Re: [Rcpp-devel] Locating an Instance of a Reference Class in the Environment

2023-03-24 Thread Dirk Eddelbuettel
On 24 March 2023 at 13:08, Matthew Supernaw - NOAA Federal wrote: | I'm sure it's possible to do from the R side, however, the requirement is to | hide this from the end user and set the reference objects name to the declared | name from the R environment. If I view the environment in RStudio,

Bug#1033410: RM: tiledb -- ROM as full builds not possible within Debian

2023-03-24 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The TileDB source package uses cmake and find_package for external resources; the upstream team maintaining the core library is going to switch to vcpkg soon. A full featured TileDB really needs the AWS SDK which we still do not have, would benefit from

Re: [Rcpp-devel] Locating an Instance of a Reference Class in the Environment

2023-03-23 Thread Dirk Eddelbuettel
On 22 March 2023 at 13:31, Matthew Supernaw - NOAA Federal wrote: | I'm trying to get an instance of a reference class (vonBertalanffyInterface) | from the R environment with the following code: | | void SetName(vonBertalanffyInterface& v) { | |     Rcpp::Environment env =

Re: [R-pkg-devel] DLL requires the use of native symbols

2023-03-20 Thread Dirk Eddelbuettel
d balances. (One micro nit for something else I noticed: you have a nice pkgdown site, but not linked to it anywhere.) Cheers, Dirk | | On 3/20/23 17:56, Dirk Eddelbuettel wrote: | > On 20 March 2023 at 12:43, Duncan Murdoch wrote: | > | It appears that you have some uses of .Call() where

Re: [R-pkg-devel] DLL requires the use of native symbols

2023-03-20 Thread Dirk Eddelbuettel
On 20 March 2023 at 12:43, Duncan Murdoch wrote: | It appears that you have some uses of .Call() where you are passing a | character variable as the first argument, instead of registering the | entry point and passing the variable containing the registration | information. Correct. And to

Re: [Rd] Request: better default R_LIBS_USER

2023-03-16 Thread Dirk Eddelbuettel
On 16 March 2023 at 17:15, Henrik Bengtsson wrote: | We're all starting out with a fresh R_LIBS_USER once a year when a new | minor version of R is released, Maybe not "we all". I don't, and I know other Linux users who don't force a rebuild unless needed (as with R 3.6.* -> R 4.0.0). R

Re: [Rd] Request: better default R_LIBS_USER

2023-03-16 Thread Dirk Eddelbuettel
On 16 March 2023 at 13:39, Felipe Contreras wrote: | I see R by default installs packages in ~/R. I know I can change the | default directory with R_LIBS_USER, but software shouldn't be | polluting the home directory. | | For example both python and node install packages to ~/.local/lib, | ruby

Bug#1032120: Upload of new upstream version before fix has migrated to testing (Was: Re: Bug#1032120: tiledb: uses atomic operations, but is not linked to libatomic)

2023-03-12 Thread Dirk Eddelbuettel
Why not wait a week on 2.15.0-1 which now 'Too young, only 4 of 10 days old'? Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1032120: Upload of new upstream version before fix has migrated to testing (Was: Re: Bug#1032120: tiledb: uses atomic operations, but is not linked to libatomic)

2023-03-12 Thread Dirk Eddelbuettel
Why not wait a week on 2.15.0-1 which now 'Too young, only 4 of 10 days old'? Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1032120: tiledb: uses atomic operations, but is not linked to libatomic

2023-02-28 Thread Dirk Eddelbuettel
Hi Graham, On 28 February 2023 at 19:36, Graham Inggs wrote: | Hi Dirk | | Thanks for the quick upload! | Already got a successful build of tiledb-py on riscv64[1]. | | On Tue, 28 Feb 2023 at 17:14, Dirk Eddelbuettel wrote: | > TileDB upstream does everything in CMake (which I do not fu

Bug#1032120: tiledb: uses atomic operations, but is not linked to libatomic

2023-02-28 Thread Dirk Eddelbuettel
Hi Graham, On 28 February 2023 at 19:36, Graham Inggs wrote: | Hi Dirk | | Thanks for the quick upload! | Already got a successful build of tiledb-py on riscv64[1]. | | On Tue, 28 Feb 2023 at 17:14, Dirk Eddelbuettel wrote: | > TileDB upstream does everything in CMake (which I do not fu

Bug#1032120: tiledb: uses atomic operations, but is not linked to libatomic

2023-02-28 Thread Dirk Eddelbuettel
(Whoops typed this hours ago but apparently did not send from Emacs. --D.) Hi Graham, On 28 February 2023 at 10:49, Graham Inggs wrote: | Source: tiledb | Version: 2.14.1-1 | Severity: serious | Tags: ftbfs patch | Control: affects -1 src:tiledb-py | | Hi Dirk | | TileDB uses atomic

Bug#1032120: tiledb: uses atomic operations, but is not linked to libatomic

2023-02-28 Thread Dirk Eddelbuettel
(Whoops typed this hours ago but apparently did not send from Emacs. --D.) Hi Graham, On 28 February 2023 at 10:49, Graham Inggs wrote: | Source: tiledb | Version: 2.14.1-1 | Severity: serious | Tags: ftbfs patch | Control: affects -1 src:tiledb-py | | Hi Dirk | | TileDB uses atomic

Re: [R-pkg-devel] Ignoring a compiler warning?

2023-02-27 Thread Dirk Eddelbuettel
On 27 February 2023 at 14:32, Duncan Murdoch wrote: | I am in the process of updating rgl to use the glad loader | (https://github.com/Dav1dde/glad). This replaces system standard gl.h | and glext.h files with new ones that include function pointers to be | filled in at run-time, so that rgl

Re: [Rcpp-devel] Problem with RCPP Paralell

2023-02-23 Thread Dirk Eddelbuettel
Hi Roberto, Very briefly: 1) We spell it Rcpp. Capital R, lowercase cpp. 2) The package you inquire about is called RcppParallel. 3) You didn't list the repo making it harder for us to help you. As a little bit of GitHub searching reveals, it is here

Re: [R-pkg-devel] Package submission rejected as it fails checks on Debian

2023-02-20 Thread Dirk Eddelbuettel
On 20 February 2023 at 22:37, Vasileios Nikolaidis wrote: | Thanks for taking the time to check it. The hint about the virtual | 'layer' class is valuable. | I will look into it. Sounds good, glad to have been of assistance. On a lark, I also tried your most recent CRAN release, and it

Re: [R-pkg-devel] Package submission rejected as it fails checks on Debian

2023-02-20 Thread Dirk Eddelbuettel
On 20 February 2023 at 21:41, Vasileios Nikolaidis wrote: | Oh yes thank you. I just realized I did not mention the repo on my | previous reply. It is | https://github.com/VNNikolaidis/nnlib2Rcpp Thanks for that -- I can confirm the error. The packages compiles all source files without issue

Re: [R-pkg-devel] Package submission rejected as it fails checks on Debian

2023-02-20 Thread Dirk Eddelbuettel
Can you share the repo URL? It may be a a fairly simple and standard issue some of us can spot easily. Hth, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list

Re: [Rcpp-devel] CRAN note about std::cout in shared library

2023-02-07 Thread Dirk Eddelbuettel
Hi Kassel, On 7 February 2023 at 02:57, Kassel Hingee wrote: | I'm running into CRAN check notes about std::cout being present in the Cpp code of a library I'm using. | | Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) | | It looks like Rcpp is automatically redirecting the std::cout

Re: [ESS] build problem

2023-02-05 Thread Dirk Eddelbuettel via ESS-help
On 5 February 2023 at 15:01, Sparapani, Rodney via ESS-help wrote: | I don�t have 28 on this machine. I am using 26 since there is not much | benefit upgrading. I am really sorry but I cannot let this stand. It is too close to FUD. As a general rule, newer *is* better. Features get added, bugs

Re: [Rcpp-devel] RInline::repl() issues

2023-02-03 Thread Dirk Eddelbuettel
Dominick, On 3 February 2023 at 20:02, Dominick Samperi wrote: | I'm sorry to say that the RInline::repl() issues are not resolved, and to | resolve them would likely require help from R core. | | Here's the test case: | library(sphereplot) | rgl.sphgrid(longtype="D") | | Under Linux there is

Re: [Rcpp-devel] R_Interactive vs R_NoEcho

2023-02-01 Thread Dirk Eddelbuettel
On 2 February 2023 at 16:02, Simon Urbanek wrote: | > On Feb 2, 2023, at 11:41 AM, Dirk Eddelbuettel wrote: | > Sounds like an r-devel question to me. Nothing Rcpp related here. Simon and | > Tomas both hang out here so if you are lucky they may see it. Else I'd try

Re: [Rcpp-devel] R_Interactive vs R_NoEcho

2023-02-01 Thread Dirk Eddelbuettel
On 1 February 2023 at 17:23, Dominick Samperi wrote: | Since I am not aware of an R-internals mailing list, and since this AFAIK there is no such mailing list. There is a manual of that name: https://rstudio.github.io/r-manuals/r-ints/ (nicer quarto rendered version) Or did you mean the

Re: [Rcpp-devel] Package RMD check warning

2023-01-30 Thread Dirk Eddelbuettel
On 30 January 2023 at 18:11, Zheng, Binghan wrote: | I’m preparing a package to be released through CRAN for Dr. Jacob Montgomery at WUSTL and I’m running into a warning that I can’t seem to resolve. | | The RCMD check is being run in R 4.2.2 on MacOS. | After running devtools::check() on the

Bug#1029917: r-cran-pbkrtest: Depends: r-cran-lme4 (>= 1.1.31) but it is not going to be installed

2023-01-28 Thread Dirk Eddelbuettel
On 29 January 2023 at 01:58, Adrian Bunk wrote: | Package: r-cran-pbkrtest | Version: 0.5.2-1 | Severity: serious | | The following packages have unmet dependencies: | r-cran-pbkrtest : Depends: r-cran-lme4 (>= 1.1.31) but it is not going to be installed | | You might want to reconsider | |

Bug#1029917: r-cran-pbkrtest: Depends: r-cran-lme4 (>= 1.1.31) but it is not going to be installed

2023-01-28 Thread Dirk Eddelbuettel
On 29 January 2023 at 01:58, Adrian Bunk wrote: | Package: r-cran-pbkrtest | Version: 0.5.2-1 | Severity: serious | | The following packages have unmet dependencies: | r-cran-pbkrtest : Depends: r-cran-lme4 (>= 1.1.31) but it is not going to be installed | | You might want to reconsider | |

Re: [Rcpp-devel] Rcpp_precious_remove again (Windows)

2023-01-23 Thread Dirk Eddelbuettel
Maintainer of affected package here: On 23 January 2023 at 12:20, Dominick Samperi wrote: | On the changes for R 4.2.0, it is not clear how to distinguish | R API functions from R internal functions (and this probably | doesn't matter for Rcpp), but you are correct, | on closer inspection these

Re: [Rd] Object are not destroy while using error (Rf_error)

2023-01-21 Thread Dirk Eddelbuettel
Antoine, I think there are few things going on here. One is that actual _R_ objects may only get destroyed when gc() gets called. Which we applications writer do not control. Another thing that may have an effect is the use of .C() which we all more or less moved away from. Anyway, if we

Re: [Rcpp-devel] Rcpp_precious_remove again (Windows)

2023-01-21 Thread Dirk Eddelbuettel
On 21 January 2023 at 10:53, Dominick Samperi wrote: | I've attached a version of RInside.cpp with my changes. The | _MSC_VER ifdefs are for Video Studio, which I am using for | debugging. I had some problems with gdb. We would love to take advantage of your hard and diligent work in trying to

Re: [R-pkg-devel] replacements of sprintf in compiled code

2023-01-21 Thread Dirk Eddelbuettel
On 21 January 2023 at 05:27, Duncan Murdoch wrote: | On 21/01/2023 5:15 a.m., Holger Hoefling wrote: | > Is there a simple replacement that I can use? | | You should use snprintf() which has an extra argument to state the size | of the buffer receiving the string. For example, | | char

Re: [Rcpp-devel] Rcpp_precious_remove again (Windows)

2023-01-20 Thread Dirk Eddelbuettel
On 20 January 2023 at 19:11, Dominick Samperi wrote: | You are right Dirk, RInside overrides what is specified because the function | myAskYesNo doesn't actually ask, so this explains why there is to | termination | prompt under Windows. This does not change what happens under Linux | because

Re: [Rcpp-devel] Rcpp_precious_remove again (Windows)

2023-01-20 Thread Dirk Eddelbuettel
On 20 January 2023 at 10:28, Tomas Kalibera wrote: | Executing then without R_LIBS set gave this error: | | " | Error: function 'Rcpp_precious_remove' not provided by package 'Rcpp' | In addition: Warning message: | In library(package, lib.loc = lib.loc, character.only = TRUE, | logical.return

Re: [Rcpp-devel] Rcpp_precious_remove again (Windows)

2023-01-19 Thread Dirk Eddelbuettel
On 19 January 2023 at 19:41, Dominick Samperi wrote: | I narrowed the problem down to the call to R_ReplDLLdo1() in RInside, and I | built R-4.3.0 pre-release version for Windows from source to investigate | further (online instructions by Tomas Kalibera were very helpful). Yes Tomas is a master

Re: [Rd] Problem installing gdb into Rtools42

2023-01-18 Thread Dirk Eddelbuettel
On 18 January 2023 at 22:44, Dominick Samperi wrote: | On second thought, there is a lot of metapramming code in Rcpp that runs | before main, so | I was wrong to say nothing can happen before main() is called. | Strategically placed print | statements may be the best strategy. Yes, and if you

Re: [Rcpp-devel] Rcpp_precious_remove again (Windows)

2023-01-17 Thread Dirk Eddelbuettel
Hi Dominick, First reflex: uh-oh as 'Rcpp_precious_remove' created some headaches for some people when mixing Rcpp and packages built with Rcpp but not the current one. We think all this got squared away an Rcpp release or two ago so as a first step please make sure _all_ involved packaes are

Bug#1028651: r-base-core: Unnecessary use of Perl in postinst

2023-01-14 Thread Dirk Eddelbuettel
On 14 January 2023 at 10:19, Gioele Barabucci wrote: | Package: r-base-core | Version: 4.2.2.20221110-1 | Tags: patch | | `r-base-core.postinst` uses Perl to set `$papersize` as a default | fallback in `Renviron`. | | Such simple processing can be achieved also with a very similar `sed` |

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

2023-01-12 Thread Dirk Eddelbuettel
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

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

2023-01-11 Thread Dirk Eddelbuettel
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: [R-pkg-devel] Current recommendations re. GitHub Action?

2023-01-02 Thread Dirk Eddelbuettel
As the error is common against your _all three_ of your Ubuntu runs, you could consider the possibility that the events are correlated. Most often it simply means a (temporary, usually) network or server outage. I would wait, and then relaunch (which these days you can do just for the failed

Re: [R-pkg-devel] How to reduce examples in a package that takes more than 5 seconds to run?

2022-12-28 Thread Dirk Eddelbuettel
On 27 December 2022 at 13:27, Duncan Murdoch wrote: | On 15/12/2022 10:25 a.m., Spencer Graves wrote: | > I know that some on this list do not like this construct, but it has | > helped me manage this problem for several years. NOTE: This CRAN | > function is NOT maintained by anyone on

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

2022-12-20 Thread Dirk Eddelbuettel
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 , MatSimple , const | MatSimple ) { | int rows = P.rows; | int nrhs = 1; | int lda = rows; | int

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

2022-12-18 Thread Dirk Eddelbuettel
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, at 8:41 AM, Dirk Eddelbuett

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

2022-12-18 Thread Dirk Eddelbuettel
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

Re: [Rcpp-devel] Printing intermediate values in C++ code used in Rcpp

2022-12-17 Thread Dirk Eddelbuettel
Good -- but next time you ask _when you already are N messages in on another help list_ have the courtesy to cross-reference the other thread. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ Rcpp-devel mailing list

Re: [Rcpp-devel] Printing intermediate values in C++ code used in Rcpp

2022-12-17 Thread Dirk Eddelbuettel
On 17 December 2022 at 17:29, Christofer Bogaso wrote: | Hi, | | I am working with a package called | | https://cran.r-project.org/src/contrib/GCPM_1.2.2.tar.gz | | The source code contains C++ codes which are available in the src folder. | | In this folder, the C++ codes are available in

Re: [R-pkg-devel] checking sizes of PDF files under‘inst/doc’ ... WARNING

2022-12-16 Thread Dirk Eddelbuettel
On 16 December 2022 at 20:30, EcoC2S - Irucka Embry wrote: | While running R CMD check on my iemisc package, I receive the following | warning: | | * checking sizes of PDF files under ‘inst/doc’ ... WARNING |‘gs+qpdf’ made some significant size reductions: | compacted

Bug#1022703: dieharder: Broken output or infinite loop after sts_runs test

2022-12-13 Thread Dirk Eddelbuettel
On 13 December 2022 at 14:23, Milan Broz wrote: | We have the same issue with empty lines, temporarily workarounded by adding -fcommon to CFLAGS (on several places) | (so yes, it was gcc-10 introduced problem). :-/ | But that off_t fix works too, thanks! But are you saying it is currently

Bug#1022703: dieharder: Broken output or infinite loop after sts_runs test

2022-12-12 Thread Dirk Eddelbuettel
On 12 December 2022 at 00:51, Bernhard Übelacker wrote: | Am 12.12.22 um 00:39 schrieb Dirk Eddelbuettel: | > | > On 11 December 2022 at 17:05, Bernhard Übelacker wrote: | > | On Mon, 24 Oct 2022 12:22:13 -0500 Dirk Eddelbuettel wrote: | > | > |diehard_birthdays| 0|

Bug#858488: dieharder segfaults when testing the XOR generator

2022-12-11 Thread Dirk Eddelbuettel
On 11 December 2022 at 22:39, Bernhard Übelacker wrote: | just for convenience: | https://github.com/eddelbuettel/rdieharder/issues/3 Yeah, but rather than piling up links to existing issue we could probably do with a fix. Ah well... Dirk -- dirk.eddelbuettel.com | @eddelbuettel |

Bug#1022703: dieharder: Broken output or infinite loop after sts_runs test

2022-12-11 Thread Dirk Eddelbuettel
On 11 December 2022 at 17:05, Bernhard Übelacker wrote: | On Mon, 24 Oct 2022 12:22:13 -0500 Dirk Eddelbuettel wrote: | > |diehard_birthdays| 0| 100| 100|0.99449351| PASSED | > | ###CUT OUT BY ME### | > | sts_runs| 2|10| 100|0.93620636

Re: [R-pkg-devel] Do you run R on Fedora or Debian?

2022-12-10 Thread Dirk Eddelbuettel
riends to make things per-session, or else you need to ask the user (once) and then store in user-supplied location. I think that was discussed here recently. Good luck, Dirk [1] Also commonly called 'attention deficit disorder' [2] A more user-friendly variant of tmux | Thanks, | | -Roy |

Re: [R-pkg-devel] Do you run R on Fedora or Debian?

2022-12-10 Thread Dirk Eddelbuettel
On 10 December 2022 at 14:00, Roy Mendelssohn - NOAA Federal via R-package-devel wrote: | CRAN has sent me a notice about the following: | | https://www.stats.ox.ac.uk/pub/bdr/donttest/rerddapXtracto.out | | I can not reproduce it. I test on my Mac, the cache space is properly handled (by

Bug#1025835: tiledb-py: build-depends on libtiledb-doc

2022-12-10 Thread Dirk Eddelbuettel
On 10 December 2022 at 22:38, Nilesh Patra wrote: | On Sat, Dec 10, 2022 at 07:56:52AM -0600, Dirk Eddelbuettel wrote: | > | > On 10 December 2022 at 09:07, Peter Green wrote: | > | Source: tiledb-py | > | Version: 0.18.2-1 | > | Severity: serious | > | Justification: rc polic

Bug#1025835: tiledb-py: build-depends on libtiledb-doc

2022-12-10 Thread Dirk Eddelbuettel
On 10 December 2022 at 22:38, Nilesh Patra wrote: | On Sat, Dec 10, 2022 at 07:56:52AM -0600, Dirk Eddelbuettel wrote: | > | > On 10 December 2022 at 09:07, Peter Green wrote: | > | Source: tiledb-py | > | Version: 0.18.2-1 | > | Severity: serious | > | Justification: rc polic

Bug#1025835: tiledb-py: build-depends on libtiledb-doc

2022-12-10 Thread Dirk Eddelbuettel
On 10 December 2022 at 09:07, Peter Green wrote: | Source: tiledb-py | Version: 0.18.2-1 | Severity: serious | Justification: rc policy - "Packages must be buildable within the same release" | x-debbugs-cc: e...@debian.org | User: debian...@lists.debian.org | Usertags: edos-uninstallable | |

Bug#1025835: tiledb-py: build-depends on libtiledb-doc

2022-12-10 Thread Dirk Eddelbuettel
On 10 December 2022 at 09:07, Peter Green wrote: | Source: tiledb-py | Version: 0.18.2-1 | Severity: serious | Justification: rc policy - "Packages must be buildable within the same release" | x-debbugs-cc: e...@debian.org | User: debian...@lists.debian.org | Usertags: edos-uninstallable | |

Re: [R-pkg-devel] Minimum macOS version ?

2022-12-08 Thread Dirk Eddelbuettel
Simon, On 9 December 2022 at 10:00, Simon Urbanek wrote: | the minimum required version for the high-sierra build is 10.13 and for big-sur build is 11.0 (as the names imply). Although it is not unrealistic to move Intel to macOS 10.14, it would be more problematic to move to 10.15 since it

[R-pkg-devel] Minimum macOS version ?

2022-12-08 Thread Dirk Eddelbuettel
One package I stand behind as maintainer does ## Take care of 10.14 requirement for Intel macOS if test x"${uname}" = x"Darwin" -a x"${machine}" = x"x86_64"; then AC_MSG_CHECKING([for Darwin x86_64 use minimum version override]) CXX17_MACOS="-mmacosx-version-min=10.14"

Re: [Rcpp-devel] C++ issue only spotted by CRAN and not locally or via rhub

2022-12-05 Thread Dirk Eddelbuettel
On 5 December 2022 at 16:34, Martyn Plummer wrote: | That's the good news. The bad news is that you have a lot of memory leaks, | so this is still not going to pass R CMD check with ASAN. You're going to | need Dirk's container. Yes, and I was actually pointing at Winston's container, and it too

Re: [Rcpp-devel] C++ issue only spotted by CRAN and not locally or via rhub

2022-12-05 Thread Dirk Eddelbuettel
On 5 December 2022 at 11:32, Sokol Serguei wrote: | I don't know what the exact source of this problem is but I can suggest | to use Armadillo which has a reputation to be better suited for | matrix/vector operation than plain Rcpp. I second that. Rcpp is great for what it does (easy

Re: [Rcpp-devel] Rcpp equivalent for Python?

2022-12-03 Thread Dirk Eddelbuettel
On 3 December 2022 at 15:08, Sparapani, Rodney wrote: | I have a tangential question. We have several R packages | based on Rcpp to call C++ code. Rcpp makes it so easy! | However, I am often asked by Python users: can we make | similar packages for that platform? I’m a newb with | respect to

Re: [R-pkg-devel] Two packages with the same name

2022-11-28 Thread Dirk Eddelbuettel
On 28 November 2022 at 12:15, Peter Carbonetto wrote: | I maintain the mashr R package (https://cran.r-project.org/package=mashr), | which has been on CRAN a little over 2 years. The mashr package depends on | another package, flashr, which is available from an external repository | (via

Re: [Rcpp-devel] Unaligned access [Was: Report of CRAN compilation problem and solution with architecture arm64]

2022-11-27 Thread Dirk Eddelbuettel
Juan, Further to Simon's comment, why is this on the rcpp-devel list? We have exactly zero choice over compiler and architecture use at CRAN. Maybe try r-devel and/or CRAN and/or R Core, but as Simon hinted that may be an uphill battle too. Best, Dirk -- dirk.eddelbuettel.com |

Re: [R-pkg-devel] Package submission error due to vignette

2022-11-22 Thread Dirk Eddelbuettel via R-package-devel
On 22 November 2022 at 14:15, Jaihee Choi wrote: | I was trying to resubmit a package but was notified that it did not pass | the initial checks due to the following error message regarding compiling | my vignette: | | Error: .onLoad failed in loadNamespace() for 'rje', details: | call:

Bug#1024628: ITP: r-cran-spdl -- GNU R package for spdlog wrapper

2022-11-22 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-spdl Version : 0.0.1 Upstream Author : Dirk Eddelbuettel * URL or Web page : https://cran.r-project.org/package=spdl * License : GPL (>= 2) Description : GNU R package for spd

Bug#1024628: ITP: r-cran-spdl -- GNU R package for spdlog wrapper

2022-11-22 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-spdl Version : 0.0.1 Upstream Author : Dirk Eddelbuettel * URL or Web page : https://cran.r-project.org/package=spdl * License : GPL (>= 2) Description : GNU R package for spd

Bug#1023731: BioC Transition blocked by new dependencies

2022-11-21 Thread Dirk Eddelbuettel
On 21 November 2022 at 16:39, Andreas Tille wrote: | Am Mon, Nov 21, 2022 at 03:05:26PM +0100 schrieb Sebastian Ramacher: | > On 2022-11-21 15:02:16 +0100, Andreas Tille wrote: | > > Some of the BioConductor packages need new dependencies. | > > I have pushed these to new queue and set the ITP

Bug#1023731: BioC Transition blocked by new dependencies

2022-11-21 Thread Dirk Eddelbuettel
On 21 November 2022 at 16:39, Andreas Tille wrote: | Am Mon, Nov 21, 2022 at 03:05:26PM +0100 schrieb Sebastian Ramacher: | > On 2022-11-21 15:02:16 +0100, Andreas Tille wrote: | > > Some of the BioConductor packages need new dependencies. | > > I have pushed these to new queue and set the ITP

Bug#1024399: xrprof: reproducible-builds: build path embedded in /usr/bin/xrprof

2022-11-18 Thread Dirk Eddelbuettel
Hi Vagrant, On 18 November 2022 at 11:49, Vagrant Cascadian wrote: | Source: xrprof | Severity: normal | Tags: patch | User: reproducible-bui...@lists.alioth.debian.org | Usertags: buildpath | X-Debbugs-Cc: reproducible-b...@lists.alioth.debian.org | | The build path is embedded in

Re: [R-pkg-devel] [UNCLASSIFIED] Remotes in description when submitting a package until a dependency is fixed

2022-11-16 Thread Dirk Eddelbuettel
On 16 November 2022 at 06:36, Duncan Murdoch wrote: | On 15/11/2022 11:59 p.m., Hugh Parsonage wrote: | > I think you've misunderstood that excerpt. By "temporary development | > state", it means _between_ CRAN releases; packages in a development | > state are not suitable for CRAN, as the

Re: [R-pkg-devel] How ton print in the console from Rcpp

2022-11-16 Thread Dirk Eddelbuettel
On 14 November 2022 at 16:34, Elysée Aristide wrote: | I was convinced that the issue is local. The warning message only appears | on MAC. | I did not try with another computer. I used CRAN macbuilder service and got | the warning message. I guess this is also the computer CRAN uses. Some

Re: [R-pkg-devel] How ton print in the console from Rcpp

2022-11-14 Thread Dirk Eddelbuettel
Ivan, Thanks for following-up but I think this issue is local to the OP as R is already setup exactly that way to skip `assert()` in builds (in perfect congruence with the CRAN Repository Policy) edd@rob:~$ grep NDEBUG /etc/R/Makeconf R_XTRA_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG

Bug#1023947: ITP: r-cran-cvar -- GNU R package to Computed Expected Shortfall and Value at Risk

2022-11-12 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-cvar Version : 0.5 Upstream Author : Georgi N. Boshnakov * URL or Web page : https://cran.r-project.org/package=cvar * License : GPL (>= 2) Description : GNU R package to Compu

Bug#1023947: ITP: r-cran-cvar -- GNU R package to Computed Expected Shortfall and Value at Risk

2022-11-12 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-cvar Version : 0.5 Upstream Author : Georgi N. Boshnakov * URL or Web page : https://cran.r-project.org/package=cvar * License : GPL (>= 2) Description : GNU R package to Compu

Re: [R-pkg-devel] R, Rust and CRAN

2022-11-12 Thread Dirk Eddelbuettel
On 13 November 2022 at 08:15, Simon Urbanek wrote: | sorry, I think you misunderstood: CRAN machines have the compilers, but the packages were not detecting it properly and/or were violating the CRAN policies as noted, so that's why I was saying that it would make sense to have a unified

Re: [R-pkg-devel] R, Rust and CRAN

2022-11-12 Thread Dirk Eddelbuettel
On 12 November 2022 at 19:27, Jeroen Ooms wrote: | On Sat, Nov 12, 2022 at 12:49 AM Simon Urbanek | wrote: | > | > this does not directly address your question, but I think it would make a lot of sense to standardize the process, given how many issues there were with packages using Rust

Re: [R-pkg-devel] vignettes - size of pdf

2022-11-11 Thread Dirk Eddelbuettel
On 11 November 2022 at 16:06, Ivan Krylov wrote: | В Fri, 11 Nov 2022 12:54:52 + | "Grose, Daniel" пишет: | | > * checking sizes of PDF files under 'inst/doc' ... WARNING | > 'gs+qpdf' made some significant size reductions: | > compacted 'cpop.pdf' from 805Kb to 547Kb | > consider

Bug#1023549: ITP: r-cran-gbutils -- R CRAN Package with Utilities for Simulation, Plots, Quantile Functions and Programming

2022-11-06 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-gbutils Version : 0.5 Upstream Author : Georgi N. Boshnakov * URL or Web page : https://cran.r-project.org/package=gbutils * License : GPL (>= 2) Description : R CRAN Pack

Bug#1023549: ITP: r-cran-gbutils -- R CRAN Package with Utilities for Simulation, Plots, Quantile Functions and Programming

2022-11-06 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-gbutils Version : 0.5 Upstream Author : Georgi N. Boshnakov * URL or Web page : https://cran.r-project.org/package=gbutils * License : GPL (>= 2) Description : R CRAN Pack

Bug#576914: sm: Kindly include (german) translation in bookworm

2022-11-06 Thread Dirk Eddelbuettel
On 6 November 2022 at 14:25, Helge Kreutzmann wrote: | Dear sm maintainer(s), | The freeze for Debian bookworm is scheduled at the beginning of 2023. | Since 2010-04-08 this bug report with a german program translation is open. | | For the benefit of the (german speaking) users it would be

Re: [R-pkg-devel] Writing to users config directory for CRAN package

2022-11-05 Thread Dirk Eddelbuettel
On 5 November 2022 at 19:32, David Hugh-Jones wrote: | I'm considering submitting the package onetime ( | https://github.com/hughjonesd/onetime/) to CRAN. | | Onetime has functions for showing a message or warning only once (ever per | user). It does this by writing to a file in the user's

Re: [R-pkg-devel] Compiled code should not call non-API entry points in R

2022-11-03 Thread Dirk Eddelbuettel
On 3 November 2022 at 21:09, Andrew Simmons wrote: | I had some R code for dealing with connections, and I was using | summary.connection(). I rewrote it in C, so I was doing something more | like: | | #include | | Rconnection Rcon = R_GetConnection(file); | Rcon->description or Rcon->class |

Re: [Rcpp-devel] Something strange with the package check and calls to C abort

2022-10-31 Thread Dirk Eddelbuettel
On 31 October 2022 at 11:01, Kevin Ushey wrote: | For posterity, what machine are you compiling the package on? If you're | using a modern Linux system, it's possible the default compilation flags | are including stack protection code during compilation that might call | abort on error. See e.g.

Re: [Rcpp-devel] Something strange with the package check and calls to C abort

2022-10-29 Thread Dirk Eddelbuettel
On 29 October 2022 at 20:41, Juan Domingo Esteve wrote: | I am new to this list and I am using Rcpp for my first large and serious package, so No worries. "By construction" we all were at that point at some point in the past. | I apologize if probably this is a naive question, but I have

Bug#1022703: dieharder: Broken output or infinite loop after sts_runs test

2022-10-24 Thread Dirk Eddelbuettel
Hi Jakub, Thanks for taking the time to write a bug report! On 24 October 2022 at 13:10, Jakub Niemczuk wrote: | Package: dieharder | Version: 3.31.1.2-1 | Severity: important | X-Debbugs-Cc: jakubniemc...@gmail.com | | Dear Maintainer, | | Every time I try to use this package on my debian

Re: [R-pkg-devel] How ton print in the console from Rcpp

2022-10-22 Thread Dirk Eddelbuettel
On 20 October 2022 at 13:16, Elysée Aristide wrote: | Thank you very much for your answers. | | I finally noticed that the issue comes from the numerical optimization, in which I use the class MFuncGrad of the package RcppNumerical. Is there any problem in using this class? This is the only

Re: [Rcpp-devel] thread safety RNG

2022-10-21 Thread Dirk Eddelbuettel
Hi Konrad, I have been meaning to look at ast2ast for some time now but alas no time yet... On 21 October 2022 at 12:15, konrad wrote: | my package ast2ast includes currently some random number generation | functions (e.g. R::dunif) within the C++ code. | | So my question is whether the RNG

Re: [R-pkg-devel] How ton print in the console from Rcpp

2022-10-20 Thread Dirk Eddelbuettel
On 20 October 2022 at 14:46, Ivan Krylov wrote: | В Thu, 20 Oct 2022 12:43:30 +0200 | Elysée Aristide пишет: | | > What I understood is that it is better to use Rcpp functions. So I | > used: | > | > Rcpp::Rcout << "beta: \n"; | > Rcpp::print(betacpp); | > Rcpp::Rcout << "log-likelihood: " <<

Re: [R-pkg-devel] Invalid UTF-8

2022-10-18 Thread Dirk Eddelbuettel
On 17 October 2022 at 13:20, Göran Broström wrote: | Thanks Ivan, | | I found two simple ways to convert this old file to UTF-8: | | (i) In emacs, C-x f (default is utf-8) That's a good ti[. I had actually hand-edited two lines down to 'seven bits' instead of this. Umlaute, accents and

Bug#1017829: elpa-ess: emacs-gtk 28.1 install fails with installed elpa-ess

2022-10-15 Thread Dirk Eddelbuettel
Salut Seb, On 15 October 2022 at 10:16, Sébastien Villemot wrote: | Thank you for your feedback, and for the good work you put into this | package over the years! | | I’m going to take it over as you suggest. Awesome! As an Emacs user I look forward to many more years with ESS on Debian and

Bug#1017829: elpa-ess: emacs-gtk 28.1 install fails with installed elpa-ess

2022-10-15 Thread Dirk Eddelbuettel
Salut Seb, On 15 October 2022 at 10:16, Sébastien Villemot wrote: | Thank you for your feedback, and for the good work you put into this | package over the years! | | I’m going to take it over as you suggest. Awesome! As an Emacs user I look forward to many more years with ESS on Debian and

Bug#1017829: elpa-ess: emacs-gtk 28.1 install fails with installed elpa-ess

2022-10-14 Thread Dirk Eddelbuettel
Salut Seb, On 14 October 2022 at 20:10, Sébastien Villemot wrote: | Hi Dirk! | | Le dimanche 21 août 2022 à 09:17 -0500, Dirk Eddelbuettel a écrit : | > That is a problem, and it is somewhat know. ESS used to release every six or | > so months, now we are many years behind with no of

Bug#1017829: elpa-ess: emacs-gtk 28.1 install fails with installed elpa-ess

2022-10-14 Thread Dirk Eddelbuettel
Salut Seb, On 14 October 2022 at 20:10, Sébastien Villemot wrote: | Hi Dirk! | | Le dimanche 21 août 2022 à 09:17 -0500, Dirk Eddelbuettel a écrit : | > That is a problem, and it is somewhat know. ESS used to release every six or | > so months, now we are many years behind with no of

Bug#1021782: ITP: r-cran-rcppspdlog -- R package for spdlog C++ logging

2022-10-14 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-rcppspdlog Version : 0.0.8 Upstream Author : Dirk Eddelbuettel * URL or Web page : https://eddelbuettel.github.io/rcppspdlog/ * License : GPL (>= 2) Description : R package for spd

Bug#1021782: ITP: r-cran-rcppspdlog -- R package for spdlog C++ logging

2022-10-14 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-rcppspdlog Version : 0.0.8 Upstream Author : Dirk Eddelbuettel * URL or Web page : https://eddelbuettel.github.io/rcppspdlog/ * License : GPL (>= 2) Description : R package for spd

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

2022-10-13 Thread Dirk Eddelbuettel
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

Re: [Rcpp-devel] sourceCpp with RcppEigen?

2022-10-10 Thread Dirk Eddelbuettel
On 10 October 2022 at 09:16, Dirk Eddelbuettel wrote: | | On 10 October 2022 at 14:02, Sparapani, Rodney wrote: | | I’m wondering what it would take to make RcppEigen functions | | work wth sourceCpp? Please let me know. Thanks | | The standard one line: add`// [[Rcpp::depends(RcppEigen

Re: [Rcpp-devel] sourceCpp with RcppEigen?

2022-10-10 Thread Dirk Eddelbuettel
On 10 October 2022 at 14:02, Sparapani, Rodney wrote: | I’m wondering what it would take to make RcppEigen functions | work wth sourceCpp? Please let me know. Thanks The standard one line: add`// [[Rcpp::depends(RcppEigen)]]` We have been doing this in that very documented and visible way

Re: [Rcpp-devel] Use cholmod modify module in an Rcpp / RcppEigen package

2022-10-06 Thread Dirk Eddelbuettel
Salut Etienne, Sorry for missing this email yesterday. On 5 October 2022 at 12:35, etienne.c...@univ-eiffel.fr wrote: | I want to use the cholmod functions from the modify module https://github.com/PetterS/SuiteSparse/tree/master/CHOLMOD/Modify inside an Rcpp/RcppEigen R package. | | >From

Re: [ESS] Debian installation bug report with current package and Emacs 28.1

2022-09-28 Thread Dirk Eddelbuettel via ESS-help
Per the email I had referenced earlier and its schedule, ESS has now been removed from Debian 'unstable' ie the rolling top of the distribution. While the existing package in the stable release (as well as previous ones) is still there for manual installation, future releases will not contain

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