similar to: Two problems building a package

Hello all: I have a protein sequence alignment in a data frame (align1, 72 x 236), where each row is a protein and each column a site in the alignment. AA is vector of amino acid symbols plus "-" (gap). I can calculate amino acid frequencies at each site by: >align1.F <- matrix(0,nrow=22,ncol=236,dimnames=list(AA,seq(1:236))) >for(i in 1:236) >

Hello: I am attempting to use R to analyze amino acid frequencies in aligned protein sequences and need some help. So far, I have imported my sequence alignment into a data frame (lets call it "alignment") with each site in one column, so that I have a data frame consisting of columns of letters (the 21 amino acid symbols plus "-") with row names being the corresponding

Greetings: In a function I'm trying to write I am multiplying each row in a matrix by a vector. When the vector extends beyond the end of the matrix I need to have the multiplication wrap around (continue with column 1 of the matrix). Initially I got this to work with a loop (old programming habits die hard). Now, after going back through MASS I've figured out how to do the multiplication

Greetings all: OK, this is bugging the @#@%* out of me. I know the answer is simple and straightforward but for the life of me I cannot find it in the documentation, in the archives, or in my notes (because I know I've encountered this in the past). My problem is: I have a data frame with columns A, B, C, D, and E. A, B, and E are factors and C and D are numeric. I need a new data frame with

This summer I and a colleague built a package for R v 1.9.1 containing C-code under Windows. That only worked for us when R was installed in c:\program files\R. Now I have R v 2.0.1 and the same package won't build. I get the following C:\Program Files\R\rw2001\bin>rcmd check "c:\program files\r\rw2001\src\library\ sag" * checking for working latex ...latex: not found NO * using

Hello everyone. I am using R 2.0.1 in windows XP sp2 and I want to create a package. I get the following errors when I run these commands at the dos prompt. Please help. Thanks. NIshan F:\Program Files\R\rw2001\bin>Rcmd build f:\testingskeke * checking for file 'f:\testingskeke/DESCRIPTION' ... OK * preparing 'f:\testingskeke': * cleaning src *

In reference to the thread http://tolstoy.newcastle.edu.au/R/devel/04/10/0859.html I have the same problem updating packages with newly-installed version of released version of R 2.0.1. Previous posts refer to a bug in windows. I wonder if there is a work-around? This probably should go to R-help but it follows on from the post in R-devel. Apologies in advance. OS: Windows XP Professional,

Dear R community, I am running R 2.0.1 on a Windoze XP OS. I recently upgraded from R 1.9x to 2.0.1 and I am currently upgrading a my personal function packages. My other packages compiled without a hitch but I am having a difficult time with my largest package. Can someone please help me with the following error message "Error in parse(file, n, text, prompt) : syntax error on line

Hello, I'm trying to create a source package (on Win2k system). I followed the instructions from R-extns.pdf, installed ActivePerl and RTools with setting the DOS path to it. Then I did "Rcmd check" and had an error: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C:\R\rw2001\bin>Rcmd check D:/prime7/SpnInstall/spectrino * checking for working latex ...latex: not found NO * using log directory

When I do a R CMD build --binary then I get the messages at the end of this post unless I specify LazyLoad: no in the DESCRIPRION file. If I do that then everything proceeds smoothly. R CMD check proceeds smoothly in either case. Is there something I should be aware of that is causing this message when I do not turn off lazy loading? I am using Windows XP and R 2.0.1 beta

I'm trying to schedule R tasks in Windows Server 2003. I can run the following from the DOS prompt without any difficulty: c:\Reports>c:\r\rw2001\bin\rterm.exe --no-restore --no-save <test.R> test.out where test.r has two lines: library(tools); Sweave("rlr.Rnw"). When I try to run the same from the task scheduler, I fill in the dialogue box as follows: Run:

I rarely use Windows, so perhaps this is a question for r-help but I don't think so. > install.packages("dse") trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 24873 bytes opened URL downloaded 24Kb trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/dse_2005.1-1.zip' Content

Hi, I recently encountered a similar problem to http://www.mail-archive.com/r-help at stat.math.ethz.ch/msg31960.html One conclusion from that thread seems to be that if XP users need to update the index, after installing a package, they have to install R into a directory for which they have got write access, either a network or local drive. This is in order to update the files 'C:Program

Hi. Day three and I’m still struggling with this. Any advice to overcome the final hurdle will be enormously appreciated. I now have all the right Java applications etc. in their right places and have managed to get rid of most errors but still get this: — Making package SJava — Building JNI header files... adding build stamp to DESCRIPTION running src/Makefile.win (cd .. ;

Hi all, I can't get my C routines running on a windows box. I have no problems at all in Linux. On windows, I have installed cygwin and the compilation works well but once I execute "dyn.load(.)" it hangs whatever I use C/C++ interfaces. In Linux it works wonderful but I need to get this code running on windows boxes. I know that the problem should be something with the

Somehow I have lost the correct file association for .RData files. They are now associated with a text file editor. When I right click on any .RData file and try to change the association, R is not listed as a choice of program. I browse to c:\Program Files\R\rw2001\bin\Rgui.exe and select that file to open .RData, but Windows does not then place Rgui.exe in the list of programs to use. I can

hello, We've got a problem with the mix package in order to impute the missing data. After importing the data, the prelim function does not work (only the stlouis data works). We have done : >library(mix) >Manq <- read.table("C:/.../file.txt") >attach(Manq) >save(Manq,file="C:/../R/rw2001/library/mix/data/Manq.rda") >data(Manq) >Manq V1 V2 V3 V4 1

I am not a techie and have been struggling 2 days solid to try and install SJava (the source from http://www.omegahat.org/RSJava/). Does anybody have a binary file for me (I am Windows XP and rw2001)? I have tried installing Perl, mingwin and the cygwin tools but still no luck. When I try “R CMD INSTALL c:\SJava_0.78-0.tar.gz” I get the following (and haven’t a clue what it could mean):

Sorry to ask a (probably) dumb question, but I am trying to install XML package on Windows XP, R 2.0.1, and I get the error: "This application has failed to start because libxml2.dll was not found. Re-installing the application may fix this problem" > library(XML) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library

I tried ot build rpvm in my own makefile. But runs into some linker errors like e.g. undefined reference to `_R_alloc' My enviornment looks like this: CYGWIN pvm 3.4 compiled under cygwin myself R installed from the rw2001.exe setup file. I guess that the R under rw2001.exe was build with some other compiler? I then tried to compile R myself under CYGWIN but runs into the following