similar to: Undocumented S4 method Warning For Bracket

Hi, While checking the package I am getting all the time the following complain about the function: Undocumented S4 methods: generic coerce and siglist matrix,Massvector I have not defined the function nowhere in the R files. My gues is that this has something to do with the following definition of the setAs function. setAs("matrix","Massvector" ,def=

Dear R-Devel subsriber, during the set-up of a package with a NAMESPACE I stumbled over the following warning during: R CMD check -l c:/R/package smem ## skipped output * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'show' and siglist 'equation' All user-level objects in a package (including S4 classes and methods) ## skipped output

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hey everyone.. been struggling with building a mailserver and i'm almost done. One of the last pieces is integrating dovecot with dspam so that I'm users can train their spam filters easily (sieve filtering is the last piece left.. that should be interesting.. lol) Anyway, I think i found an issue with memory allocation, and I'm not sure

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

Dear all, I am just writing the documentation file for S4 class 'QualTreeSet' and get the following warning with R CMD check: * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'initialize' and siglist 'QualTreeSet' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See the

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]

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 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, 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

>>>>> 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, 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 <-

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

>>>>> 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

Good day, The server administrator recently upgraded the operating system from Debian version 7 to version 8 and R from version 3.1.2 to version 3.2.2. The default font used in plots has changed and I've asked him to restore the previous font. What instructions should I tell him about restoring the font ? -------------------------------------- Dario Strbenac PhD Student University of Sydney

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")})

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()