similar to: updated R-cairo bridge, official R-3.1.*-mavericks.pkg crippled, snpMatrix 1.19.0.20

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

FYI. There is a Thai vignette - and it went a lot further doing some Thai text processing in R, than the earlier Chinese/Tibetan/LiangshanYi/Arabic vignette, which was in reality just Chinese + Cairo graphics. Managed to cross-compile an R package for Mac OS X from Linux; and it seems to be working. See screenshots below. I'd be interested to know if there are less obvious bugs; however

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 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

Hi R-help folks, I have been doing some single SNP association work using snpMatrix. This works well, but produces a lot of false positives, because of population structure in my data. I would like to correct the p-values (which snpMatrix gives me) for population structure, possibly using principle component analysis (PCA). My data is complicated, so here's a simple example of what

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")) >

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/)

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, 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 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

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

(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

I'm trying to help someone to troubleshoot possible OSX Yosemite issues, but I've only got access to OSX (< 10.9) so I cannot check myself. When building/installing binary R packages, there are different binaries depending on OSX version. For instance, CRAN provides different binaries for 'OS X Snow Leopard' and 'OS X Mavericks', e.g.

I just checked your package on a mavericks VM and it seems fine, so I wouldn't worry about it. Probably some configuration issue on the CRAN server, perhaps xquartz is outdated. Unfortunately there is no easy way anymore to check on Mavericks. Travis used to support it, but they have deprecated mavericks (along with Apple and homebrew). Hopefully CRAN will update to the current MacOS for the

We run a dovecot mailserver. One of the clients I use is a Mac Laptop. Recently I upgraded from Mountain Lion (10.8) to Mavericks (10.9). Under 10.8 it worked fine. On 10.9 it syncs up when I invoke the client, but after a while stops getting updates. Most of my mail clients are on Linux (thunderbird) or Android (K9) and I admit that several run against my very large INBOX simultaneously. The

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

[redirecting to nut-upsuser since we hardly use the packaging list anymore] On May 15, 2014, at 9:20 AM, Jose Vigil wrote: > Hi friends, > > I?m looking for an already compiled .pkg NUT Client to be installed in a Mavericks iMac. Can someone, please point me to place where I can find it? We don't have any official ones. If anyone else has compiled one, please feel free to share

Hi R-devel, I'm noticing the following behaviour: writeLines("#include <Rcpp.h>", file = "test.cpp") Rcpp::sourceCpp("~/test.cpp") ## succeeds at trivial compile Sys.setenv("USE_CXX1X" = "yes") Rcpp::sourceCpp("~/test.cpp") ## fails; CXX nor CXX1X properly set (?) IIUC, R is not propagating CXX nor CXX1X when

hello I maintain the gsl R package, and many users have recently reported that the package does not install from source under macosx 10.9 ("mavericks"). Users typically install the gnu GSL library and are able to compile and run a small "hello world" program which executes some of the Bessel functionality of the library; but under mavericks the configure script (which uses

Dear mac folks, I have started porting a large legacy toolset maintained in windows and heavily mpi laden so it can be used across platforms in R... so I am building a package out of it. On this note, I am noticing that almost all of the mpi dependent packages do not compile on the CRAN repositories.... with the basic issue that it appears it can not find mpi installed: configure: error: