[Rd] R, Wine, and multi-threadedness.

2005-10-13 Thread Hin-Tak Leung
x R is not. Is is possible to have better performance or CPU utilisation on multi-CPU systems running Win32 R under Wine rather than natively? At least on certain specific application areas? Regards, Hin-Tak Leung __ R-devel@r-project.org mailing

Re: [Rd] R, Wine, and multi-threadedness.

2005-10-13 Thread Hin-Tak Leung
R uses two threads on Windows so > that it can respond to Windows messages (repainting, etc.). It won't > really offload any substantial amount of computation to a second CPU. Wine on linux most of the time consists of at least two processes, with a "wine server" process doi

Re: [Rd] R, Wine, and multi-threadedness.

2005-10-13 Thread Hin-Tak Leung
Prof Brian Ripley wrote: > On Thu, 13 Oct 2005, Hin-Tak Leung wrote: > >> I managed to install Win32 R 2.2.0 with the CRAN Innosetup >> installer under Wine on x86 linux a few days ago. However, on trying >> to run it, MSVCP60.DLL is missing. So here is a sort of a bug &g

Re: [Rd] R, Wine, and multi-threadedness.

2005-10-13 Thread Hin-Tak Leung
Hin-Tak Leung wrote: > Prof Brian Ripley wrote: > >> On Thu, 13 Oct 2005, Hin-Tak Leung wrote: >>> (2) The interesting question: As I understand it (could be wrong), >>> R Win32 is (partly) multi-threaded, and the native linux R is not. >>> Is is pos

Re: [Rd] R, Wine, and multi-threadedness.

2005-10-13 Thread Hin-Tak Leung
xtra windows bits to view CJK pdf's)...the misleading part was that the other additional options are absolutely harmless. Thanks a lot for the discussion. If I find any interesting R issues under Wine, I'll report back. Hin-Tak Leung __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R, Wine, and multi-threadedness.

2005-10-13 Thread Hin-Tak Leung
- and since microsoft is not going bankrupt any time soon, MS office integration is fairly important to *some* people - one cannot say it is 'substantially better', because there is always one user who would judge that one missing feature, over an

Re: [Rd] R, Wine, and multi-threadedness.

2005-10-13 Thread Hin-Tak Leung
t I like alternatives, preferably covering different usage areas. Before anybody jump in again, the fact that sciview-R is somewhat .NET framework dependent (at least the binary installed by the default installer seems to be) is justifiably a development issue? Hin-Tak Leung _

Re: [Rd] R, Wine, and multi-threadedness.

2005-10-13 Thread Hin-Tak Leung
e inclined (if it bugs me enough to do something myself about it) to try porting sciview-R as a hybrid libwine application with wingcc, and I did have a look at the 14MB source code bundle - it has a lot of binary-only bits which does not look as if they belong there or be redistributed. (Sigh...

Re: [Rd] R GUI considerations (was: R, Wine, and multi-threadedness)

2005-10-17 Thread Hin-Tak Leung
ut the Tcl (or the obvious Tcl-ish stuff) in the middle. Just an idea. Hin-Tak Leung Philippe Grosjean wrote: > Hello, > > Following a discussion initiated on r-devel, that mentions SciViews-R > and other GUIs issues for R, I would like to make comments (and would be > happ

Re: [Rd] Cross compiler taqrgeting Mac OS X

2005-10-17 Thread Hin-Tak Leung
. Good luck. Hin-Tak Leung dave fournier wrote: > Hi, > > I have been asked to produce a binary of some software for somone > running R on Mac OS X. I don't have a Mac and don't know anything about > them. > The sloution would seem to be to obtain/build a crsoo compi

Re: [Rd] Embedded R in C

2005-10-17 Thread Hin-Tak Leung
NGUYEN Truong Hoan wrote: > Hello everyone, > > I would like to call the R functions from the C++ language > interface, for example from a program composed on Microsoft Visual C++. > I have referred the manual Writing R Extensions but i don't understand > exactly how to make a declarat

[Rd] Rgnome depends on obsolete components libglade/libxml (PR#8247)

2005-10-24 Thread hin-tak . leung
Full_Name: Hin-Tak Leung Version: R 2.2.0 OS: x86 linux Submission from: (NULL) (131.111.126.242) Rgnome depends libglade 0.x and libxml 1.x . They are no longer shipped with Redhat EL4. (I know they are still in fedora core 4). Just a wish-list

Re: [Rd] Rgnome depends on obsolete components libglade/libxml (PR#8247)

2005-10-24 Thread Hin-Tak Leung
Peter Dalgaard wrote: > [EMAIL PROTECTED] writes: > > >>Full_Name: Hin-Tak Leung >>Version: R 2.2.0 >>OS: x86 linux >>Submission from: (NULL) (131.111.126.242) >> >> >>Rgnome depends libglade 0.x and libxml 1.x . >> >>They are no lon

Re: [Rd] Rgnome depends on obsolete components libglade/libxml (PR#8247)

2005-10-24 Thread Hin-Tak Leung
Marc Schwartz (via MN) wrote: > On Mon, 2005-10-24 at 17:14 +0100, Hin-Tak Leung wrote: > >>Peter Dalgaard wrote: >>>You mean get it upgraded to xml2 and glade2? Patches would likely be >>>accepted... > > According to the R Admin manual (2.2.0) on page 34:

Re: [Rd] Rgnome depends on obsolete components libglade/libxml (PR#8247)

2005-10-25 Thread Hin-Tak Leung
cally significant number of sympathetic ears to offer helpful advices without the self-confessed experts coming down hard on them for being stupid. Hin-Tak Leung __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Rgnome depends on obsolete components libglade/libxml (PR#8247)

2005-10-25 Thread hin-tak . leung
cally significant number of sympathetic ears to offer helpful advices without the self-confessed experts coming down hard on them for being stupid. Hin-Tak Leung __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Microsoft help files

2005-10-26 Thread Hin-Tak Leung
re task that one must perform to get > up and running to build your own R packages on Windows. Actually, why does one need to depend on the Microsoft Help compiler? The windows build of GNU makeinfo can generate MS *.hlp file directly. That's more "native" MS

Re: [Rd] Microsoft help files

2005-10-26 Thread Hin-Tak Leung
Liaw, Andy wrote: >> From: Hin-Tak Leung >> >> Gabor Grothendieck wrote: >> >>> I wonder if the software here: >>> >>> http://morte.jedrea.com/~jedwin/projects/chmlib/ >>> >>> or at any of the links on that page might allow

[Rd] column names in pivoted matrix operations.

2005-10-27 Thread Hin-Tak Leung
during pivoting in the LAPACK/LINPACK C/fortran routines. Is this wrong, or at least, dubious? Here are two patches against the two files in "R-2.2.0/src/library/base/R" - I have tested them both myself, to obtain what I believe to be "sensible" behavior. Feedb

Re: [Rd] Classification Trees and basic Random Forest pkg using tree structures in C

2005-11-04 Thread Hin-Tak Leung
ly it uses only 2-bit for storage. (it is still work-in-process but I have got to the point of being able to get and set each 2-bit cell now). Hin-Tak Leung __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R-2.2.0 Compile problem on Slackware 10.2

2005-11-04 Thread Hin-Tak Leung
Your system is badly screwed up. On my Slackware 10.2, /usr/include/asm/errno.h is just a plain file and doesn't include anything else, unlike yours, which seems to look for "asm-generic/errno.h". The package you need to re-install is "kernel-headers-2.4.31-i386-1". It is part of the d series, on

Re: [Rd] Classification Trees and basic Random Forest pkg using t ree structures in C

2005-11-07 Thread Hin-Tak Leung
Liaw, Andy wrote: >>From: Hin-Tak Leung >>Hmm, why didn't you just post a URL? > > Isn't it a bit too much to assume that everyone has a personal web space > somewhere? Just for the sake of argument... I did assume that nih.gov is a sizeable government organizat

Re: [Rd] R build under mandriva 10.2

2005-11-09 Thread Hin-Tak Leung
Gilles GUILLOT wrote: > After upgrading from mandrake 10.1 to mandriva 10.2 > I can't build shared archive with R 2.2.0 libg2c is part of the g77 fortran runtime package in gcc 3.x. You probably have gcc 4.x (which has a new/different fortran frontend called gfortran) when you upgrade to mandriva

Re: [Rd] problem with \eqn (PR#8322)

2005-11-18 Thread Hin-Tak Leung
Your own fault. See below. It is basic LaTeX and any LaTeX person can tell you the answer...(most probably haven't bothered...) [EMAIL PROTECTED] wrote: > Full_Name: Ross Boylan > Version: 2.2.0 > OS: Linux > Submission from: (NULL) (65.175.48.58) > > > \eqn{{\bf\beta}_j}{b(j)} in my .Rd file

Re: [Rd] problem with \eqn (PR#8322)

2005-11-18 Thread Hin-Tak Leung
Martin Maechler wrote: >>>>>>"Hin-Tak" == Hin-Tak Leung <[EMAIL PROTECTED]> >>>>>>on Fri, 18 Nov 2005 16:38:28 + writes: > > > Hin-Tak> Your own fault. See below. It is basic LaTeX and any LaTeX person >

Re: [Rd] problem with \eqn (PR#8322)

2005-11-18 Thread hin-tak . leung
Martin Maechler wrote: >>>>>>"Hin-Tak" == Hin-Tak Leung <[EMAIL PROTECTED]> >>>>>>on Fri, 18 Nov 2005 16:38:28 + writes: > > > Hin-Tak> Your own fault. See below. It is basic LaTeX and any LaTeX person >

Re: [Rd] problem with \eqn (PR#8322)

2005-11-21 Thread Hin-Tak Leung
Kurt Hornik wrote: >>>>>>Duncan Murdoch writes: > > >>On 11/18/2005 12:40 PM, Hin-Tak Leung wrote: >> >>>Martin Maechler wrote: >>> >>> >>>>>>>>>"Hin-Tak" == Hin-Tak Leung <[EMAIL PROTECTED]&

Re: [Rd] problem with \eqn (PR#8322)

2005-11-21 Thread Hin-Tak Leung
Kurt Hornik wrote: > Definitely a problem in Rdconv. > > E.g., > > $ cat foo.Rd > \description{ > \eqn{{A}}{B} > } > [EMAIL PROTECTED]:~/tmp$ R-d CMD Rdconv -t latex foo.Rd | grep eqn > \eqn{{A}}{A}{{B} > > shows what is going on. There is a "work-around" - putting extra spaces between the

Re: [Rd] problem with \eqn (PR#8322)

2005-11-23 Thread Hin-Tak Leung
Ross Boylan wrote: > On Mon, 2005-11-21 at 10:27 +0000, Hin-Tak Leung wrote: > >>Kurt Hornik wrote: >> >> >>>Definitely a problem in Rdconv. >>> >>>E.g., >>> >>>$ cat foo.Rd >>>\description{ >>> \eqn{{A}}{B

Re: [Rd] [R] data.frame() size

2005-12-09 Thread Hin-Tak Leung
most hardware; this reduced version should take up only 6 words. In addition to slightly reducing memory use, this can lead to more favorable data alignment on 32-bit architectures like the Intel Pentium III where odd word alignment of doubles is allowed but much less efficient th

Re: [Rd] [R] data.frame() size

2005-12-12 Thread Hin-Tak Leung
Prof Brian Ripley wrote: > Data frames have unique row names *by definition* (White Book p.57). Yes - I happened to have the White Book on my desk (not mine...) - indeed, the first sentence on page 57 is (quote verbatim, the "never" is in italic in the book, which I have added the "*" before and

Re: [Rd] Problems with calloc function.

2006-01-05 Thread Hin-Tak Leung
ss starts at a large offset (0x4000? = 1/2 GB or 0x8000 = 1GB?), so after 4 large allocations, you run out of memory. Everything through the C interface is passed by pointer, in the fortran convention. BTW, you should use Rprintf() instead of printf(). Details below. Hin-Tak Leung Marcelo D

Re: [Rd] R plot display problem under windows when using python rpy module.

2006-01-09 Thread Hin-Tak Leung
Hi, (off topic slightly, and a slight flame-bait...). I don't have an answer or clue to your question, but I have played with PSPython briefly and it did work somewhat for me (and I have not heard of rpy until reading this through r-devel), and I was wondering what is the difference between rpy an

Re: [Rd] R plot display problem under windows when using python rpy module.

2006-01-09 Thread Hin-Tak Leung
Thanks a lot for the comment and discussion. A few of mine below. Bo Peng wrote: > The main difference is that rpy does one-way communication, is simpler > than RSPython, than is easier to use. > > > I am not an expert on RSPython. I tried RSPython and rpy and chose rpy > for the following rea

Re: [Rd] eigen()

2006-01-10 Thread Hin-Tak Leung
Peter Dalgaard wrote: > Robin Hankin <[EMAIL PROTECTED]> writes: > > >>Hi >> >>I am having difficulty with eigen() on R-devel_2006-01-05.tar.gz >> >>Specifically, in R-2.2.0 I get expected behaviour: >> >> >> > eigen(matrix(1:100,10,10),FALSE,TRUE)$values >>[1] 5.208398e+02+0.00e+00i -1.5

Re: [Rd] Section 7.1 HML documentation (PR#8484)

2006-01-17 Thread Hin-Tak Leung
[EMAIL PROTECTED] wrote: > Full_Name: Greg Kochanski > Version: 2.2.0 > OS: Debian Linux i686 > Submission from: (NULL) (212.159.16.190) > > > In /usr/share/doc/r-doc-html/manual/R-data.html (at least that's where > it is on Debian...) the documentation is unclear. Comments below. The document

Re: [Rd] Section 7.1 HML documentation (PR#8484)

2006-01-18 Thread Hin-Tak Leung
can be used. ... 7 Network interfaces Some limited facilities are available to exchange data at a lower level across network connections. 7.1 Reading from sockets ... = > Hin-Tak Leung wrote: > >> [EMAIL PROTECTED] wrote: >> >>> Full_Name: Greg Kochan

Re: [Rd] Minumum memory requirements to run R.

2006-01-23 Thread Hin-Tak Leung
gate the equivalent in Perl, the equivalent perl headers corresponding to "R/include/Rinternals.h" is located at the "-I" flags of the output of: perl -MExtUtils::Embed -e ccopts (no idea where python stores its stuff...) Hin-Tak Leung > > Kjetil > > >>Since th

Re: [Rd] Minumum memory requirements to run R.

2006-01-23 Thread Hin-Tak Leung
Prof Brian Ripley wrote: > That's a different question. I said RAM, you quote virtual. I am > suprised at your figure though, as I am used to seeing 40-50Mb virtual > at startup on an Opteron. I am somewhat surprised by it as well. But there is nothing unusual about the build - it is just re

Re: [Rd] Minumum memory requirements to run R.

2006-01-23 Thread Hin-Tak Leung
authors versus one of the users... The 32-bit/64-bit issue affects purchasing or upgrading decisions - whether one wants to spend the money on buying cheaper 32-bit machines, versus more expensive 64-bit machines. That decision would be based on information available while *not* having an operatio

[Rd] rbind/cbind unimplemented for raw (RAWSXP) types. (PR#8529)

2006-01-27 Thread hin-tak . leung
Full_Name: Hin-Tak Leung Version: R 2.2.1 OS: x86_64-redhat-linux-gnu Submission from: (NULL) (131.111.186.92) rbind/cbind is unimplemented for raw (RAWSXP) types. I have a working patch implementing the functionality, to follow. --please do not edit the information below-- Version: platform

[Rd] sub* assgnment unimplemented for raw (RAWSXP) types. (PR#8530)

2006-01-27 Thread hin-tak . leung
Full_Name: Hin-Tak Leung Version: R 2.2.1 OS: x86_64-redhat-linux-gnu Submission from: (NULL) (131.111.186.92) Matrix subset assignment and [[<- assignment are unimplemented for raw (RAWSXP) types. I have a working patch implementing the functionality, to follow. --please do not edit

Re: [Rd] rbind/cbind unimplemented for raw (RAWSXP) types. (PR#8529)

2006-01-27 Thread Hin-Tak Leung
[EMAIL PROTECTED] wrote: Full_Name: Hin-Tak Leung Version: R 2.2.1 OS: x86_64-redhat-linux-gnu Submission from: (NULL) (131.111.186.92) rbind/cbind is unimplemented for raw (RAWSXP) types. I have a working patch implementing the functionality, to follow. Attached in ready-to-patch form and

Re: [Rd] sub* assgnment unimplemented for raw (RAWSXP) types. (PR#8530)

2006-01-27 Thread Hin-Tak Leung
[EMAIL PROTECTED] wrote: Full_Name: Hin-Tak Leung Version: R 2.2.1 OS: x86_64-redhat-linux-gnu Submission from: (NULL) (131.111.186.92) Matrix subset assignment and [[<- assignment are unimplemented for raw (RAWSXP) types. I have a working patch implementing the functionality, to fol

Re: [Rd] Interfacing C-code (gets and printf) under WINDOWS (Visual C++)

2006-02-03 Thread Hin-Tak Leung
In addition to everything Prof Ripley wrote, I'd just like to add that win32 R does run under wine (in fact I am currently doing a test loading a 150MB Rdata file into win32 R under 32-bit wine under 64-bit opteron to see how slow it might be - it takes about 2 minutes natively), and I believe tha

Re: [Rd] [R] readline detection problems

2006-02-03 Thread Hin-Tak Leung
look into config.log towards the end - it gives you the details of what happened during the failed configure. (the file is created by configure as it runs). As for consistency of what --someopt should take, it is all part of the mess of autoconf. You could read it up at http://www.gnu.org/ and lo

Re: [Rd] [R] readline detection problems

2006-02-03 Thread Hin-Tak Leung
Prof Brian Ripley wrote: > On Fri, 3 Feb 2006, Benjamin Otto wrote: > > >>Dear Mr. Ripley, >> >>thanks for the quick reply. I set these flags now, however there still seem >>to be some problems with readline. The corresponding cofigure output is: >> >>checking readline/history.h usability... yes

Re: [Rd] Troubles with the function rmultinom.c of the R's Random Number Generator

2006-02-06 Thread Hin-Tak Leung
Sophie Ancelet wrote: > Thank you for the answer. However, I sought in Doc. Writing R > extensions, in particular in the paragraph 5.6 "Calling C from FORTRAN > and vice versa" (page 67) but I did not find anything which could help me to > correct my code. Indeed, rmultinom.c is a particular functi

[Rd] bug in codetools/R CMD check?

2011-02-03 Thread Hin-Tak Leung
nish’ assigned but may not be used read.HapMap.data: local variable ‘strand’ assigned but may not be used tdt.snp: local variable ‘nc.snps’ assigned but may not be used tdt.snp: local variable ‘nr.snps’ assigned but may not be used - which is more like expected check warnings. Care to

Re: [Rd] bug in codetools/R CMD check?

2011-02-08 Thread Hin-Tak Leung
--- On Tue, 8/2/11, luke-tier...@uiowa.edu wrote: > From: luke-tier...@uiowa.edu > Subject: Re: [Rd] bug in codetools/R CMD check? > To: "Hin-Tak Leung" > Cc: david.clay...@cimr.cam.ac.uk, r-devel@r-project.org > Date: Tuesday, 8 February, 2011, 15:34 > Thank

Re: [Rd] bug in codetools/R CMD check?

2011-02-08 Thread Hin-Tak Leung
--- On Tue, 8/2/11, Prof Brian Ripley wrote: > From: Prof Brian Ripley > Subject: Re: [Rd] bug in codetools/R CMD check? > To: "Hin-Tak Leung" > Cc: luke-tier...@uiowa.edu, david.clay...@cimr.cam.ac.uk, > r-devel@r-project.org > Date: Tuesday, 8 February, 2011, 17:

[Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-26 Thread Hin-Tak Leung
Current core/Recommended Matrix package (0.999375-48) has been segfaulting against R 2.13-alpha/2.14-trunk for the last week or so (since R-2.13 was branched, when I started trying) when "run with R CMD check --use-gct": -- > pkgname <- "Matrix" > source(file.path(R.home("share"), "R

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-29 Thread Hin-Tak Leung
R with > --enable-strict-barrier or set the C compilation flag > -DTESTING_WRITE_BARRIER? I think that run-time error message can only > be thrown under those circumstances (not that it isn't an error, it's > just not checked for in other circumstances). &

[Rd] "R CMD check" accepts but "R CMD INSTALL" rejects a tar ball.

2011-04-01 Thread Hin-Tak Leung
I have somehow managed to made a source tar ball which "R CMD check" accepts but "R CMD INSTALL" rejects with: -- Warning in untar2(tarfile, files, list, exdir) : checksum error for entry 'pax_global_header' Error in untar2(tarfile, files, list, exdir) : unsupported entry type ‘

[Rd] Fw: Re: core Matrix package segfaulted on R CMD check --use-gct

2011-04-01 Thread Hin-Tak Leung
repost from the subscribed address... --- On Fri, 1/4/11, Hin-Tak Leung wrote: > --- On Wed, 30/3/11, Douglas Bates > > wrote: > > > I isolated the problem and tested then committed a > fix. I > > am going to > > ask Martin to upload the new release as I h

Re: [Rd] "R CMD check" accepts but "R CMD INSTALL" rejects a tar ball.

2011-04-01 Thread Hin-Tak Leung
rious things) works and R CMD INSTALL itself does not. OTOH, should this be reported to the GIT people? > > > On Apr 1, 2011, at 10:19 AM, Hin-Tak Leung wrote: > > > I have somehow managed to made a source tar ball which > "R CMD check" accepts but &qu

Re: [Rd] "R CMD check" accepts but "R CMD INSTALL" rejects a tar ball.

2011-04-01 Thread Hin-Tak Leung
pax in several places. So git-archive's documentation (and its '--format=tar' option) is misleading; although even GNU fileutils says the ungzip'ed bundle is "posix tar". Go figure... OTOH, "R CMD check" extracts the content (and does an install) and &#x

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Hin-Tak Leung
Douglas Bates wrote: I isolated the problem and tested then committed a fix. I am going to ask Martin to upload the new release as I have gotten out of sync with some of his recent changes and he will, I hope, reconcile the branches and trunk. If you need the fixed version immediately, say for t

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Hin-Tak Leung
Martin Maechler wrote: Martin Maechler on Thu, 7 Apr 2011 12:24:32 +0200 writes: "HL" == Hin-Tak Leung on Thu, 7 Apr 2011 07:51:44 +0100 writes: HL> Douglas Bates wrote: >>> I isolated the problem and tested then committed a fix. I am >>>

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Hin-Tak Leung
--- On Thu, 7/4/11, Martin Maechler wrote: > ???  But  the prerelease version of R-2.13.0 > *contains* already > Matrix_0.999375-49  the one you claim has the bug. > > [[and you still haven't told use the exact R version you > were using]] Oh, I am tracking both R and Matrix via git-svn and re

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Hin-Tak Leung
Hin-Tak Leung wrote: Martin Maechler wrote: Martin Maechler on Thu, 7 Apr 2011 12:24:32 +0200 writes: "HL" == Hin-Tak Leung on Thu, 7 Apr 2011 07:51:44 +0100 writes: HL> Douglas Bates wrote: >>> I isolated the problem and tested then committed a fix.

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-08 Thread Hin-Tak Leung
--- On Fri, 8/4/11, peter dalgaard wrote: > On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: > > > > > Oh, I am tracking both R and Matrix via git-svn and > retrieves all revisions to all branches daily (or at least, > regularly). I.e. R svn head.  2.13.0 only forked of

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-11 Thread Hin-Tak Leung
a breakpoint in memory.c:CHK on the > line that signals > > the error gives a stack trace of the C calls involved, > and in this > > case the culprit was pretty easy to find at that > point. > > > > luke > > > > On Fri, 8 Apr 2011, Hin-Tak Leung wrote: &

[Rd] R check mis-identifying Illumina data file format as executable and other thoughts.

2011-08-03 Thread Hin-Tak Leung
This is somewhat a summary/continuation of an R bug report: (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14645) Illumina's cluster definition files (*.egt) are one of the proprietary and undocumented file formats used by their GenomeStudio line of products for genomic studies. snpMatrix

[Rd] grDevice in R HEAD been broken for 6 weeks.

2015-09-26 Thread Hin-Tak Leung
geDevice has been failing check for 6 weeks now with --enable-strict-barrier , bisected to: r69049 | murrell | 2015-08-14 00:03:12 +0100 (Fri, 14 Aug 2015) | 2 lines first hack at adding grid display list to recorded plot o

[Rd] another fix for R crashes under enable-strict-barrier, lto, trunk@72156

2017-02-11 Thread Hin-Tak Leung
I haven' t touched R for some 18 months, and so I have no idea if this is a recent problems or not; but it certainly did not segfault two years ago. Since it has been crashing (segfault) under 'make check-all' for over a month, I reckon I'll have to look at it myself, to have it fixed. I have b

Re: [Rd] another fix for R crashes under enable-strict-barrier, lto, trunk@72156

2017-02-20 Thread Hin-Tak Leung
-- On Mon, 2/20/17, Martin Maechler wrote: Subject: Re: [Rd] another fix for R crashes under enable-strict-barrier, lto, trunk@72156 To: "Hin-Tak Leung" Cc: r-devel@r-project.org, "bonsai list" Date: Monday, February 20, 2017, 9:56 AM >>>>> Hi

Re: [Rd] new window cairo bundle Re: R/Sweave/cairo/freetype bug fix.

2013-06-13 Thread Hin-Tak Leung
has a listing of versions. http://sourceforge.net/projects/outmodedbonsai/files/R/ Unix users should just upgrade. I'll get round to build R 2.15.3 (or 2.15.x) for windows and Mac OS X at some stage, but if somebody want to beat me to it, please feel free to do so. --- On Tue, 2/4/13, Hin

[Rd] new bugs and new bundles Re: R/Sweave/cairo/freetype bug fix.

2013-09-03 Thread Hin-Tak Leung
with a system font, fontconfig has problem with a system font, and cairo and R etc. Unix users should just upgrade. I'll get round to build R 2.15.3 (or 2.15.x) for windows and Mac OS X at some stage, but if somebody want to beat me to it, please feel free to do so. Hin-Tak Leung wrote: F

[Rd] freetype 2.5.1 and mono 3.2.5 (was Re: new bugs and new bundles Re: R/Sweave/cairo/freetype bug fix.)

2013-11-26 Thread Hin-Tak Leung
utine upgrade of mono 3.2 5. It is, as usual, slightly adapted to run Illumina GenomeStudio and ...-like workloads on Linux and Mac OS X better. Hin-Tak Leung wrote: The most up-to-date version of freetype (2.5.0.1) have problems with at least two of the system fonts shipped with Mac OS X. So the &q

[Rd] freetype 2.5.2, problem with the survival package, build R 2.15.x with gcc 4.8.x

2013-12-11 Thread Hin-Tak Leung
FUN = summary, maxsum = maxsum, digits = 12, ...) 7: summary.data.frame(support) ... r62430 needs a bit of adapting to apply to R 2.15.x , but you get the idea. I hope this info is useful to somebody else who is still using R 2.15.x , no doubt for very good reasons.

Re: [Rd] [R] freetype 2.5.2, problem with the survival package, build R 2.15.x with gcc 4.8.x

2013-12-17 Thread Hin-Tak Leung
-- On Fri, Dec 13, 2013 16:29 GMT David Winsemius wrote: > >On Dec 11, 2013, at 7:30 PM, Hin-Tak Leung wrote: > >> Here is a rather long discussion etc about freetype 2.5.2, problem with the >> survival package, and build R 2.15.x with gcc 4.8.x

[Rd] The URL for the replacement dll/so bundle - Re: 2 bugs in R's grDevices, and fixes.

2014-01-06 Thread Hin-Tak Leung
Hin-Tak Leung wrote: ... Somewhat related, I have finally gotten round to make two small bundles, which replace the small cairo.dll/cairo.so' in the official windows or Mac R binaries, to fix quite a few problems with them, the first of which was reported almost a year ago. Just move th

[Rd] 2 bugs in R's grDevices, and fixes.

2014-01-06 Thread Hin-Tak Leung
Just before the holiday, I asked the freetype developers what is the context of these two comments about freetype in the code of R's grDevices: === R/src/library/grDevices/src/cairo/cairoFns.c around line 720 = /* some FreeType versions have broken index support,

Re: [Rd] 2 bugs in R's grDevices, and fixes.

2014-03-09 Thread Hin-Tak Leung
Since R 3.0.3 is just around the corner and the problem is still there, here is a repost from around the new year. Hin-Tak Leung wrote: Just before the holiday, I asked the freetype developers what is the context of these two comments about freetype in the code of R's grDevices: ===

Re: [Rd] Looking for new maintainer of orphans R2HTML SemiPar cghseg hexbin lgtdl monreg muhaz operators pamr

2014-08-08 Thread Hin-Tak Leung
At least as far as I am concerned, I'll remove dependency on hexbin, if it comes to that. The dependency is only used in some vignettes, and quite non-essential, and perhaps, undesirable, in fact. On Fri, 8/8/14, Uwe Ligges wrote: Subject: Looking

[Rd] Regression and inconsistency of width of apostrophes in R vignettes

2014-09-17 Thread Hin-Tak Leung
My main dev machine died a well-deserved death a few weeks ago after six and a half years of faithful service, and refused to be re-animated. A substantial part of setting up its replacement is re-running a lot of R vignettes (mostly for timing to establish new performance baselines) - and also cl

[Rd] R build failure under gcc 4.9's link time optimization

2014-12-14 Thread Hin-Tak Leung
R fails to build with visibility on and gcc 4.9's link time optimzation, because of its practice of building part of it as archive first. Specifically it builds some bundled libraries as archive first, the symbols of which are then entirely invisible in gcc 4.9. The Matrix package also does this a

[Rd] bug fix for R, and speed gain (was Re: R build failure under gcc 4.9's link time optimization)

2014-12-23 Thread Hin-Tak Leung
nux, that covers all the major platforms. For 10% speed gain, I'll let somebody else worry about machines that are not MS windows, not mac OS X nor linux. ------------ On Mon, 15/12/14, Hin-Tak Leung wrote: R fails to build with visibility on and gcc 4.9&#

Re: [Rd] New version of Rtools for Windows

2015-01-08 Thread Hin-Tak Leung
-fopenmp -L. >> -lgfortran -lRblas -L../../bin/x64 -lRzlib -lRgraphapp -lRiconv >> -lcomctl32 -lversion >> collect2.exe: error: ld returned 5 exit status >> Makefile:150: recipe for target 'R.dll' failed >> make[3]: *** [R.dll] Error 1 >> Makefile:179: re

Re: [Rd] New version of Rtools for Windows

2015-01-08 Thread Hin-Tak Leung
fix is for passing "make check", when you finish make. -- On Thu, Jan 8, 2015 6:14 PM GMT Avraham Adler wrote: >On Thu, Jan 8, 2015 at 10:48 AM, Hin-Tak Leung > wrote: >> >> The r.dll crash is easy - you need to be using gcc-ar for ar, and gcc-

[Rd] updated R-cairo bridge, official R-3.1.*-mavericks.pkg crippled, snpMatrix 1.19.0.20

2015-01-20 Thread Hin-Tak Leung
R.framework-Versions-Resources-library-grDevices-libs-cairo_20150120.tgz in http://sourceforge.net/projects/outmodedbonsai/files/R/ are dropped in replacement to the cairo.so's in the official R binaries (2.15.3, 3.0.3, 3.1.2). updated to cairo-1.12.18 and freetype-2.5.4. The official R binaries'

Re: [Rd] updated R-cairo bridge, official R-3.1.*-mavericks.pkg crippled, snpMatrix 1.19.0.20

2015-02-01 Thread Hin-Tak Leung
are still for R 2.x. ---- On Wed, 21/1/15, Hin-Tak Leung wrote: R.framework-Versions-Resources-library-grDevices-libs-cairo_20150120.tgz in http://sourceforge.net/projects/outmodedbonsai/files/R/ are dropped in replacement to the cairo.so's in the official

[Rd] That 'make check-all' problem with the survival package

2015-05-15 Thread Hin-Tak Leung
'make check-all' for current R has been showing this error in the middle for a few months now - any thought on fixing this? I think cmprsk should be either included in the recommended bundle, or the survival vignette to not depend on it. Having 'make check-all' showing glaring ERROR's for a few mon

Re: [Rd] That 'make check-all' problem with the survival package

2015-05-16 Thread Hin-Tak Leung
nd that's is an R-devel issue. >On 16.05.2015 07:22, Hin-Tak Leung wrote: >> 'make check-all' for current R has been showing this error in the middle >> for a few months now - any thought on fixing this? I think cmprsk >> should be either included in the recom

Re: [Rd] That 'make check-all' problem with the survival package

2015-05-17 Thread Hin-Tak Leung
-- On Sat, May 16, 2015 2:33 PM BST Marc Schwartz wrote: > >> On May 16, 2015, at 6:11 AM, Hin-Tak Leung >> wrote: >> >> >> >> -- >> On Sat, May 16, 2015 8:04 AM BST Uwe Ligges wrote: >&

[Rd] a couple of small problems with current R devel branch

2011-10-12 Thread Hin-Tak Leung
These are small enough problems with R devel branch yesterday I thought I'll just post here and hope somebody will fix them soon (or may have already been fixed today), rather than filing at the bugzilla. - "R CMD check --use-valgrind --use-gct " gives: -- Error in g

[Rd] gctorture() and gzfile() doesn't get along.

2011-10-15 Thread Hin-Tak Leung
Found the simpliest way of seeing I bug I encountered doing "R CMD check --use-gct": Just launch R (with --vanilla), and do this: > ?gctorture # this work > gctorture() > ?gctorture Error in gzfile(file, "rb") : can only weakly reference/finalize reference objects # this does not It seems th

Re: [Rd] gctorture() and gzfile() doesn't get along.

2011-10-15 Thread Hin-Tak Leung
--- On Sat, 15/10/11, Hin-Tak Leung wrote: > Found the simpliest way of seeing I > bug I encountered doing "R CMD check --use-gct": Just launch > R (with --vanilla), and do this: > > > ?gctorture > # this work > > gctorture() > > ?gctorture > Erro

Re: [Rd] gctorture() and gzfile() doesn't get along.

2011-10-15 Thread Hin-Tak Leung
--- On Sat, 15/10/11, Simon Urbanek wrote: > Thanks, now fixed. It affected almost > all connections. > Simon Many thanks. Hopefully having gctorture() working would help - am having heap corruption problems and valgrind aborts :-). > On Oct 15, 2011, at 2:32 PM, Hin-Tak

[Rd] Sweave, cairo_pdf, CJK, ghostscript

2011-10-21 Thread Hin-Tak Leung
I have had some fun in the last few days trying to put together an annotated map of China with R and some public GIS data: http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download It is done, and rather nice... there are a few issues: -

[Rd] patch to add cairo support to Sweave (Re: Sweave, cairo_pdf, CJK, ghostscript)

2011-10-21 Thread Hin-Tak Leung
included in R 2.14 (already in code freeze and due in less than 10 days..), but harmless enough to go into trunk and 2.14.1? --- On Sat, 22/10/11, Hin-Tak Leung wrote: > I have had some fun in the last few > days trying to put together an annotated map of China with R > and som

Re: [Rd] Sweave, cairo_pdf, CJK, ghostscript

2011-10-23 Thread Hin-Tak Leung
--- On Sat, 22/10/11, Prof Brian Ripley wrote: > On Sat, 22 Oct 2011, Duncan Murdoch > wrote: > > > On 11-10-21 8:57 PM, Hin-Tak Leung wrote: > >> I have had some fun in the last few days trying to > put together an annotated map of China with R and some > pu

Re: [Rd] Sweave, cairo_pdf, CJK, ghostscript

2011-10-28 Thread Hin-Tak Leung
doing Tibetan and Arabic as well - needed/wanted those two for Sichuan (south-western China) and Ningxia (northern western, just south of Mongolia). --- On Sun, 23/10/11, Hin-Tak Leung wrote: > --- On Sat, 22/10/11, Prof Brian > Ripley > wrote: > > > On Sat, 22 Oct 2011, Dunc

[Rd] Sweave, cairo_pdf, xetex, CJK (Re: Sweave, cairo_pdf, CJK, ghostscript)

2011-10-31 Thread Hin-Tak Leung
r Lemberg's CJK (the LaTeX package) can work without declaring noae, so that's my preferred choice at the moment, although I have got both of them working, for doing Chinese in a LaTeX document. I think some of these information should go into the man page of cairo_pdf()... ---

Re: [Rd] Sweave, cairo_pdf, xetex, CJK (Re: Sweave, cairo_pdf, CJK, ghostscript)

2011-10-31 Thread Hin-Tak Leung
--- On Mon, 31/10/11, Simon Urbanek wrote: > On Oct 31, 2011, at 5:56 PM, Hin-Tak Leung wrote: > > > I am still doing some cosmetic things (adding > annotations with some of the really minority languages in > Sichuan), but here are a few misc tips and quirks so far: &g

Re: [Rd] Sweave, cairo_pdf, xetex, CJK (Re: Sweave, cairo_pdf, CJK, ghostscript)

2011-10-31 Thread Hin-Tak Leung
--- On Mon, 31/10/11, Simon Urbanek wrote: > Well, I don't see how most of the above is in any way > relevant. What PDF gets generated really depends on the > cairo version you are using, not on R. Only most recent > versions of Cairo (1.10.x) switched the format to PDF-1.5 > and added format res

Re: [Rd] Sweave, cairo_pdf, xetex, CJK (Re: Sweave, cairo_pdf, CJK, ghostscript)

2011-11-02 Thread Hin-Tak Leung
FWIW, this is the final outcome: Chinese, Tibetan, Arabic, Liangshan Yi (basically Chinese + 3 other languages used in Nw and Sw china). Arabic is interesting, it using a right-to-left layout - and it works in R graphics. http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.19

[Rd] non-ascii vignettes

2011-11-03 Thread Hin-Tak Leung
Hi, just saw "require vignettes to declare their encoding (trunk@57560)". Having played with non-ascii vignettes (well, a lot of Chinese...) on-and-off for almost two weeks, I noticed it was a bit odd that a *commented* \usepackage[utf8]{inputenc} had any effort at all on R's Sweave behavior -

[Rd] a couple Sweave buglets

2011-11-29 Thread Hin-Tak Leung
Just a couple of small bug-lets/stuffs in Sweave: - It stripes off the two lines starting with @ (this is a verbatim section showing plink's start-up message): === @--@ | PLINK! |v0.99p

  1   2   3   4   >