search for: mtmorgan

...58) ==25398== by 0x4E7B430: do_bind (bind.c:1113) ==25398== by 0x4F42A1B: do_internal (names.c:1116) ==25398== by 0x4EF959B: Rf_eval (eval.c:463) ==25398== by 0x4EF9F91: Rf_applyClosure (eval.c:666) gdb says (gdb) backtrace #0 0x00002b2dfe6940c9 in duplicate1 (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:134 #1 0x00002b2dfe694035 in Rf_duplicate (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:115 #2 0x00002b2dfe632555 in cbind (call=0xaaba48, args=0xb6abf0, mode=19, rho=0xb6ba40, deparse_level=1) at /home/mtmorgan/src/R-devel/src/main/b...

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: implicit declaration of function ?mktime? make[3]: *** [dounzip.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory `/home/mtmo...

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

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

...now" %in% row.names(old.packages()) [1] FALSE > library(snow) Error in library(snow) : package 'snow' does not have a NAMESPACE and should be re-installed > install.packages("snow", repos="http://cran.r-project.org") Installing package(s) into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/2.14' (as 'lib' is unspecified) trying URL 'http://cran.r-project.org/src/contrib/snow_0.3-5.tar.gz' Content type 'application/x-gzip' length 21059 bytes (20 Kb) opened URL ================================================== downloaded 2...

...lt;- function(...) .A() A NAMESPACE with import(methods) exportClasses("A") and DESCRIPTION Package: PkgA Type: Package Title: Documenting reference classes Version: 0.0.1 Date: 2012-08-05 Author: Martin Morgan Maintainer: Martin Morgan <mtmorgan at fhcrc.org> Description: This package implements a simple 'reference' class Depends: methods Imports: methods License: Apache License 2.0 Collate: binding.R R CMD INSTALL PkgA results in p$ R --vanilla CMD INSTALL PkgA * installing to library ?/home/mtmorgan/...

...otherwise) Martin Morgan ?On 5/6/20, 4:12 PM, "G?bor Cs?rdi" <csardi.gabor at gmail.com> wrote: AFAIK that API is not allowed on CRAN. It triggers a NOTE or a WARNING, and your package will not be published. Gabor On Wed, May 6, 2020 at 9:04 PM Martin Morgan <mtmorgan.bioc at gmail.com> wrote: > > 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...

...st one of economy, i.e., no use for the symbol in R routines, rather than for other nefarious reasons (?? some fundamental incompatibility with R?) I guess that most of my package users will have an R built without special attention to their lapack library, so will start with something like mtmorgan at gopher4:~> R CMD config LAPACK_LIBS -L/home/mtmorgan/arch/x86_64/R-devel/lib -lRlapack My R is built with --enable-R-shlib, so predictably enough R CMD INSTALL --clean <pkg> is 'successful' (zsysv_ is marked as unresolved in the <pkg>.so, but this doesn't stop compi...

...nce load for R Core, ...? Do we > know why? > > It sounds like it's a feature that is useful. I think we missed out on > some great enhancements in the past because of it not being part of the > public API. > > /Henrik > > On Wed, May 6, 2020, 16:26 Martin Morgan <mtmorgan.bioc at gmail.com> wrote: > > > 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 ca...

...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 https://github.com/mtmorgan/socketeer/blob/b0a1448191fe5f79a3f09d1f939e1e235a22cf11/src/connection.c#L169-L192 where connection_local_client() is called from R and _connection_local() creates and populates the appropriate structure. Probably I have done things totally wrong (e.g., by not checking the version of the API, as ad...

>>>>> 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...

--- On Sun, 13/2/11, Shing Hing Man <matmsh at yahoo.com> wrote: > From: Shing Hing Man <matmsh at yahoo.com> > Subject: Re: [R] Linked List in R > To: "Martin Morgan" <mtmorgan at fhcrc.org> > Date: Sunday, 13 February, 2011, 4:49 > Hi Martin, > ? Thanks for the pointer ! It seems quite involved to > create a > a linked list in the oo way. I need to read up on > environment. > > Thanks! > Shing > > > --- On Sun, 13/2/11, Martin M...

.../library? (as ?lib? is unspecified) Error in install.packages : Line starting '<!DOCTYPE HTML PUBLI ...' is malformed! The same error (with a different, XML response) is returned when using e.g. `https://cran.fhcrc.org`. Kevin On Tue, Aug 25, 2015 at 1:33 PM, Martin Morgan <mtmorgan at fredhutch.org> wrote: > On 08/25/2015 01:30 PM, Kevin Ushey wrote: >> >> Hi Martin, >> >> Indeed it does (and I should have confirmed myself with R-patched and >> R-devel >> before posting...) > > > actually I don't know that it does -- it a...

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 other platforms using libcurl): > > > > options(download.file.method = "lib...

...construction, is it a worry about maintenance load for R Core, ...? Do we know why? It sounds like it's a feature that is useful. I think we missed out on some great enhancements in the past because of it not being part of the public API. /Henrik On Wed, May 6, 2020, 16:26 Martin Morgan <mtmorgan.bioc at gmail.com> wrote: > 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?, >...

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 (for R version 3.1.1 Patched) but really the problem is that the package is not available at the specified repository (it is available, for the same versio...

After upgrading my servers to 2.14, log files were filled warnings that 'mem.limits' has been deprecated and to use gc instead. After reading the NEWS for R 2.14.0 and PR#14795 I learned that it is actually deprecated without replacement. Hereby I just want to voice that this function was actually in use by at least several users. Among other things, it is a useful to limit per-session

...nment 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 EDT 2010, Martin Morgan <mtmorgan at fhcrc.org> wrote: > On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote: >> Hi Martin, >> >> I am 100% sure that I set my 'PATH' environment variable >> correctly >> because all other packages can loaded correctly as well as >> because R can >>...

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) leads to incorrect dispatch (to the base class method). The attached package reproduces the problem. It has setClass("A") setClass("B", contains="A") setMethod("show", "A",

Full_Name: Ross Boylan Version: 2.10.0 OS: Windows XP Submission from: (NULL) (198.144.201.14) Some of the help for setGeneric seems to have been garbled. In the section "Basic Use", 5th paragraph (where the example counts as a single line 3rd paragraph) it says <quote> Note that calling 'setGeneric()' in this form is not strictly necessary before calling