similar to: subsetting matrix by subscript=0,x silently skips.

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: - the default pdf() device cannot do CJK with embedded fonts - and cairo_pdf() is not hooked up to

Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in

Hi, I have got a curious issue with an R package which uses zlib, against the official binary here: http://cran.r-project.org/bin/linux/redhat/el4/i386/R-2.4.1-1.rh4AS.i386.rpm on a Redhat EL4 i686 system. The problem is that at the end of reading a gzip'ed file within my C code, gzgetc() returns -1 (no more to read or error) but gzeof() doesn't return true. Now one can probably jump to

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", "examples-header.R")) >

I finally got round to look at a little problem I have - most of the time when I use R I would be using snpMatrix (now part of bioconductor, I wrote a substantial part of), so I had $HOME/.Rprofile to save some typing. Upgrading, switching versions used to work fine with R 2.8 then it broke with 2.9.. Apparently it is because most of SHLIB, INSTALL, etc used to be fairly extensive shell scripts

Hi, (somebody would probably yell at me for not checking 2.6.0rc, for which I can only apologize...) Our R package (snpMatrix in http://www-gene.cimr.cam.ac.uk/clayton/software/) is broken rather badly in 2.6.0 ; I have fixed most of it now so a new release is imminent; but I'd like to mention a few things, mostly to summarize my experience and hopefully the 'writing R extensions'

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.

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 produces this error -------------------------------------------- ! Missing $ inserted. <inserted text> $ l.7 \eqn{{\bf\beta}_j}{\bf\beta}_ jnormal-bracket5bracket-normal{b(j)} -- ! Missing $ inserted. <inserted

Hi, 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 report, and a couple of questions: (1) I think the R binary in the CRAN Innosetup installer was built with mingw. The R-windows FAQ did mention that this DLL is required *for Chinese/Japanese/Korean*

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 awful practice, with CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a . One way of fixing R is:

I wonder if the software here: http://morte.jedrea.com/~jedwin/projects/chmlib/ or at any of the links on that page might allow elimination of the need for separately downloading the Microsoft Help compiler -- which is just one more task that one must perform to get up and running to build your own R packages on Windows.

Does anybody (most probably the core team) know if there is any difference in how the official 2.4.0 and 2.4.1 binaries are built? Problem is, 2.4.0 loads with the wine (I tried a few recent versions, and also used 2.3.x under wine from time to time), but 2.4.1 won't. Thanks. Hin-Tak Leung

Hi, On Mon, Jan 19, 2015 at 03:44:45PM -0500, Duncan Murdoch wrote: > >>>>> git has an interface for cloning SVN repositories into git > >>>>> which some users might decide to use. For those users' > >>>>> surprise, the repository will always fail to build on > >>>>> svnonly target and it will exit early. >

> From: Hin-Tak Leung > > Izmirlian, Grant (NIH/NCI) wrote: > <snipped> > > The only interesting feature is that the tree structure has been > > implemented in C. Its a neater way to carry stuff around and I am > > guessing would make future implementation easier. > > > > Because of its inherent redundancy from the users standpoint, it > >

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 = x86_64-redhat-linux-gnu arch = x86_64 os = linux-gnu system = x86_64, linux-gnu status = major

------------------------------ On Sat, May 16, 2015 8:04 AM BST Uwe Ligges wrote: >Not sure why this goes to R-devel. You just could have asked the >maintainer. Terry Therneau is aware of it and promised he will fix it. > The quickest fix is to add cmprsk to the recommended list , and that's is an R-devel issue. >On 16.05.2015 07:22, Hin-Tak Leung wrote: >> 'make

On 2nd thought, I think a better fix to the segfault is something like this: --- a/src/main/memory.c +++ b/src/main/memory.c @@ -3444,6 +3444,8 @@ R_xlen_t (XTRUELENGTH)(SEXP x) { return XTRUELENGTH(CHK2(x)); } int (IS_LONG_VEC)(SEXP x) { return IS_LONG_VEC(CHK2(x)); } const char *(R_CHAR)(SEXP x) { + if(!x) + error("de-referncing null. Check the validity of your data.");

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 that when gctorture() is on gzfile() doesn't work.

From: Dirk Eddelbuettel > > On 7 March 2006 at 10:55, Hin-Tak Leung wrote: > | I have given up on "R" with any topic on Google quite some time ago > | (because bits from fragmented postscript/pdf files show up, for > | example) - but using "r-devel" with topic normally gives me enough. > | YMMV. > > Nobody seems to have mentioned the RSiteSearch()

Hello, I'm having some difficulty to understand how I could take the proper result from the following listing: -- cut --- #include <stdlib.h> #include <R.h> #include <Rmath.h> void retMat ( double **y, int *n, int *m, double *a, double *b) { int i, j; y = malloc( (*n) * sizeof( double ) ); for (i=0; i<*n; i++) { y[i] = malloc (