search for: s4vector

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 'S4Vectors' Found more...

>>>>> 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 > --------- > getClass() issues the same warning twice: > tmp <- getClass("Annotated") > Found more than one class "Annotated" in cache; using the first, from...

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 for the normal...

Good day, If the library path is changed with .libPaths, the command install.packages("/nb/dario/Biostrings_2.39.9.tar.gz", repos=NULL) fails with ** testing if installed package can be loaded Error : package ?S4Vectors? required by ?Biostrings? could not be found However, running library(S4Vectors) followed by sessionInfo() after the error shows that the package can indeed be found by R R version 3.2.3 Patched (2016-02-14 r70170) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie...

...ses setClass("S4content",representation(content="ANY",add1="ANY",add2="ANY",type="character")) S4content <- function(obj=NULL,add1=NULL,add2=NULL,type="",...){ new("S4content",content=obj,add1=add1,add2=add2,type=type) } S4vector <- function(vec,...){ new("S4content",type="vector",content=vec,...) } ### Now the test > test <- rnorm(10000) > gc() used (Mb) gc trigger (Mb) Ncells 169135 4.6 531268 14.2 Vcells 75260 0.6 786432 6.0 > (system.time(lapply(test,S3vect...

...splaying 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 arrays. Michael On Sun, Jul 7, 2019 at 4:44 PM Abby Spurdle <spurdle.a at gmail.com> wrote: > > > I am not sure if there is an existing solution to this, but I want my S4 > > objects inside a list matrix...

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 <- ifelse(mymat==1L, lowerChars, chars) keep <- mymat > 0L charList <- split(chars[keep], ro...

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

...0-17 [5] gsl_1.9-10 mvtnorm_1.0-3 grid_3.2.0 stats4_3.2.0 [9] lattice_0.20-31 stabledist_0.7-0 fortunes_1.5-2 On Wed, Oct 7, 2015 at 9:52 PM, Cook, Malcolm <MEC at stowers.org> wrote: > 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-bounce...

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

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...

...07:00, Dario Strbenac wrote: > Good day, > > If the library path is changed with .libPaths, the command > > install.packages("/nb/dario/Biostrings_2.39.9.tar.gz", repos=NULL) > > fails with > > ** testing if installed package can be loaded > Error : package ?S4Vectors? required by ?Biostrings? could not be found > > However, > > running library(S4Vectors) followed by sessionInfo() after the error shows that the package can indeed be found by R > > R version 3.2.3 Patched (2016-02-14 r70170) > Platform: x86_64-pc-linux-gnu (64-bit) > Runn...

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 : Version 1.0 installed in /Library/Frameworks/R.framework.develMav/Versions/3.2/Resources/library Version 1.29.17 available at http://bioconductor.org/packages/3.1/bioc Update (y/N/c)? y also installing the dependencies ?IRanges?, ?BiocGenerics?, ?Biobase?, ?GenomeInfoDb?, ?DBI?, ?RSQLite?, ?S4Vectors? trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.1.35.tgz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.1.35.tgz' In addition: Warning mes...

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

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

...having done super much in the way of benchmarking). What exactly is as.altrep doing? Best, ~G On Tue, Jul 23, 2019 at 9:54 AM Michael Lawrence via R-devel < r-devel at r-project.org> wrote: > Hi Kylie, > > As an alternative in the short term, you could consider deriving from > S4Vector's List class, implementing the getListElement() method to > lazily create the objects. > > Michael > > On Tue, Jul 23, 2019 at 9:09 AM Bemis, Kylie <k.bemis at northeastern.edu> > wrote: > > > > Hello, > > > > I was wondering if there were any pla...

...thods (see ?cBind) I defined >> rbind2 and cbind2 instead: >> > This needs some clarification. It certainly is possible to > define cbind and rbind methods. The BiocGenerics package > defines generics for those and many methods are defined by > e.g. S4Vectors, IRanges, etc. The issue is that dispatch > on "..." is singular, i.e., you can only specify one class > that all args in "..." must share (potentially through > inheritance). > Thus, trying to combine objects from a > different hierarchy (o...

...t; Best, > > ~G > > > > On Tue, Jul 23, 2019 at 9:54 AM Michael Lawrence via R-devel < > > r-devel at r-project.org> wrote: > > > >> Hi Kylie, > >> > >> As an alternative in the short term, you could consider deriving from > >> S4Vector's List class, implementing the getListElement() method to > >> lazily create the objects. > >> > >> Michael > >> > >> On Tue, Jul 23, 2019 at 9:09 AM Bemis, Kylie <k.bemis at northeastern.edu> > >> wrote: > >>> > >&gt...

...will universally adopted in R 11.0.0 ;-) So if we have to do with what we have IMO (1) is the scheme that makes most sense although I agree that it can do some surprising things for some unusual combinations of vector lengths. It's the scheme I adhere to in my own binary operations e.g. in S4Vector::pcompare(). The modest proposal of the 'recycle0' argument is only to let the user switch from recycling scheme (2) to (1) if they're not happy with scheme (2) (I'm one of them). Switching to scheme (3) or to a new custom scheme would be a completely different proposal. >...