similar to: install.packages() does not warn when 'lib' arg is missing on Linux or Windows

Hi, I'm running into a case where byte-compilation changes the semantic of a function. This is with R 3.4.0: foo <- function(x) { TRUE && x } foo(c(a=FALSE)) # [1] FALSE # OK foo(c(a=TRUE)) # [1] TRUE # OK foo(c(a=FALSE)) # a # ???? # FALSE The 3rd call returned a result that it different from the 1st call! After

Hi there, Is that change in R-devel intentional? library(Matrix) m <- as(matrix(c(0, 1)), "sparseMatrix") isS4(m) # [1] TRUE x <- I(m) # Warning message: # In `class<-`(x, unique.default(c("AsIs", oldClass(x)))) : # Setting class(x) to multiple strings ("AsIs", "dgCMatrix", ...); result will no longer be an S4 object

The warnings from make.packages.html() on the Apple Mac OS X platform can be dealt with as follows: ------------------------------------------------ (1) make.packages.html() uses the function tempdir() and attempts to create a temporary directory in the default location /tmp/ which fails due to the /tmp directory architecture on the Mac. I set up a .Renviron file in my user account

Hi Martin, On 10/26/20 04:52, Martin Maechler wrote: >> >> Hi there, >> Is that change in R-devel intentional? >> >> library(Matrix) >> m <- as(matrix(c(0, 1)), "sparseMatrix") >> >> isS4(m) >> # [1] TRUE >> >> x <- I(m) >> # Warning message: >> # In `class<-`(x,

Full_Name: Brian K. Boonstra Version: 2.2.1 OS: WinXP, OSX Submission from: (NULL) (63.172.178.137) The maxdrawdown function in tseries defines the maximum drawdown in terms of absolute dollars (or whatever units the input is in). Industry convention is to do this in percentage terms. I have written the code below as maximumdrawdown(), which retains backward compatibility with the current

Hi, Trying to compile one of the latest snapshot tarballs of R-devel gives me the following error (64-bit openSUSE 10.3): ... make[2]: Entering directory `/loc/home/biocbuild/bbs-2.4-bioc/R/src/library/Recommended' make[2]: *** No rule to make target `VR.ts', needed by `stamp-recommended'. Stop. make[2]: Leaving directory

Hi, The current implementation for utils::tar() seems to generate broken tarballs when some of the files to include in the tarball are >= 2GB. For example, when running 'R CMD build' on a big Bioconductor data package, we see this warning: * checking for file ?ChIPXpressData/DESCRIPTION? ... OK * preparing ?ChIPXpressData?: * checking DESCRIPTION meta-information ... OK *

Hi, I can't load XML_1.4-0.zip in last R devel (Windows): R version 2.5.0 Under development (unstable) (2007-01-05 r40386) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for

Hi, In the man page for vector(): length: A non-negative integer specifying the desired length. Double values will be coerced to integer: supplying an argument of length other than one is an error. Since long vectors are supported, it doesn't seem to be true anymore that "double values will be coerced to integer": > bigraw <-

thanks for your input Herv?. Glad to hear I'm not the only one still having this issue. In my opinion install.packages should stop with an error (instead of a warning) if this happens. However even if you want to keep the warning, at least make it so that users can set options(warn=2) to get an error if they want one. I tried setting options(warn=2) but for some reason I still get a warning.

Fine with me as long as eliminating the inconveniences associated with it can be put on the roadmap. The alias instability and the fact that the user has no way to know if s/he should do ?`foo,numeric-method` or ?`foo,numeric,ANY-method` to find the method has been a long-standing problem. H. On 3/21/19 21:29, Michael Lawrence wrote: If we started over, I'd try to avoid this sort of

The Bioconductor build for a package DirichletMultinomial on R Under development (unstable) (2013-02-26 r62077) -- "Unsuffered Consequences" at http://bioconductor.org/checkResults/devel/bioc-LATEST/DirichletMultinomial/george2-buildsrc.html shows * creating vignettes ... ERROR ... Error: processing vignette ?DirichletMultinomial.Rnw? failed with diagnostics: chunk 21 (label

Hi Michael, Thanks for looking into this. I suspect that truncation of ANY suffixes from method signatures is also the culprit behind the sudden breakage of aliases of the form \alias{foo,numeric-method} when a method without the ANY suffix in its signature gets added to the ecosystem. See my post about this to the Bioc-devel mailing list a couple of months ago:

Hi, The acrobatics that as.data.frame.factor() is going thru in order to recognize a direct call don't play nice if as.data.frame() is an S4 generic: ??? df <- as.data.frame(factor(11:12)) ??? suppressPackageStartupMessages(library(BiocGenerics)) ??? isGeneric("as.data.frame") ??? # [1] TRUE ??? df <- as.data.frame(factor(11:12)) ??? # Warning message: ??? # In

Hi Mehmet, On 11/29/2017 11:22 AM, Suzen, Mehmet wrote: > Hi Herve, > > I think you are confusing subclasses and classes. There is no > contradiction. `is` documentation > is very clear: > > `With one argument, returns all the super-classes of this object's class.` Yes that's indeed very clear. So if "list" is a super-class of "data.frame" (as

Hi, install.packages() seems to be broken in latest R-devel snapshot (2010-07-19 r52561) if you are using an R/R.version$platform-library/x.y directory. > .libPaths() [1] "/home/hpages/R/x86_64-unknown-linux-gnu-library/2.12" [2] "/home/hpages/R-2.12/library" > install.packages("car") Error in sprintf(gettext(fmt, domain = domain), ...) : too

> > Hi there, > Is that change in R-devel intentional? > > library(Matrix) > m <- as(matrix(c(0, 1)), "sparseMatrix") > > isS4(m) > # [1] TRUE > > x <- I(m) > # Warning message: > # In `class<-`(x, unique.default(c("AsIs", oldClass(x)))) : > # Setting class(x) to multiple strings ("AsIs",

Hi, Today I downloaded and compiled the last R-devel snapshot. The SVN-REVISION in the tarball contains the following: Revision: 36792 Last Changed Date: 2005-12-18 But after compiling on Unix (I compiled out of tree), I ended up with an SVN-REVSION file containing: Revision: unknown Last Changed Date: Today in the build tree. Then when I start R, I get: R : Copyright Today, The

Gabe, It's the current behavior of paste() that is a major source of bugs: ## Add "rs" prefix to SNP ids and collapse them in a ## comma-separated string. collapse_snp_ids <- function(snp_ids) paste("rs", snp_ids, sep="", collapse=",") snp_groups <- list( group1=c(55, 22, 200), group2=integer(0), group3=c(99,

Hi, I created a package as follows: > a = 1 > package.skeleton() Then I got the following output when building the package: * checking for file ?anRpackage/DESCRIPTION? ... OK * preparing ?anRpackage?: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a ?data/datalist?