[Rd] dist function in R is very slow

2017-06-17 Thread Moshe Olshansky via R-devel
Dear R developers, I am visualising high dimensional genomic data and for this purpose I need to compute pairwise distances between many points in a high-dimensional space (say I have a matrix of 5,000 rows and 20,000 columns, so the result is a 5,000x5,000 matrix or it's upper diagonal).Computi

[Rd] suggestion to fix packageDescription() for Windows users

2017-06-17 Thread Ben Marwick
Recently I was trying to cite a package where the authors have ä and ø in their names. I found that on Windows the citation() function did not return the authors' names at all, but on Linux there was no problem (sessionInfos at the bottom): On Windows, no author names are returned: #-

Re: [Rd] suggestion to fix packageDescription() for Windows users

2017-06-17 Thread Duncan Murdoch
On 17/06/2017 7:10 AM, Ben Marwick wrote: Recently I was trying to cite a package where the authors have ä and ø in their names. I found that on Windows the citation() function did not return the authors' names at all, but on Linux there was no problem (sessionInfos at the bottom): On Windows, n

Re: [Rd] suggestion to fix packageDescription() for Windows users

2017-06-17 Thread Ben Marwick
Hi Duncan, Thanks for your reply. Yes, it does seem to be specific to the CTYPE setting to Chinese on Windows. If I set it to English using Sys.setlocale() there is no problem, then back to Chinese and the authors disappear: Sys.setlocale("LC_ALL","English") citation("readr") #' To cite pac

Re: [Rd] R history: Why 'L; in suffix character‘L’ for integer constants?

2017-06-17 Thread Dirk Eddelbuettel
On 17 June 2017 at 06:40, Prof Brian Ripley wrote: | Also, int32_t | | - postdates R (it was introduced in C99, a few OSes having it earlier) | - is optional in the C99 and C11 standards (§7.20.1.1 in C11). Thanks for the C99 reference. Do you happen to know when it was added to C++? For the re

Re: [Rd] suggestion to fix packageDescription() for Windows users

2017-06-17 Thread Duncan Murdoch
On 17/06/2017 9:13 AM, Ben Marwick wrote: Hi Duncan, Thanks for your reply. Yes, it does seem to be specific to the CTYPE setting to Chinese on Windows. If I set it to English using Sys.setlocale() there is no problem, then back to Chinese and the authors disappear: Sys.setlocale("LC_ALL","Engl

Re: [Rd] dist function in R is very slow

2017-06-17 Thread Stefan Evert
> On 17 Jun 2017, at 08:47, Moshe Olshansky via R-devel > wrote: > > I am visualising high dimensional genomic data and for this purpose I need to > compute pairwise distances between many points in a high-dimensional space > (say I have a matrix of 5,000 rows and 20,000 columns, so the resul

Re: [Rd] suggestion to fix packageDescription() for Windows users

2017-06-17 Thread Ben Marwick
Thanks very much, I see your bug report here: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17291 On 18/06/2017 2:26 AM, Duncan Murdoch wrote: On 17/06/2017 9:13 AM, Ben Marwick wrote: Hi Duncan, Thanks for your reply. Yes, it does seem to be specific to the CTYPE setting to Chinese on

[Rd] Issue with memory deallocation/fragmentation on systems which use glibc

2017-06-17 Thread Dmitriy Selivanov
Hello mailing list. I'm writing to discuss issue which was already discussed here - https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14611 - OS doesn't shrink memory of the process. Thanks to Simon Urbanek for digging and explanation. However it was quite hard to find this topic after I've dis

Re: [Rd] dist function in R is very slow

2017-06-17 Thread Moshe Olshansky via R-devel
Hi Stefan, Thank you very much for pointing me to the wordspace package. It does the job a bit faster than my C code but is 100 times more convenient. By the way, since the tcrossprod function in the Matrix package is so fast, the Euclidean distance can be computed very fast: euc_dist <- function