[Rd] R compilation (revision 87083) failed after upgrade to Ubuntu 24.04 (libtirpc missing)

2024-09-01 Thread Mark Clements via R-devel
ing libtirpc-dev: > sudo apt install libtirpc-dev compilation proceeded smoothly. I understand that this may be local to my system. Sincerely, Mark. N�r du skickar e-post till Karolinska Institutet (KI) inneb�r detta att KI kommer att behandla dina personuppgifter. H�r finns information om

[Rd] User-defined RNG with the standalone Rmath library

2023-02-21 Thread Mark Clements via R-devel
. -- Mark När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result

[Rd] User-defined RNG with the standalone Rmath library

2023-02-16 Thread Mark Clements via R-devel
f_rand()); printf("%f\n", runif(0, 1)); return 0; } If we compile using -static, then we get the correct result (two values of 0.5): gcc -static -o test test.c -lRmath -lm ./test : 0.50 : 0.50 Question: does this code work for other users? Sincerely, Mark. När du skic

Re: [Rd] 1954 from NA

2021-05-23 Thread Mark van der Loo
I wrote about this once over here: http://www.markvanderloo.eu/yaRb/2012/07/08/representation-of-numerical-nas-in-r-and-the-1954-enigma/ -M Op zo 23 mei 2021 15:33 schreef brodie gaslam via R-devel < r-devel@r-project.org>: > I should add, I don't know that you can rely on this > particular en

Re: [Rd] problem adding gdb to RTOOLS40 on Windows

2021-04-15 Thread Bravington, Mark (Data61, Hobart)
. Jeroen's documentation says to do the pacman bit from mingw64, and separately from mingw32--- whereas Avraham's suggestion is to do it just from msys2. I actually did both; gdb seems to end up in the same place regardless, but tomorrow I'll find out if it's *really* worked.

[Rd] problem adding gdb to RTOOLS40 on Windows

2021-04-14 Thread Bravington, Mark (Data61, Hobart)
.9.1; I tried copying that gdb.exe into RTOOLS40 but it just exited instantly when I tried to run it from there. - NB I have absolutely no idea what is meant by msys2 or pacman or any of that, I'm just following instructions... Thanks Mark Mark

Re: [Rd] [External] setting .libPaths() with parallel::clusterCall

2020-12-23 Thread Mark van der Loo
Dear Luke, Thank you, this makes perfect sense. I find it quite hard to express this issue in a way that is both compact and understandable. In any case, below you find a proposal for an update of the documentation. Thank you again for all your work, Mark Index: src/library/parallel/man

[Rd] setting .libPaths() with parallel::clusterCall

2020-12-22 Thread Mark van der Loo
. Tested on R 4.0.3 and r-devel. Best, Mark ps: a workaround is documented here: https://www.markvanderloo.eu/yaRb/2020/12/17/how-to-set-library-path-on-a-parallel-r-cluster/ > sessionInfo() R Under development (unstable) (2020-12-21 r79668) Platform: x86_64-pc-linux-gnu (64-bit) Running

Re: [Rd] New pipe operator

2020-12-08 Thread Bravington, Mark (Data61, Hobart)
> [Duncan Murdoch responding to...] > [... Mark Bravington's proposals for placeholders and anonymous functions] > > x |> foo( _PIPE_) # placeholder > > x |> bah( otherarg, _PIPE_)# placeholder > > x |> { y <- _PIPE_+1; _PIPE_ / y

Re: [Rd] New pipe operator

2020-12-08 Thread Bravington, Mark (Data61, Hobart)
> > On 06/12/2020 8:22 p.m., Bravington, Mark (Data61, Hobart) wrote: > (and Duncan Murdoch responded, as below) It still seems to me that placeholders are viable and unambiguous (only as things in RHS of pipes), and that something like x |> foo( _PIPE_) x |> bah( otherarg, _

Re: [Rd] New pipe operator

2020-12-06 Thread Bravington, Mark (Data61, Hobart)
'expr' #2. Construct a call() to that function #3. Do the call f <- function( `_PIPE_`) NULL body( f) <- expr environment( f) <- parent.frame() # or something... yes these details are almost certainly wrong expr2 <- substitute( f( `_PIPE_`)) # or something...

Re: [Rd] vignettes present in 2 folders or won't work

2020-11-02 Thread Mark van der Loo
On Sun, Nov 1, 2020 at 10:39 PM Duncan Murdoch wrote: > On 01/11/2020 2:57 p.m., Dirk Eddelbuettel wrote: > > > > The closest to a canonical reference for a static vignette is the basic > blog > > post by Mark at > > > > > https://www.markvanderloo.eu/yaRb/

Re: [Rd] missing binaries in R-devel windows snapshot 78175

2020-04-10 Thread Bravington, Mark (Data61, Hobart)
for release soon--- bit disconcerting to hear it's actually broken! However, I suspect R4.0 [ with fixed md5sum() ] will be released before our package sees the light of day. Thanks again Mark Mark Bravington CSIRO Marine Lab Hobart Australia Fro

Re: [Rd] missing binaries in R-devel windows snapshot 78175

2020-04-09 Thread Bravington, Mark (Data61, Hobart)
> On Thu, Apr 9, 2020 at 12:44 PM Bravington, Mark (Data61, Hobart) > wrote: > > > > The "r-devel snapshot build" 78175 on Windows--- a dot-exe installer--- > > seems to be missing a couple of files in its bin/i386 folder: Rterm.exe and > > Rgui.exe. Bot

[Rd] missing binaries in R-devel windows snapshot 78175

2020-04-09 Thread Bravington, Mark (Data61, Hobart)
R version caught up. cheers Mark Mark Bravington CSIRO Marine Lab Hobart Australia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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] 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] 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] [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

2019-06-04 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). > >

[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] compairing doubles

2018-08-31 Thread Mark van der Loo
Ah, my bad, you're right of course. sum(abs(diff(diff( sort(x) < eps for some reasonable eps then, would do as a oneliner, or all(abs(diff(diff(sort(x < eps) or max(abs(diff(diff(sort(x) < eps -Mark Op vr 31 aug. 2018 om 16:14 schreef Iñaki Ucar : > El vie., 3

Re: [Rd] compairing doubles

2018-08-31 Thread Mark van der Loo
Sorry for the second e-mail: this is worth watching: https://www.youtube.com/watch?v=3Bu7QUxzIbA&t=1s It's Martin Maechler's talk at useR!2018. This kind of stuff should be mandatory material for any aspiring programmer/data scientist/statistician. -Mark Op vr 31 aug. 2018 om

Re: [Rd] compairing doubles

2018-08-31 Thread Mark van der Loo
how about is_evenly_spaced <- function(x,...) all.equal(diff(sort(x)),...) (use ellipsis to set tolerance if necessary) Op vr 31 aug. 2018 om 15:46 schreef Emil Bode : > Agreed that's it's rounding error, and all.equal would be the way to go. > I wouldn't call it a bug, it's simply part of wor

Re: [Rd] length of `...`

2018-05-03 Thread Mark van der Loo
s follows: do.call(someotherfunction, L) } -Mark Op do 3 mei 2018 om 16:29 schreef Dénes Tóth : > Hi, > > > In some cases the number of arguments passed as ... must be determined > inside a function, without evaluating the arguments themselves. I use > the following construct

Re: [Rd] data.table not available as win binary for R 3.5

2018-04-24 Thread Mark van der Loo
ing in the output on Windows: Warning: stack imbalance in '{', 39 then 40 I don't have a Windows PC handy where I can quickly reproduce this so if anyone has solved similar problems it would be nice if they could be posted here. Best, Mark [1] https://cran

Re: [Rd] Apparent bug in behavior of formulas with '-' operator for lm

2018-03-16 Thread Mark van der Loo
mprove this behavior, but perhaps one of the core authors can have a look at it. Best, Mark Op vr 16 mrt. 2018 om 13:22 schreef Joris Meys : > Technically it is used as a predictor in the model. The information is > contained in terms : > > > terms(x ~ . - z, data = d) > x ~ (

Re: [Rd] Apparent bug in behavior of formulas with '-' operator for lm

2018-03-16 Thread Mark van der Loo
Joris, the point is that 'z' is NOT used as a predictor in the model. Therefore it should not affect predictions. Also, I find it suspicious that the error only occurs when the response variable conitains missings and 'z' is unique (I have tested several other cases to confirm

[Rd] Apparent bug in behavior of formulas with '-' operator for lm

2018-03-16 Thread Mark van der Loo
vels) : factor z has new levels a It seems a bug to me, although one could argue that 'lm's documentation does not allow one to expect that the '-' operator should work generally. If it is a bug I'm happy to report it to bugzilla. Thanks for all your efforts, Mark ps:

[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

Re: [Rd] Best practices in developing package: From a single file

2018-01-31 Thread Mark van der Loo
'parent' of roxygen is Doxygen, which was already widely used (also by me) in the C/C++ community before roxygen was published. I cannot remember anyone ever complaining about C/C++ documentation deteriorating because of Doxygen. -Mark Op wo 31 jan. 2018 om 14:02 schreef Joris Meys :

Re: [Rd] Searching R Packages

2018-01-29 Thread Mark van der Loo
en of course there is the R journal and JSS, but those speak for themselves. So maybe a 'keeping up to date' section would be nice in the article? Best, Mark Op ma 29 jan. 2018 om 00:25 schreef Ravi Varadhan : > Hi Spencer, > Thank you for this wonderful service to t

Re: [Rd] Community Feedback: Git Repository for R-Devel

2018-01-04 Thread Mark van der Loo
This question has been discussed before on this list: http://r.789695.n4.nabble.com/Why-R-project-source-code-is-not-on-Github-td4695779.html See especially Jeroen's answer. Best, Mark Op do 4 jan. 2018 om 01:11 schreef Juan Telleria : > UNBIASED FACTS: > • Bugzilla & R-deve

Re: [Rd] Change to r-devel warns on #pragma

2017-12-11 Thread Mark van der Loo
nix) Best, Mark On Mon, Dec 11, 2017, 4:33 PM Patrick Perry wrote: > A recent change to r-devel causes an R CMD check warning when a C file > includes a "#pragma GCC diagnostic ignored" pragma: > > https://github.com/wch/r-source/commit/b76c8fd355a0f5b23d42aaf44a879cac0

Re: [Rd] R Configuration Variable: Maximum Memory Allocation per R Instance

2017-09-17 Thread Mark van der Loo
Dear Juan, I'm not deeply familiar with the DB's you mention but it seems to me that me that 'memory.limits' does what you want on one OS and you can use shell commands to limit R's memory usage for *nix-alike systems (see ?memory.limits). Also, Jeroen Ooms wrote a nice article about this in the J

Re: [Rd] Natural vs National in R signon banner?

2017-09-01 Thread Mark van der Loo
The way it's phrased now makes it seem that English is not a Natural language ("Natural language support *but* running in an English locale"). Why not just state: "running in an English locale" and leave it with that? Better to leave something out than to be unclear (being correct formally does not

[Rd] bugs in documentation of stats::stl

2017-08-23 Thread Mark van der Loo
not apply a low-pass filter to each subseries[2]. The subseries are reconstructed to a single series and after that a low-pass filter is applied (step 3 of the algorithm in section 2.2 of [1]) So what should it be? A literal reference to Cleveland's n_(s), n_(l), and n_(t) would be really

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] 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()

2017-07-20 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] [WISH / PATCH] possibility to split string literals across multiple lines

2017-06-14 Thread Mark van der Loo
I know it doesn't cause construction at parse time, and it was also not what I said. What I meant was that it makes the syntax at least look a little as if you have a line-breaking character within string literals. Op wo 14 jun. 2017 om 14:18 schreef Joris Meys : > Mark, that's ac

Re: [Rd] [WISH / PATCH] possibility to split string literals across multiple lines

2017-06-14 Thread Mark van der Loo
te0(x,y) "hello" %+% " pretty" %+% " world" -Mark Op wo 14 jun. 2017 om 13:53 schreef Andreas Kersting : > On Wed, 14 Jun 2017 06:12:09 -0500, Duncan Murdoch < > murdoch.dun...@gmail.com> wrote: > > > On 14/06/2017 5:58 AM, Andreas Kersti

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] 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] 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

[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] Single-threaded aspect

2016-05-12 Thread Mark van der Loo
o create R-variables from multiple threads running in C. (R's variable administration is such that the order of (un)making them from compiled code matters). I am not very savvy on Rcpp or XPtr objects, but it appears that Dirk provided answers about that in your SO-question. Best, Mark Op

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] 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] (no) circular dependency

2016-04-08 Thread Mark van der Loo
an Dușa : > Hi Mark, > > Uhm... sometimes this is not always possible. > For example I have a package QCA which produces truth tables (all > combinations of presence / absence of causal conditions), and it uses the > venn package to draw a Venn diagram. > It is debatable if one

Re: [Rd] (no) circular dependency

2016-04-07 Thread Mark van der Loo
At the risk of stating the over-obvious: there's also the option of creating just a single package containing all functions. None of the functions that create the interdependencies need to be exported that way. Btw, his question is probably better at home at the r-package-devel list. Best, M

Re: [Rd] How do I reliably and efficiently hash a function?

2015-12-11 Thread Mark van der Loo
In addition to what Charles wrote, you can also use 'local' if you don't want a function that creates another function. > f <- local({info <- 10; function(x) x + info}) > f(3) [1] 13 best, Mark Op vr 11 dec. 2015 om 03:27 schreef Charles C. Berry : > On Thu, 10

Re: [Rd] Inconsistency in treating NaN-results?

2015-12-01 Thread Mark van der Loo
1] is never much more then an arm's length away. So it all depends on what user you're aiming at when implementing such things. A (switchable) warning about loss of precision without returning NaN would probably be a reasonable compromise. Best, Mark [1] https://books.google.nl/books?

[Rd] Inconsistency in treating NaN-results?

2015-11-26 Thread Mark van der Loo
unctions (following the IEEE standard on double precision). If that's the case, the result sin(Inf)=NaN seems normal to me and a warning is unnecessary. So why the choice to have warning on sin(Inf), but not on 0/0 or exp(Nan)? Is it just historical or am I missing a reasoning or som

Re: [Rd] is R syntax closed?

2015-09-19 Thread Mark van der Loo
same way git does. Since R is free in the GNU sense you can always define your own local version, see e.g. [2]. > i'm new to R welcome, and have fun! best, Mark [1] https://www.r-project.org/contributors.html [2] https://github.com/radfordneal/pqR Op za 19 sep. 2015 om 04:02 schreef

Re: [Rd] NEWS.md support on CRAN

2015-06-04 Thread Mark van der Loo
WS.Rd? (perhaps it is already possible, I'm not sure of that). I don't maintain CRAN, but I know what I would prefer.. Cheers, Mark ​ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mai

Re: [Rd] NEWS.md support on CRAN

2015-06-04 Thread Mark van der Loo
r younger days?). In short, I think that added value of NEWS.md is fairly limited but it does increase the risk of dispersing the NEWS all over the web. Best, Mark Op wo 3 jun. 2015 om 08:32 schreef Kurt Hornik : > >>>>> Duncan Murdoch writes: > > > On 0

Re: [Rd] Development version of R: Improved nchar(), nzchar() but changed API

2015-04-27 Thread Mark van der Loo
Dear Martin, Does the work on nchar mean that bugs #16090 and #16091 will be resolved [1,2]? Thanks, Mark [1] https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16090 [2] https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16091 On Sat, Apr 25, 2015 at 11:06 PM, James Cloos wrote

Re: [Rd] Possible values for R version status

2015-03-23 Thread Mark van der Loo
In the R installation and administration manual[*] I see at least mentioned The alpha, beta and RC versions of an upcoming x.y.0 release are available [...] so 'beta' seems to be an option unless it is only used informally there. Mark [*] http://cran.r-project.org/doc/manuals/r

Re: [Rd] \U with more than 4 digits returns the wrong character

2014-12-04 Thread Mark van der Loo
I agree. You could post a documentation bug and a request here: https://bugs.r-project.org/bugzilla3/ Cheers, Mark On Thu, Dec 4, 2014 at 8:37 PM, Richard Cotton wrote: > Great spot, thanks Mark. > > This really ought to appear somewhere in the ?Quotes help page. > > Having

Re: [Rd] \U with more than 4 digits returns the wrong character

2014-12-04 Thread Mark van der Loo
Richie, The R language definition [1] says (10.3.1): \U \U{} (where multibyte locales are supported and not on Windows, otherwise an error). Unicode character with given hex code – sequences of up to eight hex digits. Best, Mark [1] http://cran.r-project.org/doc/manuals/r

Re: [Rd] R string comparisons may vary with platform (plain text)

2014-11-24 Thread Mark van der Loo
The 'stringi' package claims robust cross-platform performance. It exports much functionality of the ICU library and will attempt to install it when not present. The function 'stri_sort' accepts a collation argument that can be defined with 'stri_opts_collator'. On Sun, Nov 23, 2014 at 5:15 PM,

[Rd] nchar reporting wrong width when zero-space character is present?

2014-11-19 Thread Mark van der Loo
abstract characters) are counted, noting that some of the symbols in an alphabet represented by an encoding may be invisible (or hardly visible). Much thanks in advance, Best, Mark > sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE

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] 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] 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

[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] 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] 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] 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

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] 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

[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/

[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] 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

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 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] 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] 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

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] 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] 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] 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

[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

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

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] 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

[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] 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

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] 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] 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] 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

2009-09-16 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
.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
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

[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

[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 ___

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

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

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