
ECTED]> wrote: > Mark Kimpel wrote: > >> >> checking for gcc... gcc >> checking for C compiler default output file name... >> configure: error: C compiler cannot create executables >> See `config.log' for more details. >> > > Are you runnin

Re: [Rd] problem building R packages on RHEL 4 Linux with Intel compilers

2008-05-29 Thread Mark Kimpel
Simon, I scanned the config.log, which is too voluminous to insert below, but it seems that gcc is still being looked for as the compiler. See the lines from config.log below. Mark Thread model: posix gcc version 3.4.6 20060404 (Red Hat 3.4.6-9) configure:4824: $? = 0 configure:4831: gcc -V >

Re: [Rd] problem building R packages on RHEL 4 Linux with Intel compilers

2008-05-29 Thread Mark Kimpel
I need to know what flags to put with configure so that packages will be compiled with Intel 10.1 when I do "install.packages" from within R. Mark On Thu, May 29, 2008 at 5:54 PM, Simon Urbanek <[EMAIL PROTECTED]> wrote: > > On May 29, 2008, at 5:45 PM, Mark Kimpel

Re: [Rd] Re quest: Documentation of formulae

2008-05-31 Thread Mark Difford
that it isn't, viz in your face --- i.e. in the introductory document ---, but the operator surely deserves a mention in ?formula. So on that score I agree with you. Best, Mark. Mike Prager wrote: > > In working through material on p.272 of MASS (4th ed.), I came > across the following model

[Rd] benchmarking R installations

2008-06-02 Thread Mark Kimpel
13/bin/icpc" \ CXXFLAGS="-O3 -no-prec-div -unroll" \ FC="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort" \ FCFLAGS="-O3 -no-prec-div -unroll" \ OBJC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc" \ OBJCFLAGS="-O3 -no-pr

[Rd] configure.args from install.packages passed on to subsequent update.packages?

2008-06-02 Thread Mark Kimpel
r I am missing an argument to update.packages? Thanks, Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice

Re: [Rd] benchmarking R installations

2008-06-03 Thread Mark Kimpel
l, I think you are referring to the "with mpi", which I think he also slipped in not realizing it should more properly go with the Rmpi install. Mark On Tue, Jun 3, 2008 at 12:18 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: > On Mon, Jun 02, 2008 at 11:56:16PM -0400, Mark K

Re: [Rd] benchmarking R installations

2008-06-03 Thread Mark Kimpel
some empirical evidence as to why I am doing something, especially when it entails the extra headache of using a compiler wiith which I am not familiar. As a non-computer-scientist, however, I I wasn't sure the best way about finding the answer. Mark On Tue, Jun 3, 2008 at 11:16 AM,

Re: [Rd] benchmarking R installations

2008-06-03 Thread Mark Kimpel
Thanks, once I get my new Intel installation running in tandem with a gcc one, I'll report back. mark On Tue, Jun 3, 2008 at 7:04 PM, Martin Maechler <[EMAIL PROTECTED]> wrote: >>>>>> "SU" == Simon Urbanek <[EMAIL PROTECTED]> >>>>>>

[Rd] Rmpi segfault after install on Ubuntu Hardy Heron

2008-06-10 Thread Mark Kimpel
yone considered an R-SIG-HPC list? Anyone besides me interested? Mark R version 2.7.0 Patched (2008-05-18 r45728) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute i

Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron

2008-06-12 Thread Mark Kimpel
options. Before I make my first foray into using the R-debugger, I'd like to try you suggestion to "Check ldd on Rmpi.so" but don't have a clue how to do so. Could you instruct me? Thanks to all for the helpful comments. Mark On Wed, Jun 11, 2008 at 8:22 AM, Dirk Eddelbuett

Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron

2008-06-12 Thread Mark Kimpel
error = recover) provide any insight? Mark > require(Rmpi) Loading required package: Rmpi *** caught segfault *** address 0x2224008, cause 'memory not mapped' Traceback: 1: .Call("mpi_initialize", PACKAGE = "Rmpi") 2: f(libname, pkgname) 3: firstlib(which.lib

[Rd] RBGL not compiling on Debian Lenny with c++ (Debian 4.3.1-2) 4.3.1

2008-06-27 Thread Mark Kimpel
er attached packages: [1] graph_1.18.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 tcltk_2.7.1 tools_2.7.1 -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, &a

Re: [Rd] matching predictors and dummies

2008-07-12 Thread Mark Difford
Hi Jeroen, >> How could i use the model$terms to extract which coefficients belong to >> which factor, >> the way anova() does it? There may be a simpler ("canned") way to do it, but why don't you debug anova.lm to see how it does it? ## methods("anov

[Rd] Parameter names in nls()

2008-07-22 Thread Mark Payne
, but after the first "step", the names are dropped. I was wondering if I could please ask for a similar fix as that applied to optim() to be carried across to nls() also? Many thanks, Mark #Setup environment rm(list=ls()) counter <- 1 #Objective function for nls fitting.fn &

[Rd] error in help page of function interpSpline of package splines in R-devel

2008-08-15 Thread Mark Kimpel
, the text reads "The default action ('na.omit') is to omit any incomplete observations. " Based on today's experience, I believe the function prototype is correct and the text description should be amended. Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psyc

[Rd] specifying compiler path in configure

2008-08-27 Thread Mark Kimpel
he path to 4.2.1 ? I"m sure it's an option, but I don't see it documented in the R-admin manual. Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile &a

Re: [Rd] specifying compiler path in configure

2008-08-29 Thread Mark Kimpel
his instruction into install.packages and it failed to produce the intended result, with gcc-4.3 being used instead of 4.2. install.packages("affxparser", repos=repos,configure.args = c('CC=/usr/bin/gcc-4.2', 'CXX=/usr/bin/g++-4.2')) Thanks, Mark On Wed, Aug 27, 2008 at 4:

[Rd] splitting strings efficiently

2008-09-24 Thread Mark Kimpel
there a basic R function that handles this situation? If not, is there perhaps a faster way to do it than I currently am, which is to lapply the following function? Thanks, Mark ### string.tokenizer.func<-funct

Re: [Rd] splitting strings efficiently

2008-09-24 Thread Mark Kimpel
I knew there HAD to be a basic function, but 'help.search("split string")' and 'help("string") did not find it. Thanks for the help on this elementary question. Mark ---- Mark W. Kimpel MD ** Neuroinforma

Re: [Rd] RFC: Kerning, postscript() and pdf()

2008-10-17 Thread Mark Difford
. Regards, Mark. Bálint Czúcz-4 wrote: > > Dear Prof Ripley, > > FWIW, kerning problems seem to affect even European character sets, e.g.: > >> pdf(); plot(0,main="árvíztűrő tükörfúrógép"); dev.off() > > in a clean session produces some misaligned cha

[Rd] implementation of NULL in vectors

2009-01-03 Thread Mark Rosen
All, I was wondering if someone could point me to the location of the code in R that supports NULL values in vectors. I'm curious as to how you implemented them. The only possible solution to me seems that for a double [], you need to keep a parallel bool [] that tells you whether the value is nu

Re: [Rd] [R] Semantics of sequences in R

2009-02-24 Thread Mark Difford
things and they should not be so easily confused. Regards, Mark. Mark Difford wrote: > > Dimitris Rizopoulos wrote: > >>> in my opinion the point of the whole discussion could be summarized by >>> the question, what >>> is a design flaw? This is total

Re: [Rd] [R] Semantics of sequences in R

2009-02-24 Thread Mark Difford
r to try to compare them. Regards, Mark. Berwin A Turlach wrote: > On Tue, 24 Feb 2009 09:39:51 +0100 > Wacek Kusnierczyk wrote: > >> Berwin A Turlach wrote: > > [...] >> why not read some fortunes? > I am well aware of those fortunes and maybe you missed the

Re: [Rd] bug (PR#13570)

2009-03-05 Thread Mark Difford
Hi Uwe, This is not a problem under Vista, using "a" development version (mine now somewhat outdated). Regards, Mark. sessionInfo() R version 2.9.0 Under development (unstable) (2009-01-22 r47686) i386-pc-mingw32 locale: LC_COLLATE=English_South Africa.1252;LC_CTYPE=English_So

[Rd] installed.packages and package info cache buglet (PR#13592)

2009-03-12 Thread Mark . Bravington
in 'lib.loc', not against the one being checked. [Normally= the multiple test in '>' would flag a warning from 'if', but the &&s mean = that only the first element is used.] I can't provide a reproducible example for this, because it's so installa

[Rd] Using TCP/IP sockets in R

2006-08-15 Thread Mark Schultz
erver in R? Thanks a lot, Mark Schultz __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] rbind with auto-row-named data.frame + list (PR#9346)

2006-11-06 Thread Mark . Bravington
There's a problem new to R2.4.0 when rbinding an auto-row-named data.frame to a list: > rbind( data.frame( x=1), list( x=2)) Error in attr(value, "row.names") <- rlabs : row names must be 'character' or 'integer', not 'double' Works

[Rd] xlsReadWrite Pro and embedding objects and files in Excel worksheets

2007-02-07 Thread Mark W Kimpel
needs, but it could be a start. Well, let me know what you think. I am cc'ing R-devel to see if any of those guys have ideas as well. Thanks, Mark -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine

Re: [Rd] xlsReadWrite Pro and embedding objects and files in Excel worksheets

2007-02-08 Thread Mark W Kimpel
Thanks for the useful suggestions. I am not as CS savvy as some of you, so maybe Hans-Peter could reply? I haven't checked into it, but does his package write to files that are OpenOffice compliant? Would that satisfy more users? Mark Hin-Tak Leung wrote: > James W. MacDonald wrote:

Re: [Rd] xlsReadWrite Pro and embedding objects and files in Excel worksheets

2007-02-08 Thread Mark W Kimpel
and Windows because that is what I use. I think it would be great to come up with a common format that Linux, Mac, and UNIX users could use. Could openOffice serve that purpose? Thanks for your input. Mark Gabor Grothendieck wrote: > Its not entirely clear to me what it is that you are looking

[Rd] append within worksheet in write.xls

2007-02-08 Thread Mark W Kimpel
I can currently append an entire worksheet with write.xls, but would also like to be able to append within the same worksheet. Is this possible? It doesn't seem to work if I use append = T Thanks, Mark -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University S

[Rd] newline with cell of Excel worksheet created with write.xls

2007-02-08 Thread Mark W Kimpel
? I'm writing lots of posts on this, but trying to break up the subjects to create better threads. Mark -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine __ R-devel@r-project.org mailing list

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