similar to: Sweave, cairo_pdf, CJK, ghostscript

It was as easy as I thought it was half a day ago - here is a patch against R trunk to add cairo support to the Sweave driver, an example Sweave input, and the resulting output. A few more notes: - obviously the documentation needs to be updated... a bit more work to do. - some check to make sure "cairo" and "pdf" are not both set would be nice, as well as checking

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, fall back to index 0 */ if (!FT_New_Face(ft_library, (const char *) file, index, &face) || (index

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, fall back to index 0 */ if (!FT_New_Face(ft_library, (const char *) file, index, &face) || (index

Hi This appears to be happening (at least) because cairo_pdf() delays initialising a Cairo surface until BM_NewPage(), rather than initiliasing a Cairo surface in BM_Open(), and replayPlot() triggers some activity (set clip region) on the device BEFORE a new page is started (so the pointer to the Cairo surface is null, so BOOM). Not sure yet whether to blame replayPlot() for not starting

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

(e-mailing to R-bugs is intentional - the web itnerface seems to be down) > a<- cbind(c(1,2), c(3,4)) > a [,1] [,2] [1,] 1 3 [2,] 2 4 > a[cbind(c(2,2), c(2,1))] [1] 4 2 > a[cbind(c(2,3), c(2,1))] Error: subscript out of bounds > a[cbind(c(2,-1), c(2,1))] Error: negative values are not allowed in a matrix subscript > a[cbind(c(2,0), c(2,1))] [1] 4 Am

Hello all, When producing a plot in R using the cairo_pdf device, the resultant plot does not respect the plotting boundaries. Lines and shaded regions will spill over the lower x-axis and the right-side y-axis (sides 1 and 4). I would like to know if it is possible to fix this behaviour when using 'cairo_pdf' in R? As an example, see the image at this web link:

Hello all, When producing a plot in R using the cairo_pdf device, the resultant plot does not respect the plotting boundaries. Lines and shaded regions will spill over the lower x-axis and the right-side y-axis (sides 1 and 4). I would like to know if it is possible to fix this behaviour when using 'cairo_pdf' in R? As an example, see the image at this web link:

Hi (cc'ed to r-devel where further discussion should probably take place) Thanks Lee. I see that problem. There is a "+ 1" in the Cairo device code for setting the clipping region (https://github.com/wch/r-source/blob/ba600867f2a94e46cf9eb75dc8b37f12b08a4561/src/library/grDevices/src/cairo/cairoFns.c#L156) Remove the "+ 1" and the problem goes away (for your example

Hi, I wonder if this is expected or I'm doing a wrong thing. pdf() dev.control('enable') library("grid") plot(1) grid.text("A") res = recordPlot() dev.off() cairo_pdf() replayPlot(res) dev.off() *** caught segfault *** address 0x4, cause 'memory not mapped' > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit)

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

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.");

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'

Dear all, In grDevices R functions cairo_pdf and cairo_ps it is mentioned that when transparency (alpha channels) are used in vector output, it will rasterize the PDF or postscript exported graph at a resolution of 72 dpi : https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/cairo.html You can see the problem if you try library(ggplot2) cairo_ps(file = "test.eps",onefile =

Hi I decided to blame cairo_pdf(). There is a fix in r-devel (r72242) that works for the reported case, plus some basic sanity checks. I could not complete 'make check-devel' because it was failing on reg-tests-1d.R ... > stopifnot(length(fd) == 10, identical(fd, format(dct <- as.POSIXct(dlt)))) Error: identical(fd, format(dct <- as.POSIXct(dlt))) is not TRUE ... anyone

Dear all I've just tried the brand new 'grdevice' option in Sweave but couldn't make it work. When I declare \SweaveOpts{grdevice=pdf} or \SweaveOpts{grdevice=cairo_pdf} trying to plot something simple <<fig=T, echo=T>>= plot(1:10,1:10,main='Some title') @ would result in an Sweave error: 18:16:47.299: 1 : term verbatim 18:16:47.308: 2 : echo term verbatim

Hi Paul, Great, thank you for looking in to this, and I'm glad that you're able to reproduce it at your end too. From your reply, I'm happy that it seems like the fix may be fairly trivial, but I understand the necessity for caution. If there's anything else I can do to help, please do let me know. Thank you again, Best, Lee On Monday, 4 March 2019, Paul Murrell <paul at

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: