similar to: R Package Installation Ignores libPaths Setting

You misunderstand what .libPaths does: it changes the path in the current session only. Installation uses a different R process. Set R_LIBS to change the library path for new sessions: see ?.libPath . On 18/02/2016 07:00, Dario Strbenac wrote: > Good day, > > If the library path is changed with .libPaths, the command > >

Good day, I believe from the documentation that folders in R_LIBS should appear in the output of .libPaths, but they do not. The documentation contains "The library search path is initialized at startup from the environment variable R_LIBS ..." However, $ export R_LIBS=/users/stgrad/dario/tmp/ $ Rscript -e ".libPaths()" [1] "/dskh/nobackup/biostat/Bioconductor"

Hi, It turns out that two packages (1 Bioconductor, 1 CRAN) define an S4 class called "Annotated": library(S4Vectors) # see (*) at bottom for how to install library(RNeXML) 1st issue --------- getClass() issues the same warning twice: tmp <- getClass("Annotated") Found more than one class "Annotated" in cache; using the first, from namespace

On 06/08/2018 10:15 AM, Michael Lawrence wrote: > There probably should be an abstraction for this. In S4Vectors, we > have extractROWS(). FWIW the code in S4Vectors that does what your subset_ROW() does is: https://github.com/Bioconductor/S4Vectors/blob/04cc9516af986b30445e99fd1337f13321b7b4f6/R/subsetting-utils.R#L466-L476 (This is the default "extractROWS" method.) Except

A generic for displaying an object in a cell would be a reasonable solution for this particular problem. However, as soon as you start treating these objects as data (like putting them into a matrix), you're likely going to want vectorized operations over them, which means formalized vector and matrix classes. S4Vectors in Bioconductor facilitates this for vectors, but not for higher-order

Malcolm, I tested the code on a clean R 3.2.0 session. Not even in RStudio, just to rule that out. > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5]

Works for me. Which shell are you using? Are you setting .libPaths elsewhere? Peter-Dalgaards-MacBook-Air:F pd$ R_LIBS=~/tmp Rscript -e '.libPaths()' [1] "/Users/pd/tmp" [2] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library" Peter-Dalgaards-MacBook-Air:F pd$ export R_LIBS=~/tmp

Dear R-devs, Below is a small example of what I am trying to achieve, that is trivial in R and I would like to learn how to do in C, for very large matrices: > (mymat <- matrix(c(1,0,0,2,2,1), nrow = 2)) [,1] [,2] [,3] [1,] 1 0 2 [2,] 0 2 1 And I would like to produce: [1] "a*C" "B*c" Which can be trivially done in R via something like: foo

Hi all, Is there a better to way to subset the ROWs (in the sense of NROW) of an vector, matrix, data frame or array than this? subset_ROW <- function(x, i) { nd <- length(dim(x)) if (nd <= 1L) { x[i] } else { dims <- rep(list(quote(expr = )), nd - 1L) do.call(`[`, c(list(quote(x), quote(i)), dims, list(drop = FALSE))) } } subset_ROW(1:10, 4:6) #> [1] 4 5 6

On 05/10/2015 7:24 PM, Matt Dowle wrote: > Joris Meys <jorismeys <at> gmail.com> writes: > >> >> Hi all, >> >> I have a puzzling problem related to nchar. In R 3.2.1, the internal > nchar >> gained an extra argument (see >> https://stat.ethz.ch/pipermail/r-announce/2015/000586.html) >> >> I've been testing code using the

I recently got a request to add head() and tail() methods for Surv objects, which is quite reasonable, but not unlike other requests for logLik,? vcov, extractAIC, ...?? What they all have in common is that are methods added since creation of the survival package, and that I didn't know they existed. To try and get ahead of the curve, is there a way to list names of all of the default

>>>>> Herv? Pag?s <hpages at fredhutch.org> >>>>> on Sun, 26 Jun 2016 13:21:00 -0700 writes: > Hi, > It turns out that two packages (1 Bioconductor, 1 CRAN) define an > S4 class called "Annotated": > library(S4Vectors) # see (*) at bottom for how to install > library(RNeXML) > 1st issue >

Hi all, this question has already been posted on stackoverflow, however without success, see also http://stackoverflow.com/questions/27886535/proper-way-to-use-cbind-rbind-with-s4-classes-in-package. I have written a package using S4 classes and would like to use the functions rbind, cbind with these defined classes. Since it does not seem to be possible to define rbind and cbind directly as S4

>>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>> on Sat, 24 Jan 2015 06:39:37 -0800 writes: > On Sat, Jan 24, 2015 at 12:58 AM, Mario Annau > <mario.annau at gmail.com> wrote: >> Hi all, this question has already been posted on >> stackoverflow, however without success, see also >>

To do this in C, it would probably be easier and faster to just do the string manipulation directly. Luckily, there are already packages that have done this for you. See an example below using the S4Vectors package. foo2 <- function(mymat, colnms, tilde=FALSE) { chars <- colnms[col(mymat)] lowerChars <- if (tilde) paste0("~", chars) else tolower(chars) chars <-

>>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>> on Sun, 1 Feb 2015 19:23:06 -0800 writes: > I've implemented the proposed changes in > R-devel. Minimally tested, so please try it. It should > delegate to r/cbind2 when there is at least one S4 > argument and S3 dispatch fails (so you'll probably want to

What other packages do you have loaded? Perhaps a BioConductor one that loads S4Vectors that announces upon load: Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' Maybe a red herring... ~Malcolm > -----Original Message----- > From: R-devel [mailto:r-devel-bounces at r-project.org] On Behalf Of Duncan > Murdoch > Sent:

Are you able to create a reproducible example, somehow? Thanks, Michael On Mon, Feb 9, 2015 at 2:28 PM, Mario Annau <mario.annau at gmail.com> wrote: > Hi Michael, > I've tested your change in r67699 (using r67773) and the function now > correctly dispatches to r/cbind2 within the R-session without > bind_activation(TRUE). However, running unit tests using R CMD check I

thanks for the tip Jan. However it would be nice if I didn't have to handle this myself for all of my packages. (and teach my students how to do that) BTW I tried to disable staged installation, and the issue still happens: th798 at cmp2986 MINGW64 ~/projects/max-generalized-auc (master) $ R_INSTALL_STAGED=FALSE R --vanilla -e

Hello, I see the following issue in R-devel since 'both' has become the default pkgType for binary platforms. update.packages() fails when you set options(repos). Looks like it is trying to download a tgz file from the src/contrib section of a repository (on a mac). To reproduce this you need to have an older version of AnnotationDbi installed, which I accomplished by faking it,