similar to: Puzzling message: "no man files in this package"

Dear R users: Recently, I learn to use penalized logistic regression. Two packages (penalized and glmnet) have the function of lasso. So I write these code. However, I got different results of coef. Can someone kindly explain. # lasso using penalized library(penalized) pena.fit2<-penalized(HRLNM,penalized=~CN+NoSus,lambda1=1,model="logistic",standardize=TRUE) pena.fit2

The following R code using different packages gives the same results for a simple logistic regression without regularization, but different results with regularization. This may just be a matter of different scaling of the regularization parameters, but if anyone familiar with these packages has insight into why the results differ, I'd appreciate hearing about it. I'm new to

Hi, I am reporting what seems to be a trivial error in one of the test files (this has been failing for a few days for me): Collecting examples for package 'tools' Running examples in package 'tools' Error: testing 'tools' failed Execution halted gmake[3]: *** [test-Examples-Base] Error 1 gmake[3]: Leaving directory `/usr/local/share/R-devel/tests/Examples' gmake[2]:

Hello! I have some problems using Rcmd, bacause I get errors I do not understand. I will write down what I did. Perhaps you can help me? I have a small would-be package called "globaltest", containing only the files DESCRIPTION INDEX R/globaltest.R man/globaltest.Rd I say: C:\>Rcmd check C:/Goeman/globaltest In the output it first complains that 'sh', 'make',

Full_Name: Mike Pacey Version: 2.5.1 OS: SUSE SE Linux 9.3 Submission from: (NULL) (194.80.32.10) Versions 2.5.0 and 2.5.1 currently fail "make check" on my system due to a silent failure in the call to Rd_db("base"): ----- > ### Name: Rdutils > ### Title: Rd Utilities > ### Aliases: Rd_db Rd_parse > ### Keywords: utilities documentation > > ### **

Hi, This is a follow up to: https://stat.ethz.ch/pipermail/r-devel/2010-July/057921.html The Bioconductor daily builds have been reporting a lot of strange things lately on Windows using R-2.12. This started 2 or 3 months ago and things are not getting better with recent R-2.12. Here is a sample from today's build results. We use Windows Server 2003 R2 for the 32-bit builds, Windows

Hi, all, I just recently upgraded my computer though I'm using the same OS (XP). But now I'm having difficulty building packages and I cannot seem to solve the problem. I'm using R-2.1.1pat on Windows XP. Here is what I tried: D:\Users\sundard\slib\sundar\R>R CMD CHECK sundar * checking for working latex ... OK * using log directory

Folks, I have a personal package which used to build fine. Today when I tried to build the package again, some errors popped up. Could you please help? When I paste the offending function into an R it works correctly. But the package build breaks. $ R CMD check ansecon * checking for working pdflatex ... OK * using log directory '/Users/ajayshah/L/R/packages/ansecon.Rcheck' * using R

Hi, there, I used R CMD check to build my "ATGGS" package under window XP system. My R version is 2.7.2. But I encounter some problems. The log file is like: ********************************************************************************** installing R.css in C:/ATGGS.Rcheck ---------- Making package ATGGS ------------ adding build stamp to DESCRIPTION installing R files

Hi, there, I used R CMD check to build my "ATGGS" package under window XP system. My R version is 2.7.2. But I encounter some problems. The log file is like: ********************************************************************************** installing R.css in C:/ATGGS.Rcheck ---------- Making package ATGGS ------------ adding build stamp to DESCRIPTION installing R files

Hi! All. I want to make R package with "http://code.google.com/p/uchardet/" library. But I encountered error. Executable file with -lchardet works well but shared library didn't work with dyn.load() with Rcpp. Can any one give some tips? * installing *source* package ‘Ruchardet’ .. ** libs g++ -I/usr/share/R/include -DNDEBUG -I/usr/local/include -I/usr/include

Synopsis: I am trying to build and install a package in R, but I have run into a problem where the file names determine success or failure of the package installation. I started with a single file containing two class definitions. This package installs properly. If I split the classes into two files, the build fails. If I simply change the file name of one file with no other changes, the

Hi folks, I'm attempting to compile and install 2.5.0, and "make check" is failing one of the earlier sanity tests. I'll append the relevant portion of the Rout.fail file below, but I've narrowed it down manually to a single command: > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-unknown-linux-gnu locale:

Hi, All: What might cause "R CMD check" to report, "could not find function" for a function that has long been in the 'fda' package? Both Jim Ramsay in Ottawa, Canada, and I in San Jose, CA, get this same error. I replicated it with a fresh, anonymous checkout from R-Forge (svn checkout svn://svn.r-forge.r-project.org/svnroot/fda). With this, I did

Dear Robert, The differences have to do with diffent scaling defaults. lrm by default standardizes the covariates to unit sd before applying penalization. penalized by default does not do any standardization, but if asked standardizes on unit second central moment. In your example: x = c(-2, -2, -2, -2, -1, -1, -1, 2, 2, 2, 3, 3, 3, 3) z = c(0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1) You

I have a samll package that works well and complies nicly on WinXP, using R-2.4.1 Now I want to add a document so i make a folder inst\doc and put the .tex and .pdf in there. But the complation then crashes. Is this because the installin expects some file to be present in inst if an inst folder is there? This is how the thing progress is on my command promp:

I am not sure if this is already known. I checked BUGS and found some references to similar behavior when R_HOME is set? Here is what I get: (1) Fresh build of 1.4.1 under Linux/RH-7.2. All tests pass. > R CMD check ctest * checking for working latex ... OK * using log directory `/home/andyj/stat/R-1.4.1/library/ctest.Rcheck' Installing *source* package `ctest'

Hi, The "penalized" documentation says that "Unordered factors are turned into as many dummy variables as the factor has levels". This is done by a function in the package called contr.none. I'm trying to figure out how exactly is a model matrix created with this contrast option when the user calls the function with a formula. I typed "library(penalized) ;

Dear all, I am trying to build a home-made package (log2html) to log R output to an HTML file. The package can be build successfully under Solaris, however I am unable to build the system under Windows 2000 Professional. I read (and tried to follow to the letter) Duncan Murdoch's "Building R for Windows" (http://www.murdoch-sutherland.com/Rtools/), in combination with the newest

Hello. I've developed an algorithm in R which I need to package. The implementation uses S4 objects and it's divided in 5 files. Everything is working fine when I load the files into the R console but when I try to make a package I get an error that I don't quite understand. Here's what I do: *1.* in R console, I do and get: > package.skeleton(name='remora') Creating