similar to: Simplify and By Convert Factors To Numeric Values

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"

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

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

>>>>> 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, 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'd like to suggest the addition of an as.list method for a by object that actually returns a list of class "list". This would make it safer to do type-checking, because is.list also returns TRUE for a data.frame variable and using class(result) == "list" is an alternative that only returns TRUE for lists. It's also confusing initially that > class(x) [1]

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

I have a simple function : f <- function() { if(requireNamespace("ggplot2")) qplot(Sepal.Length, Petal.Length, data = iris, color = Species) else message("No graphics, just text.") } ggplot2 is in the Suggests field of the DESCRIPTION file. When I load the package, and run the function, I get an error : > f() Loading required namespace: ggplot2 Error in f()

Hello, I am writing an interface to some functions from the CRAN package pamr, which is poorly written. I have a S4 method I declared with setMethod. I'd like to provide a signature of "pamrtrained" which is the class of object that training creates. The last two lines of code of pamr.train are : class(junk) = "pamrtrained" junk How can I dispatch on these kinds

Good day, It is implemented by the CRAN package multicon. The function is named popsd. But it does seem like something R should provide without creating a package dependency. -------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

Hello, I have a minimal example that shows a problem I'm having with parallel processing. library(parallel) mcmapply(function(x, y) { print("Running") Sys.sleep(10) }, as.list(1:10), as.list(10:1), mc.cores = 16, SIMPLIFY = FALSE) I see "Running" printed once every ten seconds. I read the documentation for mcmapply, but I don't understand why it wouldn't

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 <-

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

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

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

Hello, The e1071 function naiveBayes gives an error when called by do.call, although it doesn't give any error if I call it manually. Browse[1]> trainParams at classifier function (x, ...) UseMethod("naiveBayes") <environment: namespace:e1071> Browse[1]> trained <- do.call(trainParams at classifier, paramList) Error in names(dimnames(tables[[i]])) <- c(Yname,

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)

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

Hello, With R version 3.0.2 Patched (2013-10-30 r64123) I don't see warnings that I get in R Under development (unstable) (2013-11-03 r64145) The warnings are like : Undocumented S4 methods: generic '[' and siglist 'BayMethList,ANY,ANY' The function actually looks like : setMethod("[", "BayMethList", function(x, i) { # Code to subset object. }