similar to: linking to package directories broken in R >= 2.10 beta

Dear R developers, I recently observed a NOTE on several MaxOS X package checks: sh: line 1: gs: command not found !!! Error: Closing Ghostscript (exit status: 127)! /usr/bin/texi2dvi: thumbpdf exited with bad status, quitting. See for details: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/simecol-00check.html or

Hello, I wonder why the control parameter REPORT is not supported by method SANN. Looking into optim.c I found an internal constant: #define STEPS 100 ... and decreasing this to 10 helped me fine-tuning the annealing parameters in an actual problem. Is there any reason why not passing nREPORT to samin and setting something like: STEPS = nREPORT / tmax Thomas P. -- Thomas Petzoldt

Dear R developers, I tried to use nlminb instead of optim for a current problem (fitting parameters of a differential equation model). The PORT algorithm converged much better than any of optim's methods and the identified parameters are plausible. However, it took me a while before spotting the reason of a technical problem that nlminb, in contrast to optim, does not pass names of the

Dear R developers, we have currently a 'mysterious' test problem with one package that successfully passed the tests on all platforms, with the only exception of Solaris x86 where obviously one of our help examples breaks the CRAN test. As we don't own such a machine I want to ask about a possibility to run a few tests on such a system: r-patched-solaris-x86 An even more recent

Dear R developers, I observed that the html help page index entry "Read overview or browse directory" for package vignettes is missing in recent R-devel. This happened on two independent computers (WinXP Prof. SP3, German) with R-devel compiled from sources svn rev. 48125 resp. 48128 It's the same for my own and also for more prominent packages as well (e.g. grid). The

Hello, first of all, thanks to LT for \pkg{codeutils}. I agree that it is indeed very useful to identify errors and also to encourage re-thinking past solutions. My problem: I want to compare different sets of related sub-functions which should be used alternatively by the same top-level function. Sets of related functions should be bound together (as lists) and the workspace should be as clean

Hello, when testing packages under R version 2.6.0 Under development (unstable), in order to discover future compatibility issues, I recently get numerous "possible problem notes" for different (own and other contributed) packages containing Tcl/Tk code, e.g.: * checking R code for possible problems ... NOTE sEdit : editVec : build: no visible global function definition

Dear R developers, if one uses package.skeleton() to create a new package, then a file anRpackage.Rd with the following entries is prepared: \name{anRpackage-package} \alias{anRpackage-package} \alias{anRpackage} \docType{package} Packages created this way have a definite entry or overview page, so: ?anRpackage gives new users of a certain package a pointer where to start reading. This is

Hello, is it *really intentional* that the "silent" option of try() does only apply to the outer call in nested try constructs? I would assume that a silent try() should suppress all error messages regardless where they occur, even if they are already handled with other try()'s. The error message itself should be (and is in both cases) reported by the return value of try().

Dear useRs, a new and completely re-worked version of the "simecol" package SIMulatiion of ECOLogical (and other) dynamic systems is now available on CRAN. Compared to the S3 based 0.2-x versions an improved object model using S4 classes was employed. Please ask me for assistance in case of incompatibility. Comments are welcome, Thomas Petzoldt

Dear useRs, a new and completely re-worked version of the "simecol" package SIMulatiion of ECOLogical (and other) dynamic systems is now available on CRAN. Compared to the S3 based 0.2-x versions an improved object model using S4 classes was employed. Please ask me for assistance in case of incompatibility. Comments are welcome, Thomas Petzoldt

Dear R developers, I've got an information from Prof. Ripley regarding a bug found with AdressSanitizer in one of our packages. It is now fixed, thank you for this information. Now, I would like to run AddressSanitizer myself before submitting the patched package to CRAN. Is there a recommendation of a suitable Linux distribution with gcc 4.8, ideally an ISO image or (even better) a

Hello, I want to do simulations with an external simulation model. For this purpose I wrote a R-script which makes the pre- and post-processing of the data (generate scenarios, analyze results). The R-script writes the input file for the simulation with e.g. write(x, file="test.dat", ncolumns=10) The problem is, however, that this command (and even constructions with cat) will add a

Special Volume on Spectroscopy and Chemometrics in R Guest Edited by Katharine M. Mullen and Ivo H.M. van Stokkum 11 contributions, with software packages and examples Similar volumes on R in Psychometrics (guest edited by Jan de Leeuw) and R in Political Methodology (guest edited by Micah Altman and Simon Jackman) are close to being finished. Additional volumes are being worked on. Proposals

Dear list The deSolve package allows you to specify the model code in C or Fortran. Thanks to the excellent vignette this works fine. However I have not yet managed to use forcing functions in C code. In pure R code this works very well with approxfun() specified outside the model: ############################################### #Model lvml <- function(t, x, parms) {

Dear all, The default plotting method for hclust trees looks just fine for few objects like in the example dataset. But when it comes to many features (eg some 1000 and more - I'm trying to visualize clustered microarray data) it renders a tree, that one cannot inspect, because of overlapping text and lines. My question is, is there a way or a plotting parameter for plotting a tree which is

On 2 September 2016 at 14:54, Thomas Petzoldt wrote: | Hi, | | I have the same problem and, at a first look, the issues reported by the | CRAN checks seemed easy to fix. However, after checking it again locally | and on http://win-builder.r-project.org it appeared that GCC 4.9.3 | (Windows, Rtools 3.4), same also on win-builder reports even more | issues, especially legacy Fortran (mainly

Dear list - Does anyone have any ideas / comments about why I am receiving the following warning when I run lsoda: 1: lsoda-- at t (=r1), too much accuracy requested in: lsoda(start, times, model, parms) 2: for precision of machine.. see tolsf (=r2) in: lsoda(start, times, model, parms) I have tried changing both rtol and atol but without success. I saw the thread in the

I have a problem, that the plot of mathematical formula sometimes crashes R on Linux (SuSE 6.2 and 7.0 on a Dual PIII/500 machine with 1GB RAM). The problem occurs for example in demo("graphics"), i.e. in the last part were the mathematical symbols are plotted. There are several circumstances to reproduce this segmentation fault, but the following is one of the most simple examples. The

Dear R developers, I found a small issue while plotting contours of data containing both "usual" and "very small" numbers. It appeared with both R 3.0.1 and R-Devel on Windows, and I could reproduce it on Linux. Would it be possible to solve this before the upcoming release? Thanks a lot for developing this great software! Thomas Example: ######## set.seed(357) z1 <-