similar to: list2env() is broken

Hi, Currently object.size() is not very useful on environments as it always returns 56 bytes, no matter how big the environment is: env1 <- new.env() object.size(env1) # 56 bytes env2 <- new.env(hash=TRUE, size=75000000L) object.size(env2) # 56 bytes env3 <- list2env(list(a=runif(25000000), L=LETTERS)) object.size(env3) # 56 bytes This makes it pretty useless on

Hi Gabe, On 09/29/2015 02:51 PM, Gabriel Becker wrote: > Herve, > > The problem then would be that for A a refClass whose fields take up N > bytes (in the sense that you mean), if we do > > B <- A > > A and B would look like the BOTH take up N bytes, for a total of 2N, > whereas AFAIK R would only be using ~ N + 2*56 bytes, right? Yes, but that's still a *much*

Hi, 'R CMD build' (with R 2.12.0 RC) fails to clean the src/ folder on Windows: D:\biocbld\bbs-2.7-bioc>ls meat/BUS/src BUS.cpp BUS.h D:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\BUS * checking for file 'meat\BUS/DESCRIPTION' ... OK * preparing 'BUS': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package

Hi, The cleanup_pkg() function defined the big tools:::.build_packages() function in tools/R/build.R is currently broken. When Makefiles are used cleanup_pkg() doesn't clean anything because of the way system2() is called. For example, the call to Ssystem() on line 304 (Ssystem is a silent version of system2) is basically trying to do this: >

Hi, When 'x' is a vector of doubles, it's not clear how 'factor(x)' compares its values in order to determine the levels. For example, here all the values in 'x' are "conceptually" the same: x <- c(11/3, 2/3 + 4/3 + 5/3, 50 + 11/3 - 50, 7.00001 - 1000003/300000) However, due to machine rounding errors, they are not

I get this (with R-2.12 and R-2.13, didn't try with earlier versions): > max(c(NaN, NA)) [1] NA > max(c(NA, NaN)) [1] NaN I get the same thing with min(). The fact that the result of 'max(x)' or 'min(x)' depends on the order of the elements in 'x' is surprising. It also seems to contradict the man page: By definition the min/max of a numeric vector

Hi, According to its man page substring() "expands (its) arguments cyclically to the length of the longest _provided_ none are of zero length". So, as expected, I get an error here: > substring("abcd", first=2L, last=integer(0)) Error in substring("abcd", first = 2L, last = integer(0)) : invalid substring argument(s) But I don't get one here:

Hi, Today we've seen the following problem with the R-2.12 that we use for our Windows builds: > installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure was that 1 of the 890 packages currently installed on the machine (Windows Server 2003 R2) had its DESCRIPTION file empty:

Hi, On both Unix and Windows there is a mechanism to add variables to the environment when R is started. I noticed that, on Unix, this mechanism is not used when R is started normally at the command line but only when it's started using the 'R CMD' syntax. One problem with this is some lack of consistent cross-platform behaviour. For example: On Linux: $ echo $TEXINPUTS $

Hi, Already reported here: https://stat.ethz.ch/pipermail/r-devel/2010-September/058636.html but it doesn't seem to be related (at least not in an obvious way) to the problems described in that previous thread. So the problem is that, with recent versions of R 2.12 (i.e. current R-alpha but I've observed this with R-devel for at least 2-3 months now), 'R CMD build

Hi, Trying to access files on the ftp server at ftp.ncbi.nih.gov will either give a time out or sometimes even a segfault on Linux. The 2 following methods give the same results: f <- url("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", open="r") download.file("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", destfile=tempfile())

I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R on Ubuntu 8.1. I had no errors before! > install.packages("XML") Warning in install.packages("XML") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL

Hi, I just realized that a named empty list is displayed the same way as an empty list: > list(aa=2:5)[0] list() > list() list() For empty atomic vectors, the print method makes the difference: > c(aa=3L)[0] named integer(0) > integer(0) integer(0) Maybe lists could do that too? Thanks, H. > sessionInfo() R version 2.12.0 Under development (unstable)

Hi list, This looks similar to the problem reported here https://stat.ethz.ch/pipermail/r-devel/2006-April/037199.html by Henrik Bengtsson a long time ago. It is very sporadic and non-reproducible. Henrik, do you remember if your code was using reg.finalizer()? I tend to suspect it but I'm not sure. I've been hunting this bug for months but today, and we the help of other Bioconductor

Hi, After updating R-2.12 on the Bioconductor build system about 1 week ago (we update R every 4-6 weeks for our devel builds), we've started to see something never seen before on Windows: for some BioC packages, 'R CMD build' would produce no output at all (0 byte) and, of course, no source tarball. Even though, the code returned by the command is 0! See an example of this is here:

Hi, Installing from binaries on Windows: > install.packages("multtest") Warning: dependency 'Biobase' is not available trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip' Content type 'application/zip' length 1645590 bytes (1.6 Mb) opened URL downloaded 1.6 Mb package 'multtest' successfully unpacked

Hi, > x <- charToRaw("ABCDEFGx") > x[c(1:3, NA, 6)] <- x[8] *** caught segfault *** address 0x8402423f, cause 'memory not mapped' Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Cheers, H. > sessionInfo() R version 2.10.0 Under development

Not sure why the performance penalty of nonstandard evaluation would be more of a concern here than for something like switch(). If that can't/won't be fixed, what about fixing the man page so it's in sync with the current behavior? Thanks, H. On 05/03/2017 02:26 AM, peter dalgaard wrote: > The first line of stopifnot is > > n <- length(ll <- list(...)) > >

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, I'm subsetting a named vector using character indices. My vector of indices (or keys) is 10x longer than the vector I'm subsetting. All my keys are distinct and only 10% of them are valid (i.e. match a name of the vector being subsetted). It is surprisingly slow: x1 <- 1:1000 names(x1) <- paste("a", x1, sep="") keys <- sample(c(names(x1),