similar to: write.csv performance improvements?

Hi all, (and especially hi to Tomas Kalibera who accepted my patch sent yesterday) I believe that I have found another bug, this time in the substring function. The use case that I am concerned with is when there is a single (character scalar) text/subject, and many substrings to extract. For example substring("AAAA", 1:4, 1:4) or more generally, N=1000

On 2/20/19 7:55 PM, Toby Hocking wrote: > Update: I have observed that stringi::stri_sub is linear time complexity, > and it computes the same thing as base::substring. figure > https://github.com/tdhock/namedCapture-article/blob/master/figure-substring-bug.png > source: > https://github.com/tdhock/namedCapture-article/blob/master/figure-substring-bug.R > > To me this is a

Hi all, Several people have noticed that gregexpr is very slow for large subject strings when perl=TRUE is specified. - https://stackoverflow.com/questions/31216299/r-faster-gregexpr-for-very-large-strings - http://r.789695.n4.nabble.com/strsplit-perl-TRUE-gregexpr-perl-TRUE-very-slow-for-long-strings-td4727902.html - https://stat.ethz.ch/pipermail/r-help/2008-October/178451.html I figured out

Hi all, I'm on Ubuntu 18.04, running R-4.0.0 which I compiled from source, and using valgrind I am always seeing the following message. Does anybody else see that? Is that a known false positive? Any ideas how to fix/suppress? Seems related to TRE, do I need to upgrade that? (base) tdhock at maude-MacBookPro:~/R/binsegRcpp$ R --vanilla -d valgrind -e 'extSoftVersion()' ==9565==

Hello, I've been using R for about 3 years now and I'm pretty sure this is a bug. I'm using R 2.2.0. The way R is set up to get packages from CRAN using install.packages is really convenient --- if you are installing to your system's main package directory. However, I observe the following problem: I want package X but it requires package Y. Further, I have neither package

Dear R-devel, I am running mclapply with many iterations over a function that modifies nothing and makes no copies of anything. It is taking up a lot of memory, so it seems to me like this is a bug. Should I post this to bugs.r-project.org? A minimal reproducible example can be obtained by first starting a memory monitoring program such as htop, and then executing the following code while

Update: I have observed that stringi::stri_sub is linear time complexity, and it computes the same thing as base::substring. figure https://github.com/tdhock/namedCapture-article/blob/master/figure-substring-bug.png source: https://github.com/tdhock/namedCapture-article/blob/master/figure-substring-bug.R To me this is a clear indication of a bug in substring, but again it would be nice to have

It is known, with a known workaround, see e.g. https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt . Set suppressions in ~/.valgrindrc, e.g. the CRAN check machine has --suppressions=/data/blackswan/ripley/wcsrtombs.supp It is an issue in your OS (glibc), not TRE nor R. On 10/06/2020 00:21, Toby Hocking wrote: > Hi all, > > I'm on Ubuntu 18.04, running R-4.0.0 which I

Hi Hilmar and Ivan, I have used your code examples to write a blog post about this topic, which has figures that show the asymptotic time complexity of the various approaches, https://tdhock.github.io/blog/2023/df-partial-match/ The asymptotic complexity of partial matching appears to be quadratic O(N^2) whereas the other approaches are asymptotically faster: linear O(N) or log-linear O(N log N).

Hi all, I am having an issue related to installing packages on windows with R-3.6.0. When installing a package that is in use, I expected R to stop with an error. However I am getting a warning that the DLL copy was not successful, but the overall package installation IS successful. This is quite dangerous because the old DLL and the new R code could be incompatible. I am definitely not the

Well it's only a leak if you don't get the memory back after it returns, right? Anyway, one (untested by me) possibility is the copying of memory pages when the garbage collector touches objects, as pointed out by Radford Neal here: http://r.789695.n4.nabble.com/Re-R-devel-Digest-Vol-149-Issue-22-td4710367.html If so, I don't think this would be easily avoidable, but there may be

Dear R-devel, A number of people have observed anecdotally that read.csv is slow for large number of columns, for example: https://stackoverflow.com/questions/7327851/read-csv-is-extremely-slow-in-reading-csv-files-with-large-numbers-of-columns I did a systematic comparison of read.csv with similar functions, and observed that read.csv is quadratic time (N^2) in the number of columns N, whereas

Toby, > On Sep 2, 2015, at 1:12 PM, Toby Hocking <tdhock5 at gmail.com> wrote: > > Dear R-devel, > > I am running mclapply with many iterations over a function that modifies > nothing and makes no copies of anything. It is taking up a lot of memory, > so it seems to me like this is a bug. Should I post this to > bugs.r-project.org? > > A minimal reproducible

If anybody else has this issue, please add a comment on https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17478 so we are more likely to get R-core to address this. Thanks Toby On Tue, Jun 4, 2019 at 2:58 PM Pages, Herve <hpages at fredhutch.org> wrote: > On 5/31/19 08:41, Toby Hocking wrote:... > > In my opinion install.packages should stop with an error (instead of a >

Hi Toby, AFAIK it has not been addressed in R. You can handle the problem on your package side, see https://github.com/Rdatatable/data.table/pull/3237 Regards, Jan On Thu, May 30, 2019 at 4:46 AM Toby Hocking <tdhock5 at gmail.com> wrote: > > Hi all, > > I am having an issue related to installing packages on windows with > R-3.6.0. When installing a package that is in use, I

Dear WINE Users/Programmers/Developers, I am currently starting a new project called BoxOS. We are going to try port the WINE System to a FreeDOS Enviroment. Here is a more information on the project: The BoxOS Kernel is based upon FreeDOS Beta 7 ("SPEARS"). That version of FreeDOS includes the Kernel 2023b and sys updated to 2024h and the FreeCom 0.82 updated to 0.83beta28. We have

Hello all, I would like to recreate the plot shown here (from a useR 2009 presentation): http://www.agrocampus-ouest.fr/math/useR-2009/abstracts/pdf/Hocking.pdf I downloaded the code for that image, and discovered that it relies on external web services, and also having PERL installed on the computer. I believe this could be done "locally" using the "seqLogo"

thanks for the tip Jan. However it would be nice if I didn't have to handle this myself for all of my packages. (and teach my students how to do that) BTW I tried to disable staged installation, and the issue still happens: th798 at cmp2986 MINGW64 ~/projects/max-generalized-auc (master) $ R_INSTALL_STAGED=FALSE R --vanilla -e

I am sorry if this question is vague or uninformed. I am just learning R and struggling. I am using the book Hierarchical Modeling and Inference in Ecology and they provide examples of R code. I have the following code from the book but when I run it I don't get any output. I cannot get the values of 'out' to show up. Basically, I just want to see my estimates for b0,

Can someone please add documentation for that environment variable to Writing R Extensions? An appropriate place would be section https://cloud.r-project.org/doc/manuals/r-release/R-exts.html#Suggested-packages which already discusses _R_CHECK_DEPENDS_ONLY_=true [[alternative HTML version deleted]]