similar to: R 2.8->2.9 change that breaks some upgrade scenarios

This is the change I suggested earlier - it should just disable more of user/site customization during package installation/removal, and getting more of R 2.8-like behavior back. Attached and inlined below. Against svn r48897 (svn HEAD AFAIK). -------------------------------------------------- diff --git a/src/scripts/INSTALL b/src/scripts/INSTALL index 42470c2...4c7bae9 100755 ---

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, 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

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

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

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

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:

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")) >

(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

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

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

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, (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'

All, I have an ActiveRecord object that I need to be able to uniquely identify _before_ I actually save the object (I may not end up saving the object based on conditions). This is because I want to use the ID in another context (a file name in the filesystem). Depending on conditions, I may or may not need to do a lot of stuff between the time that I generate the object ID and actually

Dear R-devel, I think the following describes a bug in R. It seems to be associated with dyn.load() and/or something that happens at start-up. I have not filed a bug report yet (because I doubt my ability to rule out other explanations) but would happily do so if requested. Observation: If two dlls are loaded as a result of dyn.load() calls in .Rprofile, subsequent calls to dyn.load()

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/)

Hi, I am interested in customizing the installation of R. I have gone through the ?R Installation and Administration? manual. But some of the stuff is not clear to me and I would like to get clarifications on the following points (for a Windows installation with R_HOME=C:\\R\\R-2.9.1 ) : 1. I understand that I need to create a file, .Renviron with the following path : R_HOME\\etc\\.Renviron where

--- On Thu, 3/9/09, Vinh Nguyen <vinhdizzo at gmail.com> wrote: > hi hin-tak, > > i'm trying to build r packages for windows on a > mac/linux. i guess > this used to possible and supported, but is no longer > supported. i > ran into this post of yours, > https://stat.ethz.ch/pipermail/r-devel/2009-July/053971.html, > and hope > u don't mind me

TL:DR there are at least three maybe four ways to address this depending on what you plan to do. I usually adjust PATH to add Rtools using .Rprofile. But if you do that then if you want to use the command line to invoke R then you need to set the PATH separately when you start the shell. For this reason some people like to set it in the User Environment Variables control panel... but some Rtools

Michael, I've implemented a LOADABLE_MODULE feature in the makefiles: http://mail.cs.uiuc.edu/pipermail/llvm-commits/Week-of-Mon-20050110/023147.html The approach taken is almost what you described below. However, I want to retain the distinction between a "regular" shared library and one that can be dlopened. So, if you specify SHARED_LIBRARY=1 you get a regular shared library