similar to: requiring NAMESPACE re-installation marked as old.packages?

The following code results in a seg fault. > sessionInfo() R version 2.6.0 Under development (unstable) (2007-06-21 r42013) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] stats graphics

as.factor / as.ordered is not written as a generic. This differs from as.numeric, as.matrix, and other as.*. The following seems to address this and does not break make check-all. FWIW, the patch is against r55563, because with r55564 I see /home/mtmorgan/src/R-devel/src/main/dounzip.c:75:15: error: storage size of ?dt? isn?t known /home/mtmorgan/src/R-devel/src/main/dounzip.c:88:5: warning:

R developers, I am trying to understand how symbols are resolved, so that I can configure a package that I contributed to, and so that I can provide guidance to (linux / OSX) users of the package. To be concrete, my package uses the LAPACK Fortran symbol zsysv. This is not in libRlapack, but is defined on my system in the library /usr/lib64/liblapack.so. * I suspect that the reason the symbol is

https://github.com/jimhester/archive was not allowed on CRAN when I submitted it 3 years ago due to this restriction. Being able to write custom connections is a useful feature for a number of applications, I would love this policy to be reconsidered. On Wed, May 6, 2020 at 10:30 PM Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote: > What's the gist of the problem of

yep, you're right, after some initial clean-up and running with or without --as-cran R CMD check gives a NOTE * checking compiled code File ?socketeer/libs/socketeer.so?: Found non-API calls to R: ?R_GetConnection?, ?R_new_custom_connection? Compiled code should not call non-API entry points in R. See 'Writing portable packages' in the 'Writing R

>>>>> Martin Morgan <mtmorgan at fredhutch.org> >>>>> on Mon, 11 May 2015 10:18:07 -0700 writes: > On 05/10/2015 08:19 AM, Martin Morgan wrote: >> Loading an S4 object from a file without first loading the library sometimes (?, >> the example below and actual example involves a virtual base class and the show >> generic)

In fact, this does reproduce on R-devel: > options(download.file.method = "libcurl") > options(repos = c(CRAN = "https://cran.rstudio.com/", CRANextra = + "http://www.stats.ox.ac.uk/pub/RWin")) > install.packages("lattice") ## could be any package Installing package into ?/Users/kevinushey/Library/R/3.3/library? (as ?lib? is

Hi Martin, It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. Thank you and Duncan so much for your great help. Howard On Tue Mar 30 18:12:54

Dear Luke and others, I have many R versions on my machine and want to start a particular one when snow builds its cluster. (The same version I start snow from.) It seems that everything is set up correctly in defaultClusterOptions: > mget(ls(defaultClusterOptions), defaultClusterOptions) $homogeneous [1] TRUE $manual [1] FALSE $master nodename "maya.unil.ch" $outfile [1]

The public connection API is defined in https://github.com/wch/r-source/blob/trunk/src/include/R_ext/Connections.h I'm not sure of a good pedagogic example; people who want to write their own connections usually want to do so for complicated reasons! This is my own abandoned attempt

In the context of installing a Bioconductor package using our biocLite() function, install.packages() warns > install.packages("RUVSeq", repos="http://bioconductor.org/packages/2.14/bioc") Installing package into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1-2.14' (as 'lib' is unspecified) Warning message: package 'RUVSeq' is not available

Thanks for the reports. Will look into it soon and report back. Luke Sent from my iPhone > On Jan 3, 2019, at 2:15 PM, Martin Morgan <mtmorgan.bioc at gmail.com> wrote: > > For what it's worth this also introduced > >> df = data.frame(v = package_version("1.2")) >> rbind(df, df)$v > [[1]] > [1] 1 2 > > [[2]] > [1] 1 2

Hi Martin, Indeed it does (and I should have confirmed myself with R-patched and R-devel before posting...) Thanks, and sorry for the noise. Kevin On Tue, Aug 25, 2015, 13:11 Martin Morgan <mtmorgan at fredhutch.org> wrote: > On 08/25/2015 12:54 PM, Kevin Ushey wrote: > > Hi all, > > > > The following fails for me (on OS X, although I imagine it's the same >

On Tue, Aug 25, 2015 at 10:33 PM, Martin Morgan <mtmorgan at fredhutch.org> wrote: > > actually I don't know that it does -- it addresses the symptom but I think there should be an error from libcurl on the 403 / 404 rather than from read.dcf on error page... Indeed, the only correct behavior is to turn the protocol error code into an R exception. When the server returns a status

During vignette generation on Windows, Sweave seems to clean up before all graphics files are completely processed. For instance, if tmp.Rnw is: \documentclass[12pt]{article} \begin{document} <<>>= bitmap("afile.png") plot(1:100) dev.off() @ \end{document} Then: C:\R\tmp>R CMD Sweave tmp.Rnw Writing to file tmp.tex Processing code chunks ... 1 : echo term verbatim

A post on the Bioconductor mailing list https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html suggests that install.packages now references .Rprofile (?), whereas in R-2-8 it did not. Is this intentional? The example is, in .Rprofile library(utils) install.packages("Biobase", repos="http://bioconductor.org/packages/2.4/bioc") then

A package uses VignetteEngine: knitr; the package itself does not Suggests: knitr, but it Suggests: BiocStyle which in turn Suggests: knitr. Nonetheless, R CMD check fails indicating that a package required for checking is not declared. Is it really the intention that the original package duplicate Suggests: knitr? This is only with a recent R. In detail, with $ Rdev --version|head -3 R Under

PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods indicates that one should setGeneric("unique") setClass("A") unique.A <- function(x, incomparables=FALSE, ...) {} setMethod(unique, "A", unique.A) Both S3 and S4 methods need to be exported in the NAMESPACE import(methods) S3method(unique, A)

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

Dear all, I had a R segmentation fault, and then invoked debug mode and ran step by step. When I reached "terms(Y~X1*X2*...*X16)", I would then have "segmentation" fault. However, if I just ran this under regular "R interactive" mode, it would be fine though taking long time. My questions are: 1. Is there a known limit of terms for a formula? 2. Why does the