[Rd] Package Version Checking

This is a feature suggestion. My apologies if it's already been raised. I recently noticed that dplyr's behaviour has changed: > *dplyr 0.4.0* > df <- data_frame(x = c(1, 1, 1, 2, 2), y = 1:5) > result <- df %>% dplyr::distinct(x) %>% sum > *# result == 8* > > *dplyr 0.5.0* > df <- data_frame(x =

Re: [Rd] Crash after (wrongly) applying product operator on object from LIMMA package

Hi, following up on my own question, I found smaller example that does not require LIMMA: setClass("FOOCLASS", representation("list") ) ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10))) > ma * ma$M Error: C stack usage 7970512 is too close to the limit > library(xlsx) Loading

Re: [Rd] Crash after (wrongly) applying product operator on S4 object that derives from list

Dear Hilmar Perhaps this gives an indication of why the infinite recursion happens: ## after calling `*` on ma and a matrix: showMethods(classes=class(ma), includeDefs=TRUE, inherited = TRUE) Function: * (package base) e1="FOOCLASS", e2="matrix" (inherited from: e1="vector", e2="structur

Re: [Rd] R 3.4 has broken C++11 support

Hi! Well, my linux distribution has very recent versions of everything, so a working C++11 compiler exists: $ gcc --version | head -n1 gcc (GCC) 6.3.1 20170306 Could wrong ./configure options be at fault here? See: https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=r-devel#n40 My sessionIn

Re: [Rd] R 3.4 has broken C++11 support

On Wed, 2017-04-19 at 12:42 +0200, Angerer, Philipp wrote: > Hi! > > Well, my linux distribution has very recent versions > of everything, so a working C++11 compiler exists: > > $ gcc --version | head -n1 > gcc (GCC) 6.3.1 20170306 I am on Fedora 25 which also uses gcc 6.3.1. The default standa

Re: [Rd] R 3.4 has broken C++11 support

On Wed, 2017-04-19 at 13:17 +0200, Angerer, Philipp wrote: > Hmm, doesn’t look like my R was configured incorrectly: That looks fine. Can you please give a reproducible example of a package that compiles correctly on R 3.3.3 but not with R 3.4.0 or R- devel. Martyn > > > R is now configured fo

Re: [Rd] R 3.4 has broken C++11 support

On 19 April 2017 at 12:42, Angerer, Philipp via R-devel wrote: | Well, my linux distribution has very recent versions | of everything, so a working C++11 compiler exists: | | $ gcc --version | head -n1 | gcc (GCC) 6.3.1 20170306 | | Could wrong ./configure options be at fault here? See: | | htt

[Rd] ask.yes.no() function

As described in , R base functions are currently inconsistent in asking interactive "yes/no" type questions. One solution to this is to have a function to do it, and to use it consistently. Rather than just writing such a function a

[Rd] Default R-3.4.0 RC CXXFLAGS without -O2 on x86_64-linux-gnu with g++-5.4.0 causes WARNING from stl_list.h

Hi r-devel, a recent install of R-3.4.0 RC (2017-04-13 r72510)  on Linux (Ubuntu 16.04.1 LTS) x86_64-linux-gnu  with g++ (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609 (see  http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-NodeInfo.html  for more)  results in CXXFLAGS not containing

Re: [Rd] R 3.4 has broken C++11 support

Hmm, doesn’t look like my R was configured incorrectly: R is now configured for x86_64-pc-linux-gnu Source directory: . Installation directory:/opt/r-devel C compiler:gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-siz

Re: [Rd] Crash after (wrongly) applying product operator on S4 object that derives from list

I think this is a known issue with Java messing with the stack, see e.g. http://r.789695.n4.nabble.com/Error-memory-exhausted-limit-reached-td4729708.html. I'll fix the infinite recursion caused by the methods package. Michael On Wed, Apr 19, 2017 at 1:12 AM, Wolfgang Huber wrote: > Dear Hilma

Re: [Rd] Crash after (wrongly) applying product operator on S4 object that derives from list

We're working on a workaround for the JVM issue, it should be available in rJava soon. (the JVM issue is only on Linux and it turns infinite/deep recursion into a crash of R; it also effectively reduces the R stack size) Best Tomas On 04/19/2017 02:56 PM, Michael Lawrence wrote: I think thi

Re: [Rd] R 3.4 has broken C++11 support

Hi Dirk and Martyn, > That looks fine. Can you please give a reproducible example of a package > that compiles correctly on R 3.3.3 but not with R 3.4.0 or R-devel. here you go, it’s pretty much the simplest package possible that needs C++11: https://github.com/flying-sheep/cxx11test > Maybe yo

Re: [Rd] R 3.4 has broken C++11 support

On Wed, 2017-04-19 at 16:32 +0200, Angerer, Philipp wrote: > Hi Dirk and Martyn, > > > That looks fine. Can you please give a reproducible example of a > > package > > that compiles correctly on R 3.3.3 but not with R 3.4.0 or R-devel. > > here you go, it’s pretty much the simplest package possib

Re: [Rd] R 3.4 has broken C++11 support

FWIW works for me too, with or without my ~/.R/Makevars edd@max:~/git$ git clone https://github.com/flying-sheep/cxx11test Cloning into 'cxx11test'... remote: Counting objects: 13, done. remote: Compressing objects: 100% (10/10), done. remote: Total 13 (delta 0), reused 13 (delta 0), pack-reused

Re: [Rd] R 3.4 has broken C++11 support

Hi Philipp, Fellow Archlinux user here. I think the problem is with the r-devel PKGBUILD file, rather than anything wrong in R itself. The PKGBUILD file does this: ln -s /etc/R/${i} ${i} when it should do ln -s /etc/R-devel/${i} ${i} You can fix your installed version with cd /opt/r-devel/lib

[Rd] c documentation after change

In R 3.4.0 RC, argument list of 'c' as S4 generic function has become (x, ...) . However, "S4 methods" section in documentation of 'c' (c.Rd) is not updated yet. Also, in R 3.4.0 RC, 'c' method of class "Date" ('c.Date') is still not explicitly documented. ___

Re: [Rd] system/system2 and open file descriptors

In addition to the issue of a child process holding onto open files, the child process can also manipulate a file descriptor in a way that affects the parent process. For example, calling lseek() in the child process will move the file offset in the parent process. Here is a set of commands that d