similar to: Thai vignette, cross-compile for Mac OS X, universal/multiarch (Fwd: Mac OS X builds of CelQuantileNorm, vcftools/samtools/tabix, and snpStats)

The windows replacement is R-library-grDevices-libs-winCairo_20150122.zip in http://sourceforge.net/projects/outmodedbonsai/files/R/ The cairo replacements are just two bundles, windows or OS X - containing replacements for R 2.15.3, 3.0.3 and 3.1.2. You just extract the relevant one for your R version. The windows builds of R packages snpStats x.x.x.8 and snpMatrix 1.19.0.20 were done with

------------------------------ 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. Please feel free to skip forward. >> >> - freetype 2.5.2: >> >> the fix to cope with

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' were built with early freetype 2.4.x and cairo 1.11(?) and had a number of issues with some

Hi, Does anybody know how to obtain the imputed SNP genotype probabilities from the snpStats package? I am interested in using an imputation method implemented in R to be further used in a simulation study context. I have found the snpStats package that seems to contain suitable functions to do so. As far as I could find out from the package vignette examples and its help, it gives the

Hi All, Well, it <http://goo.gl/hzxyw> was too good to be true. Under extreme, extended IO on a 48core node, some part of the the NFS stack collapses and leads to an IO lockup thru NFS. We've replicated it on 48core and 64 core nodes, but don't know yet whether it acts similarly on lower-core-count nodes. Tho I haven't had time to figure out exactly /how/ it collapses, I

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

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 1.17.0.7 onwards (http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/)

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

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.");

Hello *, I'm currently migrating a friend to Kubuntu 7.10. He's forced to use a service which works with IE only (no other browser can display their website). Fortunately, IE6 works with Wine (I used ies4linux 2.99.0 (http://www.tatanka.com.br/ies4linux) to set it up), but unfortunately only with the English keyboard layout: When we switch to Thai (KDE shortcut Ctrl-Alt-K), the focused

Anybody know where to find Thailand DIDs that can ring in to my * in the USA on SIP? Oh, and a good price, too! ;) Chris Coulthurst chris@shuksan.com

Full_Name: Hutcha Sriplung Version: 2.1.0 OS: windows Submission from: (NULL) (202.12.74.9) In R-2.1.0, I found that 'example' function does not work properly and report an error message as shown below on a Windows machine (running r-devel release) but not on Linux. > example(attach) Error in switch(x[2], "1250" = return("ISO 8859-2"), "1251" =

Hi there, I have some problems reading in a Thai text. Some of the newlines are skipped. (see the contents of my file below) R>count.fields ("my.txt", sep='\n', quote="") [1] 1 1 1 Three lines with one item each, right? R> scan("my.txt", what="", sep="\t", quote="") Read 2 items [1] "?\x83???\x88

Package: klibc Version: 1.5.20-1 Severity: normal Tags: patch User: ubuntu-devel at lists.ubuntu.com Usertags: origin-ubuntu natty ubuntu-patch Hi maks, Since the Ubuntu linux-libc-dev is now installing its asm headers to the multiarch /usr/include/<triplet>/ directory to allow co-installability, I've pushed the attached patch to Ubuntu so klcc knows to include this path when searching

Package: gcc-4.7 Version: 4.7.0-12 Severity: serious Justification: breaks unrelated software The following scenario is broken: I would expect the link to fail. This is a carefully nailed-down testcase to figure out that the fault is with gcc not binutils. tg at zigo:~ $ echo 'int login_tty(int); void _exit(int); void _start() { _exit(login_tty(0)); }' >test.c tg at zigo:~ $ rm -f

Hi, Why isn't 'R CMD check --force-multiarch' installing the package for all the architectures that are going to be checked? For some packages, it only installs for the default arch ('i386'). Then testing the package for 'x64' fails. For example, Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz: ----------------------------------------------------------- *

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")) >

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

Dear experts, I am trying to perform an association using snpStats. I have a snp matrix called 'plink' which contains my genotype data (as a list of $genotypes, $map, $fam), and a phenotype data frame which contains the outcomes (outcome1, outcome2,...) I would like to associate with the genotype. My question is, how do I loop through the outcomes? This type of data seems different from