similar to: as.list method for by Objects

Dario, What version of R are you using. In my mildly old 3.4.0 installation and in the version of Revel I have lying around (also mildly old...) I don't see the behavior I think you are describing > b = by(1:2, 1:2, identity) > class(as.list(b)) [1] "list" > sessionInfo() R Under development (unstable) (2017-12-19 r73926) Platform: x86_64-apple-darwin15.6.0 (64-bit)

by() does not always return a list. In Gabe's example, it returns an integer, thus it is coerced to a list. as.list() means that it should be a VECSXP, not necessarily with "list" in the class attribute. Michael On Tue, Jan 30, 2018 at 2:41 PM, Herv? Pag?s <hpages at fredhutch.org> wrote: > Hi Gabe, > > Interestingly the behavior of as.list() on by objects seem to

I just meant that the minimal contract for as.list() appears to be that it returns a VECSXP. To the user, we might say that is.list() will always return TRUE. I'm not sure we can expect consistency across methods beyond that, nor is it feasible at this point to match the semantics of the methods package. It deals in "class space" while as.list() deals in "typeof() space".

>>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>> on Tue, 30 Jan 2018 10:37:38 -0800 writes: > I agree that it would make sense for the object to have c("by", "list") as > its class attribute, since the object is known to behave as a list. Well, but that (list behavior) applies to most non-simple S3 classed

Good day, The use of "rounding" also doesn't make sense. If The number is halfway between two integers, it is rounded to the nearest even integer. > round(2.5) [1] 2 -------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

On 01/30/2018 02:50 PM, Michael Lawrence wrote: > by() does not always return a list. In Gabe's example, it returns an > integer, thus it is coerced to a list. as.list() means that it should be > a VECSXP, not necessarily with "list" in the class attribute. The documentation is not particularly clear about what as.list() means for list derivatives. IMO clarifications

Hi Gabe, Interestingly the behavior of as.list() on by objects seem to depend on the object itself: > b1 <- by(1:2, 1:2, identity) > class(as.list(b1)) [1] "list" > b2 <- by(warpbreaks[, 1:2], warpbreaks[,"tension"], summary) > class(as.list(b2)) [1] "by" This is with R 3.4.3 and R devel (2017-12-11 r73889). H. On 01/30/2018 02:33 PM,

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"

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

Good day, Could the documentation of graphics devices give some explanation of how big the bitmap limits are? For example, > png("Figure1A.png", h = 7, w = 7, res = 1000, units = "cm") Results in Error: unable to start png() device, but the help page of devices doesn't explain that there are any limits or how they are determined. The wording of the error message could

Good day, I'm trying the example cl <- makeCluster(2, type = "SOCK") from the makeCluster documentation and the R command prompt never returns. I am using a 32-bit Windows 10 computer. The problem doesn't happen on another 64-bit Windows 10 computer but does happen on another 32-bit Windows 7 computer. Can anyone reproduce it? Are there any other options that can be passed to

I agree that it makes sense to expect as.list() to perform a "strict coercion" i.e. to return an object of class "list", *even* on a list derivative. That's what as( , "list") does by default: # on a data.frame object as(data.frame(), "list") # object of class "list" # (but strangely it drops the names)

Good day, I have been unable to solve this issue. Do you get grainy fonts when running the test case plot(1:10, main = "abcedfghijklmnopqrstuvwxyz", cex.main = 4, cex.lab = 4, cex.axis = 4) What version of libcairo is on your system ? -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Good day, If there's a library folder of the latest R packages and a particular package from it is loaded using the lib.loc option, the dependencies of that package are still attempted to be loaded from another folder of older packages specified by R_LIBS, which may cause errors about version requirements not being met. The documentation of the library function doesn't explain what the

Good day, Sometimes, sparse.model.matrix outputs a dgCMatrix which has column names consisting of factor levels that were not in the original dataset. The first factor appears to be correctly transformed, but the following factors don't. For example: diamonds <- as.data.frame(ggplot2::diamonds) > colnames(sparse.model.matrix(~ . -1, diamonds)) [1] "carat"

Hello, I have a seemingly simple problem that a tab-delimited file can't be read in. > annoTranscripts <- read.table("matched.txt", sep = '\t', stringsAsFactors = FALSE) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 5933 did not have 12 elements However, all lines do have 12 columns. > lines <-

>>>>> Benjamin Tyner >>>>> on Sat, 21 Jul 2018 13:42:43 -0400 writes: > Not sure whether it is the same issue as was raised here: > https://stat.ethz.ch/pipermail/r-devel/2010-October/058729.html > but in any case perhaps the problem could partially be remedied on line > 245 of src/library/base/R/library.R by passing the lib.loc to

>>>>> Benjamin Tyner >>>>> on Fri, 20 Jul 2018 19:42:09 -0400 writes: > Here's a trick/workaround; if lib.loc is the path to your > library, then prior to calling library(), >> environment(.libPaths)$.lib.loc <- lib.loc Well, that is quite a "trick" -- and potentially a pretty dangerous one, not intended when making

Hello, capture.output produces a different result if the S4 object was created with a constructor than if the body of the constructor is copied and pasted. setClass("TransformParams", representation( transform = "function", otherParams = "list") ) setGeneric("TransformParams", function(transform, ...) {standardGeneric("TransformParams")})

Note that there are at least 5 separate png() devices, so Linux was not using the (default) device used on Windows. In general, the device-limits info is not on the help page because we do not know it. On Windows the default device limits depend on the OS version, 32/64-bit, RAM and the graphics hardware. This sounds like the last: you were asking for 49 megapixels which is far larger than