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

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

2022-09-26 Thread Dirk Eddelbuettel
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

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

2022-09-25 Thread Dirk Eddelbuettel
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 --

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

2022-09-13 Thread Dirk Eddelbuettel via ESS-help
A follow-up to this bug report: Due to the breakage caused by the (old) ess package, I (as maintainer of the Debian package) now received the note that the ess / elpa-ess packages will be archived away from Debian unstable as they make Emacs 28.1 uninstallable. So future Debian releases will

Re: [R-pkg-devel] Error checking in an independent C code and printing (perror, printf, etc.)

2022-09-07 Thread Dirk Eddelbuettel
On 7 September 2022 at 11:58, Ivan Krylov wrote: | there at all. On the other hand, my package that uses the | R_InitOutPStream and R_Serialize entry points seems to have passed the | CRAN review. A table of all public entry points including short | descriptions and whether they allocate could

Re: [R-pkg-devel] [Solved, sort-of] CRAN valgrind reports with zero leaks - actionable?

2022-08-29 Thread Dirk Eddelbuettel
Based on further (off-list) follow-ups with Simon and Uwe, the situation can now be summarized as follows: - there appears to be no word about non-leak errors reported by valgrind in the official documentation; I will have to plead that those with the power to amend these documents maybe

Re: [R-pkg-devel] CRAN valgrind reports with zero leaks - actionable?

2022-08-24 Thread Dirk Eddelbuettel
Dear CRAN Team, On 18 August 2022 at 06:55, Dirk Eddelbuettel wrote: | | [ Five days ago, I sent (most) of the message below to a CRAN team member. I | have not had a reply, and it now appears that we are asked to email here so I | am resending. ] An answer would be much appreciated after

Re: [R-sig-Debian] Font issue under X11() (Ubuntu 20.04)

2022-08-23 Thread Dirk Eddelbuettel
On 23 August 2022 at 15:04, Viechtbauer, Wolfgang (NP) wrote: | Hi all, | | Using R under (X)ubuntu 20.04 here. I just noticed that the equal symbol (and other symbols like <>) are hanging kinda low under X11(). For example, if I run this code: | | plot(NA, xlim=c(0,2), ylim=c(0,2)) |

Bug#1017684: tiledb-r: ftbfs on riscv64("undefined symbol: __atomic_compare_exchange_1")

2022-08-21 Thread Dirk Eddelbuettel
On 22 August 2022 at 10:20, Bo YU wrote: | Hi, | On Sun, Aug 21, 2022 at 09:41:39AM -0500, Dirk Eddelbuettel wrote: | > | >| Oh, yes, It is applied to debian/rules and I forget to mention it.:) | > | >No worries :) Do you have easy-enough access to the platform? Could you | >

Bug#1017684: tiledb-r: ftbfs on riscv64("undefined symbol: __atomic_compare_exchange_1")

2022-08-21 Thread Dirk Eddelbuettel
On 21 August 2022 at 22:27, Bo YU wrote: | Hi, | On Sun, Aug 21, 2022 at 09:14:14AM -0500, Dirk Eddelbuettel wrote: | >| > | >| >So what is the proper architecture name for riscv64, and please remind me | >| >what the best way to determine it is (uname -m ? Or uname

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

2022-08-21 Thread Dirk Eddelbuettel via ESS-help
Hi all, I just got a fresh (and detailed) bug reports at https://bugs.debian.org/1017829 which details issue with the package I look after ("frozen" at the last official release) and the current emacs-gtk 28.1. I find myself between a rock and a hard place here. I would prefer an updated

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

2022-08-21 Thread Dirk Eddelbuettel
Gregory, 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 official release. Your best bet may be to install directly from melpa and removing the package. I will bring this to the ESS list but last time this was

Bug#1017684: tiledb-r: ftbfs on riscv64("undefined symbol: __atomic_compare_exchange_1")

2022-08-21 Thread Dirk Eddelbuettel
On 21 August 2022 at 10:57, Bo YU wrote: | Hi, | On Sat, Aug 20, 2022 at 06:22:17PM -0500, Dirk Eddelbuettel wrote: | > | >On 19 August 2022 at 07:21, Bo YU wrote: | >| Source: tiledb-r | >| Version: 0.15.0-1 | >| Severity: normal | >| Tags: ftbfs, patch | >| User: debian-r

Bug#1017684: tiledb-r: ftbfs on riscv64("undefined symbol: __atomic_compare_exchange_1")

2022-08-20 Thread Dirk Eddelbuettel
On 19 August 2022 at 07:21, Bo YU wrote: | Source: tiledb-r | Version: 0.15.0-1 | Severity: normal | Tags: ftbfs, patch | User: debian-ri...@lists.debian.org | Usertags: riscv64 | X-Debbugs-Cc: debian-ri...@lists.debian.org | | Dear Maintainer, | | The tiledb-r has a ftbfs on riscv64 due to

Re: [Rcpp-devel] cost of .Call

2022-08-10 Thread Dirk Eddelbuettel
Hi Konrad, On 10 August 2022 at 08:22, konrad wrote: | I have a question regarding the cost of .Call. If I implement the | rosenbrock function in R and in Rcpp. The R version is substentially | faster then the C++ version. The Rcpp function is basically an R | function which calls the C++

Bug#1016880: fbasics: FTBFS on hppa - /usr/bin/ld: cannot find /usr/lib/gcc/hppa-linux-gnu/11/libgcc.a

2022-08-09 Thread Dirk Eddelbuettel
On 9 August 2022 at 10:27, John David Anglin wrote: | On 2022-08-08 8:17 p.m., Dirk Eddelbuettel wrote: | > Will I need an explicit depends or is gcc-12 now the default in unstable (as | > I suspect it is)? | It is now default. That's what I thought. I'll send up a -2 build.

Bug#1016880: fbasics: FTBFS on hppa - /usr/bin/ld: cannot find /usr/lib/gcc/hppa-linux-gnu/11/libgcc.a

2022-08-08 Thread Dirk Eddelbuettel
On 8 August 2022 at 19:53, John David Anglin wrote: | On 2022-08-08 3:32 p.m., Dirk Eddelbuettel wrote: | > The problem is the build now uses the gcc-12 toolchain. I think the R | > | build environment needs updating. | > | > Could you test with a local binary rebuild of r-base on

Bug#1016880: fbasics: FTBFS on hppa - /usr/bin/ld: cannot find /usr/lib/gcc/hppa-linux-gnu/11/libgcc.a

2022-08-08 Thread Dirk Eddelbuettel
On 8 August 2022 at 19:10, John David Anglin wrote: | Source: fbasics | Version: 3042.89.2-1 | Severity: normal | | Dear Maintainer, | | The fbasic build on hppa fails here: | gcc -shared -L/usr/lib/R/lib -o fBasics.so gld.o init.o nig.o -lblas -lgfortran -lm

Bug#1016688: dieharder -h segfaults

2022-08-05 Thread Dirk Eddelbuettel
On 5 August 2022 at 13:20, Milan Broz wrote: | Actually this patch is better, just displays usage and also check upper boundary (another segault with -d 10 ...) | | https://github.com/mbroz/dieharder/commit/7d60208c8a8beabe6d3d5a88399b83ebf03240a5 Thanks for both. I will try to fold

Re: [R-pkg-devel] No news entries found

2022-07-08 Thread Dirk Eddelbuettel
On 8 July 2022 at 14:23, Plamen Mirazchiyski wrote: | to what actual the problem is. Unfortunately, the r-svn repository on | GitHub does not have the possibility to report this as an issue. Please see https://bugs.r-project.org/but also see old mailing list (and elsewhere) posts on how

Bug#1013891: RM: foptions -- RoM: Retired upstream

2022-06-26 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The foptions package (binary: r-cran-foptions) is no longer on CRAN and can be removed from unstable as well. It had two dependencies (fasianoptions, fexoticoptions) which were already removed in #1013234 and #1013235. If needed, old versions remain at

Re: [Rcpp-devel] Help reading libzma file

2022-06-23 Thread Dirk Eddelbuettel
is part of that set. Portable development is hard for a reason. Operating systems are idiosyncratic. Dirk | | Em qui., 23 de jun. de 2022 às 07:59, Dirk Eddelbuettel | escreveu: | | > | > On 23 June 2022 at 10:05, Serguei Sokol wrote: | > | Le 23/06/2022 à 04:07, Roberto Spadim a écr

Re: [Rcpp-devel] Rcpp shared libraries (?)

2022-06-23 Thread Dirk Eddelbuettel
One belated follow-up: one can in general control visibility so - a function can be in C(++) and used by other C(++) functions (and we have examples) - a function can be exported to R easily via [[Rcpp::export()]] thanks to magic of Rcpp::compileAttributes() - a function can also be

Re: [Rcpp-devel] Help reading libzma file

2022-06-23 Thread Dirk Eddelbuettel
On 23 June 2022 at 10:05, Serguei Sokol wrote: | Le 23/06/2022 à 04:07, Roberto Spadim a écrit : | > Hi folks | > | > I have a .xz file and need to read it and "convert" to a DataFrame using | > Rcpp if possible. | > | > But... I'm with a problem (first time testing this) using liblzma with |

Bug#1013235: RM: fexoticoptions -- RoM: Retired upstream

2022-06-19 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The fexoticoptions package (binary: r-cran-fexoticoptions) is no longer on CRAN and can be removed from unstable as well. If needed, old versions remain at https://cran.r-project.org/web/packages/fExoticOptions/index.html Dirk -- dirk.eddelbuettel.com

Bug#1013234: RM: fasionoptions -- RoM: Retired upstream

2022-06-19 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The fasianoptions package (binary: r-cran-fasianoptions) is no longer on CRAN and can be removed from unstable as well. If needed, old versions remain at https://cran.r-project.org/web/packages/fAsianOptions/index.html Dirk -- dirk.eddelbuettel.com |

Re: [R-sig-Debian] How to open an access mdb using the rodbc package under Ubuntu 22.04

2022-06-17 Thread Dirk Eddelbuettel
Postscriptum: We absolutely don't mind helping here, use on Ubuntu is *very much* on charter for r-sig-deb (which is, loosely, for help with any .deb-based OS and R). However, the question really had little to do with the OS and a lot with 'how do I do OBDC' which Ivan answered admirably. Next

Re: [Rcpp-devel] Assertion error in ud_ep.c, when running with MPI

2022-06-14 Thread Dirk Eddelbuettel
On 14 June 2022 at 09:38, Serguei Sokol wrote: | Hi, | | Probably, this issue would be better posted here | https://github.com/openucx/ucx/issues Seconded. I don't have much to add: these MPI examples are ten years old, worked all the time as far as we know, and haven't changed. Maybe some

Re: [Rcpp-devel] [R-pkg-devel] moving from C to C++ with Rcpp in R package

2022-06-03 Thread Dirk Eddelbuettel
rcppsimdjson/src/simdjson_example.cpp:// [[Rcpp::export(.cppVersion)]] rcppsimdjson/src/simdjson_example.cpp:// [[Rcpp::export(.unsupportedArchitecture)]] edd@rob:~/git$ Hope this helps, Dirk | Thanks | Jean | | | > Le 2 juin 2022 à 15:49, Dirk Eddelbuettel a écrit : | >

Re: [Rcpp-devel] [R-pkg-devel] moving from C to C++ with Rcpp in R package

2022-06-02 Thread Dirk Eddelbuettel
On 2 June 2022 at 08:32, Dirk Eddelbuettel wrote: | | (Removed CC to r-package-devel) | | On 2 June 2022 at 16:24, Ivan Krylov wrote: | | Unfortunately, this means editing RcppExports.R, which (I think) | | prevents you from enjoying the way Rcpp::compileAttributes() sets | | everything up

Re: [Rcpp-devel] [R-pkg-devel] moving from C to C++ with Rcpp in R package

2022-06-02 Thread Dirk Eddelbuettel
(Removed CC to r-package-devel) On 2 June 2022 at 16:24, Ivan Krylov wrote: | Unfortunately, this means editing RcppExports.R, which (I think) | prevents you from enjoying the way Rcpp::compileAttributes() sets | everything up for you. Yes. I think that is the best I came up with once too in a

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

2022-05-24 Thread Dirk Eddelbuettel
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 |

Bug#1011476: beancounter: Please drop alternative dependency on libdbd-sqlite2-perl

2022-05-23 Thread Dirk Eddelbuettel
Hi Gregor, On 23 May 2022 at 21:05, gregor herrmann wrote: | Package: beancounter | Severity: minor | X-Debbugs-Cc: 998...@bugs.debian.org | | beancounter has "libdbd-pg-perl | libdbd-mysql-perl | | libdbd-odbc-perl | libdbd-sqlite3-perl | libdbd-sqlite2-perl" in | Depends, as it apparantly

Re: [Rd] CRAN webserver down

2022-05-23 Thread Dirk Eddelbuettel
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

Re: [R-sig-Debian] Ubuntu Impish (21.10) repository complains about weak security information

2022-05-16 Thread Dirk Eddelbuettel
On 16 May 2022 at 22:24, Lennart C. Karssen wrote: | Thanks Dirk, that gets me one step further. However, there is still a | hurdle. It seems that (at least at the time of writing) the | impish-cran40/ repo is broken. You are correct, sorry. I rushed earlier to help you on the key issue, and

Bug#1011044: libtiledb2.8 needs Breaks+Replaces: libtiledb2.7

2022-05-15 Thread Dirk Eddelbuettel
On 16 May 2022 at 04:48, Adrian Bunk wrote: | Package: libtiledb2.8 | Version: 2.8.3-2 | Severity: serious | | Unpacking libtiledb2.8:amd64 (2.8.3-2) ... | dpkg: error processing archive /var/cache/apt/archives/libtiledb2.8_2.8.3-2_amd64.deb (--unpack): | trying to overwrite

Bug#1011044: libtiledb2.8 needs Breaks+Replaces: libtiledb2.7

2022-05-15 Thread Dirk Eddelbuettel
On 16 May 2022 at 04:48, Adrian Bunk wrote: | Package: libtiledb2.8 | Version: 2.8.3-2 | Severity: serious | | Unpacking libtiledb2.8:amd64 (2.8.3-2) ... | dpkg: error processing archive /var/cache/apt/archives/libtiledb2.8_2.8.3-2_amd64.deb (--unpack): | trying to overwrite

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-15 Thread Dirk Eddelbuettel
Hi Nilesh, On 15 May 2022 at 07:48, Dirk Eddelbuettel wrote: | On 15 May 2022 at 14:10, Nilesh Patra wrote: | | Can I ask you to please take a look at my changes once? | | I will try that a little later. They look good. They are even more minimal than what I attempted (i.e. you knew to only

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-15 Thread Dirk Eddelbuettel
Hi Nilesh, On 15 May 2022 at 07:48, Dirk Eddelbuettel wrote: | On 15 May 2022 at 14:10, Nilesh Patra wrote: | | Can I ask you to please take a look at my changes once? | | I will try that a little later. They look good. They are even more minimal than what I attempted (i.e. you knew to only

Bug#1011012: tiledb-r FTBFS with tiledb 2.8.3

2022-05-15 Thread Dirk Eddelbuettel
Adrian, On 15 May 2022 at 13:38, Adrian Bunk wrote: | Source: tiledb-r | Version: 0.12.0-1 | Severity: serious | Tags: ftbfs | | https://buildd.debian.org/status/logs.php?pkg=tiledb-r=0.12.0-1%2Bb1 | | ... | g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/

Bug#1011012: tiledb-r FTBFS with tiledb 2.8.3

2022-05-15 Thread Dirk Eddelbuettel
Adrian, On 15 May 2022 at 13:38, Adrian Bunk wrote: | Source: tiledb-r | Version: 0.12.0-1 | Severity: serious | Tags: ftbfs | | https://buildd.debian.org/status/logs.php?pkg=tiledb-r=0.12.0-1%2Bb1 | | ... | g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-15 Thread Dirk Eddelbuettel
Hi Nilesh, On 15 May 2022 at 14:10, Nilesh Patra wrote: | | Hi Dirk, | | On Fri, 13 May 2022 19:57:11 -0500 Dirk Eddelbuettel wrote: | > As noted in a mail to debian-python [1], the tiledb-py package is creating a | > few issues I do not currently have time to work through. | | I sa

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-15 Thread Dirk Eddelbuettel
Hi Nilesh, On 15 May 2022 at 14:10, Nilesh Patra wrote: | | Hi Dirk, | | On Fri, 13 May 2022 19:57:11 -0500 Dirk Eddelbuettel wrote: | > As noted in a mail to debian-python [1], the tiledb-py package is creating a | > few issues I do not currently have time to work through. | | I sa

Re: Need a hand with tiledb-python

2022-05-13 Thread Dirk Eddelbuettel
I have now orphaned the package [1] as this one needs more attention that I can currently give it due to 180+ other packages I have, and other work and open source commitments. Dirk [1] https://bugs.debian.org/1010953 -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-13 Thread Dirk Eddelbuettel
Package: wnpp Severity: normal As noted in a mail to debian-python [1], the tiledb-py package is creating a few issues I do not currently have time to work through. I will continue to look after the tiledb package, and after the R bindings in package tiledb-r. If someone can devote some time to

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-13 Thread Dirk Eddelbuettel
Package: wnpp Severity: normal As noted in a mail to debian-python [1], the tiledb-py package is creating a few issues I do not currently have time to work through. I will continue to look after the tiledb package, and after the R bindings in package tiledb-r. If someone can devote some time to

Re: [R-pkg-devel] advice on a rejected package (I think, because time was 13min, in excess of 10min limit)

2022-05-11 Thread Dirk Eddelbuettel
On 11 May 2022 at 19:07, Daniel Kelley wrote: | Today I tried to update the CRAN oce package to version 1.7-3, to address a problem with 1.7-2 on one of the CRAN build platforms. I used devtools::release() to submit it. I just received the text I've pasted at the bottom of this email. I've

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