similar to: a couple Sweave buglets

Hi All, does anyone know how to import binary .bed files generated by Plink (http://pngu.mgh.harvard.edu/~purcell/plink/ ) into R? the Plink FAQ explains how to conver other types of files, not the .bed. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax

I note that "current implementations of R use 32-bit integers for integer vectors," but I am working with large arrays that contain integers from 0 to 3, so they could be stored as unsigned 8-bit integers. Can R do this? (FYI -- This is for storing minor-allele counts for genetic studies. There are 0, 1 or 2 minor alleles and 3 would represent missing.) It is theoretically possible

Hi, ? I am very new to R. So, pardon my dumb question. I was trying to write my own function to run a different model (perform an ordered logistic regression) using the example in website http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml But R returns a error `R Error in eval(expr, envir, enclos) : object 's' not found' when I run it. What am I doing wrong here? Here's

R CMD check <package> gives me below message at the end. There does not seem to be a problem with my TeX installation. Is it possible that R CMD check is not looking in the correct location? How can this problem be fixed? Thanks, Naresh * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX

This is about LaTeX install and not about R. My problem was multiple installations of LaTeX: first using MacTex, then newer version using texlive. I had also tried to install then uninstall using MacPorts. It seems MacPorts uninstall was not clean. I had to manually delete several sym links. MacTex install inserts /etc/paths.d/TeX, which has the path /Library/TeX/texbin. So to get TeX to use

Hi, just saw "require vignettes to declare their encoding (trunk at 57560)". Having played with non-ascii vignettes (well, a lot of Chinese...) on-and-off for almost two weeks, I noticed it was a bit odd that a *commented* \usepackage[utf8]{inputenc} had any effort at all on R's Sweave behavior - while it is understandable (probably no check is made whether a "%" is before

I a using plink on a large SNP dataset with a .map and .ped file. I want to get some sort of file say a list of all the SNPs that plink is saying that I have. ANyideas on how to do this? -- Thanks, Jim. [[alternative HTML version deleted]]

Hello Because I want to use different true type fonts with latex, I''m using the XeTeX typesetting engine for my sweave-documents. I''m using Lyx with Sweave on a Windows 7 PC and have set up LyX to work with XeTeX according to the following instructions: http://wiki.lyx.org/LyX/XeTeX Because the input file for XeTeX is assumed to be in UTF-8 encoding, I set the encoding

Hi there, I tried to compile some trivial LaTeX file with the shipped XeLaTeX: $ xelatex trivial.tex This is XeTeX, Version 3.1415926-2.5-0.9999.3 (TeX Live 2013) restricted \write18 enabled. kpathsea: Running mktexfmt xelatex.fmt /usr/bin/mktexfmt: line 395: /usr/share/texlive/texmf/texconfig/tcfmgr: No such file or directory fmtutil: config file `fmtutil.cnf' not found. I can't find

On 05/29/2018 04:53 PM, Dirk Eddelbuettel wrote: > I noticed it with a local, not-public package -- but it appears to apply with > any source package. I replicated with pkgKitten straight off CRAN and after > checking that it has a six page manual there. I'm having trouble reproducing this one. In my fresh CentOS 7 VM, I can pull the pkgKitten source down, and run R CMD Rd2pdf

Tom, On 30 May 2018 at 11:34, Tom Callaway wrote: | On 05/29/2018 04:53 PM, Dirk Eddelbuettel wrote: | > I noticed it with a local, not-public package -- but it appears to apply with | > any source package. I replicated with pkgKitten straight off CRAN and after | > checking that it has a six page manual there. | | I'm having trouble reproducing this one. In my fresh CentOS 7 VM, I

Hi list, When using R CMD Rd2pdf, it is possible to set environment variable RD2PDF_INPUTENC to value "inputenx" and enjoy better support for UTF-8 characters (see ?Rd2pdf). This enables LaTeX package "inputenx" instead of "inputenc". Even better support for UTF-8 encoded characters can be had by better using the facilities provided by inputenx and making R CMD

Processing commands for control at bugs.debian.org: > found 661471 3.4.1-2 Bug #661471 [gnome-themes-standard] gnome-themes-standard: removal of gnome-themes-standard makes files disappear from gnome-accessibility-themes Marked as found in versions gnome-themes-standard/3.4.1-2. > found 670105 libdrmaa-dev/6.2u5-4 Bug #670105 {Done: Dominique Belhachemi <domibel at debian.org>}

Dear all, I have a problem with an Rd file containing French accentuated characters. I have uploaded the file at http://filex.cirad.fr/get?k=cjW7lImMaNC6Ci2vX0H I have declared Encoding: latin1 in the package DESCRIPTION file and I have added \encoding{latin1} in the header of the Rd file. When I compile the package manual, I have LaTeX errors: ! Package inputenc Error: Unicode char \u8:?F

Cameron and I are pleased to announce version 0.6.0 of the tikzDevice package which should be available shortly at your local CRAN mirror! The tikzDevice makes it possible to export R graphics as LaTeX code that can be included in other documents or compiled into stand alone figures. The full power of LaTeX is available for typesetting text and mathematical expressions inside figures produced

Cameron and I are pleased to announce version 0.6.0 of the tikzDevice package which should be available shortly at your local CRAN mirror! The tikzDevice makes it possible to export R graphics as LaTeX code that can be included in other documents or compiled into stand alone figures. The full power of LaTeX is available for typesetting text and mathematical expressions inside figures produced

Dear list, Latex/Sweave has trouble processing Sveave-output coming from the summary-command of a linear Model. >summary(lmRub) The output line causing the trouble looks in R like this Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 In my Sweaved Tex-file that line looks like this Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1? (actually in the editor the

Dear users, I'm struggling with encoding issues for documenting some functions. The Rd format is incradible simple, however, because I'm dealing with diacritic strings, I seted up encoding in several Rd files as latin1. Under R, using the checks available in the package 'tools it performs pretty well. But when check the package as cran, I got several encoding issues. Have any one

On 10/31/23 10:05, Duncan Murdoch wrote: > On 31/10/2023 4:32 a.m., Tomas Kalibera wrote: >> >> On 10/30/23 19:07, Yihui Xie wrote: >>> Sure. I'm not sure if it's possible to make it easier to reproduce, >>> but for now the example would require installing TinyTeX (via >>> tinytex::install_tinytex(), which can be later uninstalled cleanly via

Hello, I am not sure whether this is a bug or lack of R experience. However, I am using your Sweavelistingutil package, which is very nice. Obviously I use it to create LaTeX files. These are encoded in utf8. However, when I use the Sweavelistingutil is uses some funky character for "`" and "'" that is not recognized. Here is an example from my tex-file: ,---- |