Re: [Rd] ask.yes.no() function

On 20 April 2017 at 09:33, Michael Sumner wrote: | Perhaps worth pointing out "yesno" as a candidate: | | https://CRAN.R-project.org/package=yesno | Not really as i) base R will not have dependencies outside of it ii) more importantly, Duncan asked

Re: [Rd] tempdir() may be deleted during long-running R session

On 21 April 2017 at 15:13, Mikko Korpela wrote: | Despite my obvious failure to read the manual and report this properly, | I will try to make a case. I understand that data stored in a temporary | file may disappear, and for that reason using an alternative TMPDIR | might be advisable. However

Re: [Rd] tempdir() may be deleted during long-running R session

On 21 April 2017 at 10:34, frede...@ofb.net wrote: | Hi Mikko, | | I was bitten by this recently and I think some of the replies are | missing the point. As I understand it, the problem consists of these | elements: | | 1. When R starts, it creates a directory like /tmp/RtmpVIeFj4 | | 2. Right

Re: [Rd] tempdir() may be deleted during long-running R session

On 24 April 2017 at 12:34, frede...@ofb.net wrote: | As it is, I don't even know what distributions are affected. I'm not | sure how to look up the contents of a "default" configuration on other | distributions. So how do you think R can automate that? Hint: It can't. Dirk -- http://dirk.edde

Re: [Rd] tempdir() may be deleted during long-running R session

On 26 April 2017 at 08:29, Duncan Murdoch wrote: | This seems like the wrong approach. The problem occurs as soon as the | tempdir() gets cleaned up: there could be information in temp files | that gets lost at that point. So the solution should be to prevent the | cleanup, not to continue o

Re: [Rd] tempdir() may be deleted during long-running R session

On 26 April 2017 at 16:39, Tomas Kalibera wrote: | I agree this should be solved in configuration of | systemd/tmpreaper/whatever tmp cleaner - the cleanup must be prevented Yep. | in configuration files of these tools. Moving session directories under | /var/run (XDG_RUNTIME_DIR) does not se

Re: [Rd] xrealloc namespace conflict

On 11 May 2017 at 12:16, Patrick Perry wrote: | I've done a bit more investigation into this issue. Here is my current | understanding of the situation: | | 1. I have a package on CRAN (corpus-0.3.1) that passes tests on all | platforms except for Linux. | 2. My package defines a C function, "x

Re: [Rd] bug report: nlme model-fitting crashes with R 3.4.0

On 11 May 2017 at 10:17, Erwan Le Pennec wrote: | Dear all, | | I've stumbled a similar issue with the package cluster when | compiling the 3.4.0 version with the settings of Fedora RPM specs. | Compiling R with the default setting of configure yields a version that | works for clust

Re: [Rd] problem running test on a system without /etc/localtime

On 17 May 2017 at 03:35, Kirill Maslinsky wrote: | I'm packaging R for Sisyphus repository and package build environment, | by design, doesn't have /etc/localtime file present. This causes failure | with Sys.timeone during test run: [...] | It seems that the best solution will be to patch Sys.time

Re: [Rd] Rounding in print.summaryDefault()

On 28 May 2017 at 17:37, Arne Henningsen wrote: | Dear all | | I am happy that summary.default() no longer rounds since R 3.4.0. | | However, in R 3.4.0, in a few cases, print.summaryDefault() rounds the | mean value (and the median value) differently on my GNU/Linux machine | and on my colleagu

Re: [Rd] Creating a private CRAN with webpages

On 9 June 2017 at 02:44, Joshua Bradley wrote: | repo. I like the CRAN web pages that allow a user to browse the various | packages from a browser without having to first install them. I want to | duplicate the process that CRAN goes through when it generate the webpages. As your initial email co

Re: [Rd] Creating a private CRAN with webpages

On 9 June 2017 at 15:47, Prof Brian Ripley wrote: | On 09/06/2017 07:44, Joshua Bradley wrote: | > I'm not trying to create a mirror of the CRAN. I also do not want to create | > a "subset" of CRAN packages. Sorry if my explanation was confusing. There | > are internal proprietary R packages that

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

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] R_LIBS_USER on Ubuntu 16.04

On 3 July 2017 at 15:35, Stefan Lüdtke wrote: | the recent update to R-3.4.1 kind of screwed the path to the libraries | installed on a user basis. | | The previous version of the file /etc/R/Renviron had the following line | activated: | | R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-li

Re: [Rd] reproducible segmentation fault installing packages on FreeBSD 11.1

On 31 July 2017 at 19:38, Joseph Mingrone wrote: | This happens when attempting to install any package. There were no such | problems on 11.0. | | Some other ways to trigger the problem: [...] | trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_0.12.12.tar.gz' | [New LWP 100854 of process

Re: [Rd] Help to create bugzilla account

On 12 August 2017 at 15:10, luke-tier...@uiowa.edu wrote: | As the Python posts poitns out, it is possible to use alternate malloc | implementations, either rebuilding R to use them or using LD_PRELOAD. | On Ubuntu for example, you can have R use jemalloc with | | sudo apt-get install libjemalloc

Re: [Rd] Help to create bugzilla account

On 13 August 2017 at 15:15, Dmitriy Selivanov wrote: | Very interesting information about switching glibc malloc to jemalloc. | | So I see action plan as following: | |1. set up some benchmark (need to think about design) |2. Run it on ubuntu machine with default glibc malloc |3. Run

Re: [Rd] Missing y label

On 1 September 2017 at 14:28, Therneau, Terry M., Ph.D. wrote: | Martin, |Thanks for taking a quick look. Yes it looks like it must be something local. | I've done the following to make sure I have a clean box: |reboot |sudo apt-get update |sudo apt-get upgrade | | Rerun the "sv

Re: [Rd] Missing y label

On 1 September 2017 at 15:50, Therneau, Terry M., Ph.D. wrote: | The system admins here ... I suggest you get these local admins to help you. These CRAN repos for Ubuntu are used by thousands of people every day, and they "just work", for both the recent releases and the most recent LTS. Dirk

Re: [Rd] Suggestion: Create On-Disk Dataframes

On 4 September 2017 at 11:35, Suzen, Mehmet wrote: | It is not needed. There is a large community of developer using SparkR. | https://spark.apache.org/docs/latest/sparkr.html | It does exactly what you want. I hope you are not going to mail a sparkr commercial to this list every day. As the coun

Re: [Rd] R and Visual Studio

On 19 September 2017 at 12:53, lille stor wrote: | I am trying to build R using Visual Studio 2010 but without success. My question is if it possible build R with this compiler anyway? In general, no. [ I believe there is an exception if you're a true compiler expert and really know what you're

Re: [Rd] R and Visual Studio

On 19 September 2017 at 07:07, Dirk Eddelbuettel wrote: | [ I believe there is an exception if you're a true compiler expert and really | know what you're doing. No such person is part of the wider R community as | far as I know. ] This was missing an important qualifier for "

Re: [Rd] what do you think about write.table(... qmethod = "excel")?

On 19 September 2017 at 12:04, Paul Johnson wrote: | They showed me a CSV file from Excel that looked like this | | x1,x2,x3,x4 5 6 | fred,barney,betty,x | bambam,"fred,wilma",pebbles,y | | Note how the quotes only happen on row 2 column 2. I was surprised it | did that, but now I have some pres

Re: [Rd] Debate: Shall some of Microsoft R Open Code be ported to mainstream R?

On 29 October 2017 at 22:01, Kenny Bell wrote: | User here: incorporating Intel's MKL, as MRO does, would be a very welcome | addition. | | I was an MRO user before and it improved my experience with medium data | immensely. | | They did, however, leave behind bugs here and there, especially rel

Re: [Rd] Bug: Issues on Windows with SFN disabled

On 7 December 2017 at 17:56, Tomas Kalibera wrote: | | An update on this. Writing R Extensions does not recommend to have a | space character in R_HOME. This means that on Windows one either should | have SFN enabled (which is still the common case), or install into a | directory that does not

Re: [Rd] Bug: Issues on Windows with SFN disabled

On 8 December 2017 at 08:52, Kevin Ushey wrote: | For what it's worth, the Windows installers for other programming | language runtimes often install outside of Program Files, so at least | there is 'prior art' to motivate having R install directly into the | root of the home drive: | | - Act

Re: [Rd] OpenBLAS in everyday R?

Kenny, On 17 December 2017 at 09:28, Kenny Bell wrote: | Hi R-devel list, | | OpenBLAS is readily available for unix-likes: | | https://cloud.r-project.org/web/packages/gcbd/vignettes/gcbd.pdf Please consider re-reading this vignette of mine. BLAS is an interface, OpenBLAS is but one implement

Re: [Rd] Rcpp - Linking to DLL from another package?

(Moderately wrong list: r-package-devel for packaging questions, rcpp-devel for Rcpp questions) On 18 December 2017 at 13:24, Stravs, Michael wrote: | I am trying to make a package B that extends another package A. Package A uses Rcpp, and I want to extend a class X used there. It doesn't reall

Re: [Rd] Rcpp - Linking to DLL from another package?

On 18 December 2017 at 16:10, Jeroen Ooms wrote: | On Mon, Dec 18, 2017 at 2:40 PM, Dirk Eddelbuettel wrote: | > | > (Moderately wrong list: r-package-devel for packaging questions, rcpp-devel | > for Rcpp questions) | > | > On 18 December 2017 at 13:24, Stravs, Michael wrote: |

[Rd] Change in package.skeleton behavior from R 3.6.3 to R 4.0.0 ?

The Rcpp package and some related packages such as RcppArmadillo make use of (local) wrappers around the utils::package.skeleton() function for creating (basic yet functional) packages using Rcpp or RcppArmadillo. RStudio also exposes this under the graphical menu as a nice way to construct a pac

Re: [Rd] Change in package.skeleton behavior from R 3.6.3 to R 4.0.0 ?

On 6 June 2020 at 15:44, Duncan Murdoch wrote: | On 06/06/2020 3:06 p.m., Dirk Eddelbuettel wrote: | > | > The Rcpp package and some related packages such as RcppArmadillo make use of | > (local) wrappers around the utils::package.skeleton() function for creating | > (basic ye

Re: [Rd] Change in package.skeleton behavior from R 3.6.3 to R 4.0.0 ?

On 6 June 2020 at 15:53, Duncan Murdoch wrote: | This change happened in August, 2019, about 10 months ago. Perhaps this | message asking people to test R-devel is relevant: | | https://stat.ethz.ch/pipermail/r-devel/2020-May/079484.html Touche :) And fully agree. Rcpp's unit tests covered Rc

Re: [Rd] Possible Bug: file.exists() Function. Due to UTF-8 Encoding differences on Windows between R 4.0.1 and R 3.6.3?

On 10 June 2020 at 13:06, Juan Telleria Ruiz de Aguirre wrote: | I am having an issue with the renv package and R 4.0.1, which I | suspect is related to base R and not the renv package itself, as with | R 3.6.3 such an "error" does not appear. So a bug in `renv` as it does not account for change

Re: [Rd] Build a R call at C level

On 30 June 2020 at 14:42, Morgan Morgan wrote: | Thanks Jan and Tomas for the feedback. | Answer from Jan is what I am looking for. | Maybe I am not looking in the right place buy it is not easy to understand | how these LCONS, CONS, SETCDR...etc works. a) There are alternatives, and if memory s

Re: [Rd] Speed-up/Cache loadNamespace()

On 19 July 2020 at 20:47, Mario Annau wrote: | Am So., 19. Juli 2020 um 20:11 Uhr schrieb Hugh Parsonage < | hugh.parson...@gmail.com>: | > 3. Keep an R session running in perpetuity and source the scripts within | > that everlasting session | However, 3. sounds interesting - how would this work

Re: [Rd] CAR0 vs. EXTPTR_PTR

On 22 July 2020 at 16:29, William Dunlap via R-devel wrote: | I know that binary packages are R-version specific, but it was a bit | surprising that Rcpp 1.0.5 built with R-4.0.2 cannot be loaded into | R-4.0.0. | | % R-4.0.0 --quiet | > library(Rcpp, lib="lib-4.0.2") | Error: package or namespa

Re: [Rd] Rust bindings to nmath

On 1 September 2020 at 13:01, Richard Dodd wrote: | I needed some statistical functions for a project I was working on in | Rust, and I've used the R math library as a standalone solution. I That's its purpose as far as I can tell. We have provided it as a Debian package alongside the "normal" R

Re: [Rd] Rgui never processes ~/.Renviron

On 2 September 2020 at 23:38, Henrik Bengtsson wrote: | WORKAROUND: | Setting R_USER or HOME prior to calling Rgui will cause Rgui to | process ~/.Renviron, e.g. AFAICR one _always_ had to manually set $HOME on Windows as the convention of having it comes from the some other OSs and is not nativ

Re: [Rd] Issue with data() function

On 24 October 2020 at 05:28, Duncan Murdoch wrote: | they are and ignore the warnings about package size. I think that's a | negotiation you should have with R Core. s/R Core/CRAN/ ? Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __

Re: [Rd] vignettes present in 2 folders or won't work

The closest to a canonical reference for a static vignette is the basic blog post by Mark at https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/ which I follow in a number of packages. Back to the original point by Alexandre: No, I do _not_ think we can do

Re: [Rd] formatting issue with gcc 9.3.0 on Ubuntu on WSL2

On 17 November 2020 at 12:34, Bill Dunlap wrote: | I just got a new Windows laptop (i7, 10th generation CPU), installed | 'Windows Subsystem for Linux 2' and then installed Ubuntu 20.04 and | used 'apt-get install' to install packages that the R build seems | to require. In particular, I am usin

Re: [Rd] Two ALTREP questions

On 21 November 2020 at 20:56, Jiefei Wang wrote: | Hello, | | I have two related ALTREP questions. It seems like there is no way to | assign attributes to an ALTREP vector without using C++ code. To be more | specifically, I want to make an ALTREP matrix, I have tried the following R | code but

Re: [Rd] Ignore Sites Option For libPaths

On 8 December 2020 at 23:00, Dario Strbenac wrote: | Could .libPaths gain an option to ignore all values other than the user-specified new parameter? Currently, it takes the union of new and .Library and .Library.site and there is no way to turn it off. Are you use? It is constructed from loo

Re: [Rd] Ignore Sites Option For libPaths

On 9 December 2020 at 02:00, Dario Strbenac wrote: | That seems like a straightforward and reasonable thing to do, but: | | ~$ R_LIBS="/tmp" R_LIBS_SITE="/var" Rscript -e 'print(.libPaths())' | [1] "/dora/nobackup/biostat/Rpackages/v4" "/dora/users/course/splus/library/R" | [3] "/usr/lib/R/sit

Re: [Rd] Ignore Sites Option For libPaths

On 9 December 2020 at 09:49, Martin Maechler wrote: | Also, R allows the user to remove their own home directory, it | should also allow to get a .libPaths() which contains nothing compulsory | but R's own .Library {as only that can contain 'base' !} That would be a very nice-to-have feature! Bu

Re: [Rd] [External] R crashes when using huge data sets with character string variables

On 12 December 2020 at 21:26, luke-tier...@uiowa.edu wrote: | If R is receiving a kill signal there is nothing it can do about it. | | I am guessing you are running into a memory over-commit issue in your OS. | https://en.wikipedia.org/wiki/Memory_overcommitment | https://engineering.pivotal.io

Re: [Rd] URL checks

The idea of 'white lists' to prevent known (and 'tolerated') issues, note, warnings, ... from needlessly reappearing is very powerful and general, and can go much further than just URL checks. I suggested several times in the past that we can look at the format Debian uses in its 'lintian' packa

Re: [Rd] [External] brief update on the pipe operator in R-devel

On 12 January 2021 at 20:38, Iñaki Ucar wrote: | On Tue, 12 Jan 2021 at 20:23, wrote: | > | > After some discussions we've settled on a syntax of the form | > | > mtcars |> subset(cyl == 4) |> d => lm(mpg ~ disp, data = d) | > | > to handle cases where the pipe lhs needs to be passed to an

Re: [Rd] Inconsistency of c.Date: non-commutativity and non-integer Value

On 22 January 2021 at 21:35, Jens Heumann wrote: | Dear r-devel, | | Today I came across what I would call inconsistencies in the `c.Date` | method compared to what happens when concatenating other classes: 1. | Non-commutativity: The type in the arrangements of the elements does | matter (fi

[Rd] r-devel windows gcc10-UCRT machine questions

I saw two (unchanged, long-existing) tests of main fail narrowly on this new platform (relative to the tolerance argument set). Attempting to change the tolerance if .Platform$OS.type == "windows" failed (any idea why that test would evaluate to FALSE?). Could it be that capabilities("long.doub

Re: [Rd] Potential improvements of ave?

On 16 March 2021 at 10:50, Martin Maechler wrote: | I vaguely remember (from Luke's docs/presentation on ALTREP) | that there are some "missing parts" here. | One of them the not-existing R level functionality, another may be | the C code below R's is.unsorted() ... maybe is.unsorted() | could

Re: [Rd] boneheaded BLAS questions

Ben, This stuff has worked unchanged since the 1990s when we had a _really_ far sighted fellow in Debian come up with the 'switch the links' scheme which was (and is) subsequently deployed by many numerical applications within Debian, R and e.g. Octave included. And I used this ability to switc

Re: [Rd] boneheaded BLAS questions

On 17 March 2021 at 22:53, Ben Bolker wrote: |Thanks. I know it's supposed to Just Work (and I definitely | appreciate all the work that's gone into making it Just Work 99% of the | time!). And for what it is worth, the aforementioned 'switching from within' solution is using FlexiBLAS (n

Re: [Rd] boneheaded BLAS questions

On 18 March 2021 at 09:15, Tomas Kalibera wrote: | This is documented in R Admin manual, section A.3, and there is also | "configure --help". | | On my Ubuntu 20.04, using "--with-blas --with-lapack" when a BLAS/LAPACK | implementation is installed via "apt" works for me: | | with libblas3, l

[Rd] Possible x11 window manager window aggregation under one icon?

[ I hope the Subject: is arcane enough to reduce readership to a handful :) ] Running the default window manager in the Linux distribution I am running, multiple 'windows' of the same program are usually aggregated under one icon. I typically have numerous (gnome) terminals, several top-level em

Re: [Rd] Possible x11 window manager window aggregation under one icon?

(Group reply to three emails at once) On 22 March 2021 at 10:27, Balasubramanian Narasimhan wrote: | Confession: haven't done this in decades. Equally green here. | Isn't the usual way to use 'xwininfo' to figure out the information | about any X window and set a specific resource in the .X1

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 00:01, Ivan Krylov wrote: | The surrounding code and | | proved to be enough of an example. The following patch makes it | possible to group x11() windows on my PC with Xfce running: [...] | Some ver

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 22 March 2021 at 16:57, Dirk Eddelbuettel wrote: | | On 23 March 2021 at 00:01, Ivan Krylov wrote: | | The surrounding code and | | <https://tronche.com/gui/x/xlib/ICC/client-to-window-manager/wm-hints.html> | | proved to be enough of an example. The following patch makes it | | possi

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 13:18, Ivan Krylov wrote: | On Mon, 22 Mar 2021 16:57:48 -0500 | Dirk Eddelbuettel wrote: | | > Do you want to send a proper patch to bugzilla? | | Would be glad to, especially if we manage to solve that problem you | uncovered while I was asleep. | | On Mon, 22 Mar 2

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 07:44, Dirk Eddelbuettel wrote: | On 23 March 2021 at 13:18, Ivan Krylov wrote: | | Apparently Xfce uses libwnck [*] which groups windows by WM_CLASS in | | addition to WM_HINTS (as far as understand the code). | | | | Here is what GNOME Shell does [**] besides looking at

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 08:15, Dirk Eddelbuettel wrote: | Only one small downside: the regrouped icon switches to the old R icon (which | is probably the one we bitmapped). Would you know how we could force the new | one? Could well be my fault. =:-) I still ship /usr/share/icons/hicolor/48x48

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 17:13, Ivan Krylov wrote: | В Tue, 23 Mar 2021 08:58:49 -0500 | Dirk Eddelbuettel пишет: | | > I still ship /usr/share/icons/hicolor/48x48/apps/rlogo_icon.png which | > is from the 2012 patch, and I vaguely recall the .desktop file being | > unhappy without it. Re

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 09:38, Dirk Eddelbuettel wrote: | | On 23 March 2021 at 17:13, Ivan Krylov wrote: | | В Tue, 23 Mar 2021 08:58:49 -0500 | | Dirk Eddelbuettel пишет: | | | | > I still ship /usr/share/icons/hicolor/48x48/apps/rlogo_icon.png which | | > is from the 2012 patch, and I v

Re: [Rd] [Solved] Possible x11 window manager window aggregation under one icon?

-base (4.0.4-1.2010.3) groovy; urgency=medium * debian/r-base-core.dirs: Also create the directory usr/share/icons/hicolor/scalable/apps for the svg logo -- Dirk Eddelbuettel Tue, 23 Mar 2021 11:05:17 -0500 r-base (4.0.4-1.2010.2) groovy; urgency=medium * icon-class-patch/R.desktop: Add

Re: [Rd] [Solved] Possible x11 window manager window aggregation under one icon?

On 24 March 2021 at 10:30, Martin Maechler wrote: | For this reason I've committed to R (the trunk, i.e., R-devel, | for R 4.1.0 in a month or so) in svn rev 80110. I just saw that via the (still extremely helpful) RSS feed of SVN changes and then pulled. You may have missed that Ivan conclude

Re: [Rd] custom allocators, Valgrind and uninitialized memory

Andreas, Can you briefly describe what it is you are trying to do? In general, no R package would use valgrind directly; it is an optional debugger. Also note _Writing R Extensions_ has a few things to say about how memory destined for R object can and cannot be allocated -- I presume your cust

Re: [Rd] custom allocators, Valgrind and uninitialized memory

Andreas, Thanks for the clarification. On 26 March 2021 at 20:48, Andreas Kersting wrote: | Sure, let me try to explain: | | CRAN ran the tests of my package using R which was configured --with-valgrind-instrumentation > 0. Valgrind reported many errors related to the use of supposedly unini

Re: [Rd] R extension memory leak detection question

On 5 April 2021 at 18:27, xiaoyan yu wrote: | Thank you all for your help. | We embedded R in our program and found the memory in the process | accumulated while our expectation is that the memory will go down after | each R evaluation. | I started to write a test program with only a few lines of

Re: [Rd] [External] memory consumption of nested (un)serialize of sys.frames()

On 7 April 2021 at 16:06, Andreas Kersting wrote: | Hi Luke, | | Please see https://github.com/akersting/dumpTest for the package. | | Here a session showing my issue: | | > library(dumpTest) | > sessionInfo() | R version 4.0.5 (2021-03-31) | Platform: x86_64-pc-linux-gnu (64-bit) | Running un

Re: [Rd] Testing R build when using --without-recommended-packages?

On 4 May 2021 at 09:31, Henrik Bengtsson wrote: | I'm on Linux (Ubuntu 18.04). How do I check an R build when using | --without-recommended-packages? 'make check' assumes 'recommended' | packages are installed, so that fails without them available. [...] | BTW, isn't this a bug? Shouldn't this

Re: [Rd] Testing R build when using --without-recommended-packages?

On 4 May 2021 at 11:07, Henrik Bengtsson wrote: | Thanks, but I don't understand. That's what I usually do when I build | R with 'recommended' packages. But here, I explicitly do *not* want | to build and install 'recommended' packages with the R installation. | So, I'm going down the --without-

Re: [Rd] Testing R build when using --without-recommended-packages?

On 4 May 2021 at 11:25, Henrik Bengtsson wrote: | FWIW, | | $ ./configure --help | ... | --with-recommended-packages | use/install recommended R packages [yes] Of course. But look at the verb in your Subject: no optionality _in testing_ there. You obviously need to

Re: [Rd] Testing R build when using --without-recommended-packages?

On 4 May 2021 at 14:10, Gabriel Becker wrote: | A couple of things. Firstly, so far asI have ever heard, it's valid that a | package have hard dependencies in its tests for packages listed only in | Suggests. In fact, that is one of the stated purposes of Suggests. An | argument could be made, I

Re: [Rd] Testing R build when using --without-recommended-packages?

On 5 May 2021 at 05:42, Duncan Murdoch wrote: | I think it would be useful to issue some kind of warning if tests are | skipped. As mentioned earlier, this is impossible in user-contributed | packages, which can only return OK or ERROR from their tests. Seconded! Dirk -- https://dirk.eddel

Re: [Rd] {splines} package gone missing?

Randall, On 20 May 2021 at 07:12, Ben Bolker wrote: | splines is 'recommended' ( not sure about capitalization), not "base' If you install 'r-base' rather than just the narrower 'r-base-core' you also get 'r-recommended'. So please do that, or just do sudo apt install r-recommended The gra

[Rd] R-Forge http link redirection setup busted

(Sorry for posting here but the top-level r-forge page does not make it all that clear where to contact its admins.) When an old-style 'http' URL at r-forge is resolved / redirected to 'https', it is corrupted and the redirect breaks. That required a package re-upload for me a few days ago (as

Re: [Rd] R-Forge http link redirection setup busted

Hi Gennadiy, On 20 July 2021 at 10:25, Gennadiy Starostin wrote: | Thank you for your feedback. There was a misconfigured redirection | indeed. It should work well now. Fabulous, thanks as always. | The top page does say "If you experience any problems or need help you | can submit a suppor

Re: [Rd] Feature request: Change default library path on Windows

On 24 July 2021 at 15:53, Steve Haroz wrote: | I'd like to propose moving the default library install location on Windows from: | %USERPROFILE%/Documents/R | to some other location such as: | %USERPROFILE%/R Can you not set .Library.site in R_HOME/etc/Rprofile.site (or maybe setting R_LIBS_SITE

Re: [Rd] Rprofile.site function or variable definitions break with R 4.1

On 12 August 2021 at 15:19, Andrew Piskorski wrote: | Ok, but what's the recommended way to actually USE Rprofile.site now? | Should I move all my local configuration into a special package, and | do nothing in Rprofile.site except require() that package? Exactly as before. I set my mirror as I

Re: [Rd] [External] svd For Large Matrix

Dario, On 14 August 2021 at 00:00, Dario Strbenac via R-devel wrote: | Good day, | | Ah, I was confident it wouldn't be environment-specific but it is. My environment is | | R version 4.1.0 (2021-05-18) | Platform: x86_64-pc-linux-gnu (64-bit) | Running under: Debian GNU/Linux 10 (buster) |

Re: [Rd] [External] Re: Update on rtools4 and ucrt support

As I type this, we are eight messages into this thread -- but I am not sure it has been made clear what the actual contentious issues are. There appear to be two toolchains, and they appear to be interoperate (though Duncan stated he had issues with an (arguably demanding) package). Now, I have

Re: [Rd] Environment setting _R_CHECK_DEPENDS_ONLY_='true'

On 20 October 2021 at 09:31, Sebastian Meyer wrote: | If you set the environment variable inside a running R process, it will | only affect that process and child processes, but not an independent R | process launched from a shell like you seem to be doing here: Yes. That is somewhat common, i

Re: [Rd] How can a package be aware of whether it's on CRAN

This may be more of a question for r-package-devel than for r-devel. On 23 November 2021 at 14:11, Dipterix Wang wrote: | I recently received an email from Prof. Ripley. He pointed out that my package seriously violates the CRAN policy: "using 8 threads is a serious violation of the CRAN polic

Re: [Rd] How can a package be aware of whether it's on CRAN

On 23 November 2021 at 12:19, Hervé Pagès wrote: | But why would you need to check for anything in the first place? | | If you only use 2 cores in your examples, vignettes, and unit tests, 'R | CMD check' will run fine everywhere and not eat all the CPU power of the | machine where it's runnin

Re: [Rd] * checking CRAN incoming feasibility ... NOTE

On 26 November 2021 at 14:40, Witold E Wolski wrote: | I am submitting a package to CRAN and I am asked to fix 2 NOTE's | I am not sure how I should ask the following NOTE? | | | * this is package 'sigora' version '3.0.9' | * checking CRAN incoming feasibility ... NOTE | Maintainer: 'Witold Wol

Re: [Rd] * checking CRAN incoming feasibility ... NOTE

Hi Witold, On 26 November 2021 at 17:09, Witold E Wolski wrote: | We have been using the package at work since 2018. We made some | feature requests in 2019 to the maintainer and Author Amir B.K. | Foroushani and was so kind to | implement them for us and release a new version in 2019. But then

Re: [Rd] string concatenation operator (revisited)

On 8 December 2021 at 00:06, Simon Urbanek wrote: | Hence it's much easier to ban a package than to hack it out of R ;). Paging Achim for suggested `fortunes` inclusion. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-d

[Rd] Status of '=>'

R 4.1.0 brought the native pipe and the related ability to use '=>' if one opted into it by setting _R_USE_PIPEBIND_. I often forget about '=>' and sadly can never find anything in the docs either (particularly no 'see als' from '|>' docs) which is not all that heplful. Can we anticipate a chang

[Rd] R-devel tarball at ETH is zero

Dear Martin as our trusted ETH point person, I have some automated builders fall over as the tarball of R-devel is currently empty: edd@rob:/tmp$ wget https://stat.ethz.ch/R/daily/R-devel.tar.bz2 --2022-05-03 06:52:20-- https://stat.ethz.ch/R/daily/R-devel.tar.bz2 Resolving stat.ethz.ch (stat

Re: [Rd] R-devel tarball at ETH is zero

On 4 May 2022 at 11:32, Martin Maechler wrote: | I'm really sorry for this experience. Stuff happens -- thanks for fixing it. The weekly build for the rocker/drd container of r-devel (and r-patched) worked fine now that you restored the mirror, so big thanks! Dirk -- dirk.eddelbuettel.com |

Re: [Rd] CRAN webserver down

On 23 May 2022 at 10:29, peter dalgaard wrote: | Apparently resurrected now. As another maintainer told me, the submission page appears to be down. Going to https://cran.r-project.org/submit.html (and then refreshing over the stale iframe) gets me The webpage at https://xmpalantir.wu.a

Re: [Rd] How to access to internal header files

On 24 May 2022 at 15:23, Martin Maechler wrote: | Well, if you want to explore how R is written ... and that's the | only good reason for looking into such private header files ... | then get the sources of R and explore... | | The official sources (and even daily snapshots from both | "R-patche

Re: [Rd] Better 'undefined columns' error for data.frame

Andre, On 25 September 2022 at 18:09, GILLIBERT, Andre wrote: | Please, find the patch attached, based on the latest R SVN trunk code. Well the mailing list software tends to drop attachments. There is a reason all these emails suggest to use bugs.r-project.org. Dirk -- dirk.eddelbuettel.co

Re: [Rd] Proposal to limit Internet access during package load

Regarding 'system' libraries: Packages like stringi and nloptr download the source of, respectively, libicu or libnlopt and build a library _if_ the library is not found locally. If we outlaw this, more users may hit a brick wall because they cannot install system libraries (for lack of permissi

Re: [Rd] Rscript -e EXPR fails to launch if stdin is closed

On 10 October 2022 at 09:34, Henrik Bengtsson wrote: | Thank you Peter for the quick fix. Will this make it into R-patched | to become R 4.2.2 soon? I checked when you posted this and didn't reply -- but this is also not an issue for littler so if you need alternative there is one $ Rscript

[Rd] Repeated segfault at installing sysdata.rda with clang/san build

I have maintained two SAN/UBSAN builds (one gcc, one clang) for many years (even though I also happily use Winston's newer/bigger container and generally recommend its use) and still have GitHub actions build them on a weekly schedule (as they follow r-devel). The clang one started to fail a lit

Re: [Rd] Repeated segfault at installing sysdata.rda with clang/san build

y it suddenly appeared - perhaps some changes in toolchain or glibc? Yep. And as I had on schedule for some time with no issues it likely is external. No obvious how to minimize it to a smaller reproducible example though. Best, Dirk | Cheers, | Simon | | | > On 19/12/2022, a

Re: [Rd] F77_CALL(dgetrs) C++ call in R-devel

On 20 December 2022 at 12:33, Lars Relund wrote: | In my package, I have the method: | | /** Solve equations transpose(P)w = r. */ | int LASolveT(MatSimple &P, MatSimple &w, const | MatSimple &r) { | int rows = P.rows; | int nrhs = 1; | int lda = rows; | i

Re: [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack

On 11 January 2023 at 17:35, RICHET Yann wrote: | Thank you all, for these advices. | | So I try to fix OMP_THREADS, cleanup tests, and display explicitly what test is running by moving in tests/ instead of tests/testthat/... | Next step should be to investigate blocking test using a reporter (

Re: [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack

On 12 January 2023 at 08:54, RICHET Yann wrote: | Thank you, Dirk. | But I also tried with ccache, without fails... can you give some details about you reverse-depend configuration ? docker image ? Mine was a standard ubuntu 20.04 packages... Nothing special -- I just the standard functions in

<    1   2   3   4   5   6   7   8   9   10   >