Re: [R-pkg-devel] macOS results not mirrored/updated at CRAN

2023-08-08 Thread Dirk Eddelbuettel
Simon, This is still an issue for arm64. Uploaded tiledb and RQuantLib yesterday, both already built binaries for macOS (thank you!) but on the x86_64 ones are on the results page. Can you take another peek at this? Thanks so much, Dirk -- dirk.eddelbuettel.com | @eddelbuettel |

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

2023-08-07 Thread Dirk Eddelbuettel
On 8 August 2023 at 13:17, Simon Urbanek wrote: | To be honest I think the motivation of this thread is dubious at best: it is a bad idea to use detectCore() blindly to specify parallelization and we explicitly say it's a bad idea - any sensible person will set it according to the demands,

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

2023-08-07 Thread Dirk Eddelbuettel
On 8 August 2023 at 11:21, Simon Urbanek wrote: | First, detecting HT vs cores is not necessarily possible in general, Linux may assign core id to each HT depending on circumstances: | | $ grep 'cpu cores' /proc/cpuinfo | uniq | cpu cores : 32 | $ grep 'model name' /proc/cpuinfo | uniq |

Re: [R-pkg-devel] [External] Re: clang issue

2023-08-07 Thread Dirk Eddelbuettel
On 7 August 2023 at 13:55, Grose, Daniel wrote: | As I say - I cannot reproduce the error myself. I will try asking Uwe Ligges | for more information. Methinks you are doing it wrong. We created the r-package-devel list years ago to take load away from the overworked CRAN maintainers who are

Re: [Rd] A demonstrated shortcoming of the R package management system

2023-08-07 Thread Dirk Eddelbuettel
Hi Ivan, I usually 'mentally applaud' when reading your replies on list but not here. On 7 August 2023 at 16:15, Ivan Krylov wrote: | SeuratObject 4.1.3. The breakage definitely exists, but not on the | source package level. You seem to overlook that a large part of the R Universe only works

Re: [R-pkg-devel] [External] Re: clang issue

2023-08-07 Thread Dirk Eddelbuettel
On 7 August 2023 at 13:38, Grose, Daniel wrote: | No - unfortunately not. I cannot reproduce the error locally so I posted the | snippet that Uwe Ligges sent me regarding the failed CRAN submission. That is | all of the information I have. | | For now I will follow Dirk's advice and see if the

Re: [R-pkg-devel] clang issue

2023-08-07 Thread Dirk Eddelbuettel
Daniel, This is not new, and not related to clang. On 7 August 2023 at 12:58, Grose, Daniel wrote: | Any ideas ? Add a line #define R_NO_REMAP 1 before _any_ inclusion of R headers. See Section 6 of Writing R Extensions. If you use eg Rcpp it is done for you when you include Rcpp

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

2023-08-07 Thread Dirk Eddelbuettel
On 7 August 2023 at 08:48, Nils Kehrein wrote: | I recently noticed that `detectCores()` ignores the `logical=FALSE` | argument on Linux platforms. This means that the function will always | return the number of logical CPUs, i.e. it will count the number of threads | that theoretically can run

[Rd] A demonstrated shortcoming of the R package management system

2023-08-06 Thread Dirk Eddelbuettel
CRAN, by relying on the powerful package management system that is part of R, provides an unparalleled framework for extending R with nearly 20k packages. We recently encountered an issue that highlights a missing element in the otherwise outstanding package management system. So we would like

Re: [R-sig-Debian] Ubuntu packages on s390x

2023-08-03 Thread Dirk Eddelbuettel
On 4 August 2023 at 00:06, Jeroen Ooms wrote: | On Thu, Aug 3, 2023 at 9:16 PM Vivian Kong wrote: | > | > Hello, | > | > Are there any plans to add R packages for Ubuntu on other architectures in addition to amd64? We are looking for s390x packages as the version from the distro's package

Re: [R-sig-Debian] Ubuntu packages on s390x

2023-08-03 Thread Dirk Eddelbuettel
Hi Vivian, On 3 August 2023 at 19:15, Vivian Kong wrote: | Are there any plans to add R packages for Ubuntu on other architectures in addition to amd64? We are looking for s390x packages as the version from the distro's package manger is 4.2.2. I'm happy to help in any way I can. Ok, now I

Bug#1042889: vm breakage with Emacs 29

2023-08-02 Thread Dirk Eddelbuettel
On 2 August 2023 at 14:41, Ian Jackson wrote: | Dirk Eddelbuettel writes ("Re: vm breakage with Emacs 29"): | > On 2 August 2023 at 13:17, Ian Jackson wrote: | > | Hi. Since you were helpful with #1039105 "Fails to start with Emacs | > | 28" I thought I would dr

Bug#1042889: vm breakage with Emacs 29

2023-08-02 Thread Dirk Eddelbuettel
On 2 August 2023 at 14:41, Ian Jackson wrote: | Dirk Eddelbuettel writes ("Re: vm breakage with Emacs 29"): | > On 2 August 2023 at 13:17, Ian Jackson wrote: | > | Hi. Since you were helpful with #1039105 "Fails to start with Emacs | > | 28" I thought I would dr

Bug#1038405: Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74

2023-08-01 Thread Dirk Eddelbuettel
On 31 July 2023 at 23:13, Adrian Bunk wrote: | On Mon, Jun 19, 2023 at 04:37:22PM +0300, Adrian Bunk wrote: | > On Tue, Jun 13, 2023 at 03:30:18PM -0500, Dirk Eddelbuettel wrote: | > > | > > On 13 June 2023 at 13:15, Steve Langasek wrote: | > > | Control: reassign -1 r

Bug#1038405: Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74

2023-08-01 Thread Dirk Eddelbuettel
On 31 July 2023 at 23:13, Adrian Bunk wrote: | On Mon, Jun 19, 2023 at 04:37:22PM +0300, Adrian Bunk wrote: | > On Tue, Jun 13, 2023 at 03:30:18PM -0500, Dirk Eddelbuettel wrote: | > > | > > On 13 June 2023 at 13:15, Steve Langasek wrote: | > > | Control: reassign -1 r

Bug#1042040: quantlib-swig: FTBFS: QuantLib/quantlib_wrap.cpp:9493:19: error: ‘LexicographicalView’ in namespace ‘QuantLib’ does not name a template type

2023-07-25 Thread Dirk Eddelbuettel
On 25 July 2023 at 23:05, Lucas Nussbaum wrote: | Source: quantlib-swig | Version: 1.30-2 | Severity: serious | Justification: FTBFS | Tags: trixie sid ftbfs | | Hi, | | During a rebuild of all packages in sid, your package failed to build | on amd64. I'll get on this -- it is lagging behind

Bug#1042040: quantlib-swig: FTBFS: QuantLib/quantlib_wrap.cpp:9493:19: error: ‘LexicographicalView’ in namespace ‘QuantLib’ does not name a template type

2023-07-25 Thread Dirk Eddelbuettel
On 25 July 2023 at 23:05, Lucas Nussbaum wrote: | Source: quantlib-swig | Version: 1.30-2 | Severity: serious | Justification: FTBFS | Tags: trixie sid ftbfs | | Hi, | | During a rebuild of all packages in sid, your package failed to build | on amd64. I'll get on this -- it is lagging behind

Bug#1041835: gretl: installs empty directory /usr/lib/pkgconfig

2023-07-24 Thread Dirk Eddelbuettel
On 24 July 2023 at 06:47, Helmut Grohne wrote: | Source: gretl | Version: 2023b-1 | Severity: important | Tags: patch | | gretl contains an empty directory /usr/lib/pkgconfig. Due to having | implemented the /usr-merge using directory aliasing, this directory is | prone to loss. Are we sure

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-23 Thread Dirk Eddelbuettel
On 23 July 2023 at 11:03, Dirk Eddelbuettel wrote: | Note that the mlmRev authors / maintainers are the same as / a subset of the | lme4 authors. They may have an idea. | | https://cran.r-project.org/package=mlmRev I just ran `R CMD check mlmRev_*tar.gz` on my amd64 (under Ubuntu 23.04

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-23 Thread Dirk Eddelbuettel
On 23 July 2023 at 11:03, Dirk Eddelbuettel wrote: | Note that the mlmRev authors / maintainers are the same as / a subset of the | lme4 authors. They may have an idea. | | https://cran.r-project.org/package=mlmRev I just ran `R CMD check mlmRev_*tar.gz` on my amd64 (under Ubuntu 23.04

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-23 Thread Dirk Eddelbuettel
On 23 July 2023 at 15:07, Graham Inggs wrote: | Hi | | On Sun, 23 Jul 2023 at 13:11, Nilesh Patra wrote: | > How do you conclude that? | > The versions of affected packages are same in unstable and testing. They | > fail in i386 with a newer version of lme4. | | For what it's worth,

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-23 Thread Dirk Eddelbuettel
On 23 July 2023 at 15:07, Graham Inggs wrote: | Hi | | On Sun, 23 Jul 2023 at 13:11, Nilesh Patra wrote: | > How do you conclude that? | > The versions of affected packages are same in unstable and testing. They | > fail in i386 with a newer version of lme4. | | For what it's worth,

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-23 Thread Dirk Eddelbuettel
On 23 July 2023 at 18:42, Nilesh Patra wrote: | On Sun, 23 Jul 2023 07:15:09 -0500 Dirk Eddelbuettel wrote | > Is this is not an example of a release manager override? The affectect | > packages all work together in unstable and could migrate. | | How do you conclude that? | The ve

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-23 Thread Dirk Eddelbuettel
On 23 July 2023 at 18:42, Nilesh Patra wrote: | On Sun, 23 Jul 2023 07:15:09 -0500 Dirk Eddelbuettel wrote | > Is this is not an example of a release manager override? The affectect | > packages all work together in unstable and could migrate. | | How do you conclude that? | The ve

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-23 Thread Dirk Eddelbuettel
Paul, Is this is not an example of a release manager override? The affectect packages all work together in unstable and could migrate. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-23 Thread Dirk Eddelbuettel
Paul, Is this is not an example of a release manager override? The affectect packages all work together in unstable and could migrate. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: [R-pkg-devel] DESCRIPTION file question

2023-07-22 Thread Dirk Eddelbuettel
On 22 July 2023 at 16:07, Dirk Eddelbuettel wrote: | | Taylor, | | I believe we have been over this at StackOverflow but you may by now have | deleted the question/ | | On 21 July 2023 at 20:51, taylor brown via R-package-devel wrote: | | I have a question about the DESCRIPTION file of an R

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-22 Thread Dirk Eddelbuettel
On 22 July 2023 at 21:45, Paul Gevers wrote: | Source: lme4 | Version: 1.1-31-1 | Severity: serious | Control: close -1 1.1-34-1 | X-Debbugs-CC: debia...@lists.debian.org | Tags: sid trixie | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The

Bug#1041738: src:lme4: fails to migrate to testing for too long: causes timeout in autopkgtests on i386

2023-07-22 Thread Dirk Eddelbuettel
On 22 July 2023 at 21:45, Paul Gevers wrote: | Source: lme4 | Version: 1.1-31-1 | Severity: serious | Control: close -1 1.1-34-1 | X-Debbugs-CC: debia...@lists.debian.org | Tags: sid trixie | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The

Re: [R-pkg-devel] DESCRIPTION file question

2023-07-22 Thread Dirk Eddelbuettel
Taylor, I believe we have been over this at StackOverflow but you may by now have deleted the question/ On 21 July 2023 at 20:51, taylor brown via R-package-devel wrote: | I have a question about the DESCRIPTION file of an R package that has some c++ dependencies. | | This package of mine

Re: [R-pkg-devel] macOS results not mirrored/updated at CRAN

2023-07-22 Thread Dirk Eddelbuettel
Simon, This still persists. As Murray reported, it happened for a while now, it is still happening eg package tiledb has been rebuilt everywhere [1] since the upload a few days ago -- yet the results page still reports builds two uploads ago [2] for both arm64 variants of your macOS setup. Can

Re: [R-pkg-devel] macOS results not mirrored/updated at CRAN

2023-07-15 Thread Dirk Eddelbuettel
On 16 July 2023 at 14:31, Simon Urbanek wrote: | I looked into it and there was no issue on the build machine or staging server, so it will require some more digging in the international waters .. hopefully sometime next week… Thanks for checking, sometimes one-offs happen. Dirk --

Re: [R-pkg-devel] macOS results not mirrored/updated at CRAN

2023-07-15 Thread Dirk Eddelbuettel
Simon, On 12 July 2023 at 19:02, Dirk Eddelbuettel wrote: | | Simon, | | It looks like some result mirroring / pushing from your machines to CRAN fell | over. One of my packages, digest 0.6.33, arrived on CRAN about a week ago, | is built almost everywhere (apart from macOS_release_x86_64

Re: [R-pkg-devel] Feedback on "Using Rust in CRAN packages"

2023-07-13 Thread Dirk Eddelbuettel
The concerns over github going away (!!) (or altering references, tags, releases, ...) may be somewhat alleviated by Software Heritage [1] covering and 'preserving' it. FWIW I briefly spoke about that iniative and a possible CRAN connection at useR! in Toulouse four years ago [2]. I think I

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-13 Thread Dirk Eddelbuettel
Graham, On 13 July 2023 at 18:59, Graham Inggs wrote: | I believe the attached patch should do the trick. It's basically | Paul's list from message #210, plus r-cran-interval and | r-cran-maldiquant. I've also used a << relationship against the | versions in unstable, and appended a tilde at

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-13 Thread Dirk Eddelbuettel
Graham, On 13 July 2023 at 18:59, Graham Inggs wrote: | I believe the attached patch should do the trick. It's basically | Paul's list from message #210, plus r-cran-interval and | r-cran-maldiquant. I've also used a << relationship against the | versions in unstable, and appended a tilde at

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-13 Thread Dirk Eddelbuettel
Hi Graham, On 13 July 2023 at 11:14, Graham Inggs wrote: | On Wed, 12 Jul 2023 at 19:07, Dirk Eddelbuettel wrote: | > On 12 July 2023 at 19:47, Paul Gevers wrote: | > | Yes, you only need to carry the Breaks until in the next release. So | > | every Breaks that's present in the r-bas

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-13 Thread Dirk Eddelbuettel
Hi Graham, On 13 July 2023 at 11:14, Graham Inggs wrote: | On Wed, 12 Jul 2023 at 19:07, Dirk Eddelbuettel wrote: | > On 12 July 2023 at 19:47, Paul Gevers wrote: | > | Yes, you only need to carry the Breaks until in the next release. So | > | every Breaks that's present in the r-bas

[R-pkg-devel] macOS results not mirrored/updated at CRAN

2023-07-12 Thread Dirk Eddelbuettel
Simon, It looks like some result mirroring / pushing from your machines to CRAN fell over. One of my packages, digest 0.6.33, arrived on CRAN about a week ago, is built almost everywhere (apart from macOS_release_x86_64 stuck at 0.6.32) but the result page still has nags from the 0.6.31 build

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-12 Thread Dirk Eddelbuettel
Hi Paul, On 12 July 2023 at 19:47, Paul Gevers wrote: | On 12-07-2023 16:02, Dirk Eddelbuettel wrote: | > I can add the Breaks as a 'best of the worse alternative'. And, I presume, I | > can remove the existing four-year breaks? [1] | | Yes, you only need to carry the Breaks until in th

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-12 Thread Dirk Eddelbuettel
Hi Paul, On 12 July 2023 at 19:47, Paul Gevers wrote: | On 12-07-2023 16:02, Dirk Eddelbuettel wrote: | > I can add the Breaks as a 'best of the worse alternative'. And, I presume, I | > can remove the existing four-year breaks? [1] | | Yes, you only need to carry the Breaks until in th

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-12 Thread Dirk Eddelbuettel
Hi Paul, On 11 July 2023 at 20:36, Paul Gevers wrote: | On 11-07-2023 02:43, Dirk Eddelbuettel wrote: | I'm totally on board for technical excellence, although I think we have | different things in mind when we say that. | | In Debian, with more QA than we ever had before, we're finding

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-12 Thread Dirk Eddelbuettel
Hi Paul, On 11 July 2023 at 20:36, Paul Gevers wrote: | On 11-07-2023 02:43, Dirk Eddelbuettel wrote: | I'm totally on board for technical excellence, although I think we have | different things in mind when we say that. | | In Debian, with more QA than we ever had before, we're finding

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-10 Thread Dirk Eddelbuettel
On 10 July 2023 at 19:43, Dirk Eddelbuettel wrote: | Someone simply didn't update our Debian package, so it lacks this change and | fingers point at r-base when the fault, if there is one, is to let our | package slip behind a compilation and code standard established at CRAN for | the R 4.3.0

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-10 Thread Dirk Eddelbuettel
On 10 July 2023 at 19:43, Dirk Eddelbuettel wrote: | Someone simply didn't update our Debian package, so it lacks this change and | fingers point at r-base when the fault, if there is one, is to let our | package slip behind a compilation and code standard established at CRAN for | the R 4.3.0

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-10 Thread Dirk Eddelbuettel
Paul, Here is a case in point from looking at the current excluses list (which is by now indeed a little shorter). One package that jumps out is r-cran-maldiquant. We are at version 1.22, with Debian build 1.22-1. But one second at the CRAN site and the page for the package shows that it is

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-10 Thread Dirk Eddelbuettel
Paul, Here is a case in point from looking at the current excluses list (which is by now indeed a little shorter). One package that jumps out is r-cran-maldiquant. We are at version 1.22, with Debian build 1.22-1. But one second at the CRAN site and the page for the package shows that it is

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-09 Thread Dirk Eddelbuettel
Hi Paul, On 9 July 2023 at 20:11, Paul Gevers wrote: | On 09-07-2023 18:41, Dirk Eddelbuettel wrote: | > On 9 July 2023 at 17:40, Paul Gevers wrote: | > | Did we already discuss that r-cran-ps also seems to be impacted by the | > | r-base change of the symbols thingy, as can be seen

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-09 Thread Dirk Eddelbuettel
Hi Paul, On 9 July 2023 at 20:11, Paul Gevers wrote: | On 09-07-2023 18:41, Dirk Eddelbuettel wrote: | > On 9 July 2023 at 17:40, Paul Gevers wrote: | > | Did we already discuss that r-cran-ps also seems to be impacted by the | > | r-base change of the symbols thingy, as can be seen

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-09 Thread Dirk Eddelbuettel
On 9 July 2023 at 11:41, Dirk Eddelbuettel wrote: | For spacetime and stars I suspect (based on past experience) possible | interaction from the underlying graphics libraries. Absent-minded typing error: "geospatial", of course. Not "graphics". Dirk -- dirk.eddelbuettel

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-09 Thread Dirk Eddelbuettel
On 9 July 2023 at 11:41, Dirk Eddelbuettel wrote: | For spacetime and stars I suspect (based on past experience) possible | interaction from the underlying graphics libraries. Absent-minded typing error: "geospatial", of course. Not "graphics". Dirk -- dirk.eddelbuettel

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-09 Thread Dirk Eddelbuettel
Paul, On 9 July 2023 at 17:40, Paul Gevers wrote: | Did we already discuss that r-cran-ps also seems to be impacted by the | r-base change of the symbols thingy, as can be seen in r-cran-xopen [1]. Correct me if I am wrong but the "symbols thingy" was not a change in R 4.2.* to R 4.3.*. It

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-09 Thread Dirk Eddelbuettel
Paul, On 9 July 2023 at 17:40, Paul Gevers wrote: | Did we already discuss that r-cran-ps also seems to be impacted by the | r-base change of the symbols thingy, as can be seen in r-cran-xopen [1]. Correct me if I am wrong but the "symbols thingy" was not a change in R 4.2.* to R 4.3.*. It

Bug#1039721: r-base: 4.3 causes many autopkgtests to fail

2023-07-06 Thread Dirk Eddelbuettel
Thanks for closing it. I think in due course as you will see there a) new tag does not help today (we already took care of the six packages needing a rebuild because of the graphics engine constant changing) and b) what is likely being the exact same sets of packages having issue

Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing (Was: Bug#1040001: transition: r-base)

2023-07-06 Thread Dirk Eddelbuettel
On 7 July 2023 at 00:33, Nilesh Patra wrote: | I think we are hitting this issue here: https://github.com/tidyverse/dplyr/issues/6793 | The comment says "Looks like some package in the stack sets R_forceSymbols(dll, TRUE)" and that package is tibble | | | $ grep -rnw R_forceSymbols | |

Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing (Was: Bug#1040001: transition: r-base)

2023-07-06 Thread Dirk Eddelbuettel
On 7 July 2023 at 00:33, Nilesh Patra wrote: | I think we are hitting this issue here: https://github.com/tidyverse/dplyr/issues/6793 | The comment says "Looks like some package in the stack sets R_forceSymbols(dll, TRUE)" and that package is tibble | | | $ grep -rnw R_forceSymbols | |

Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Dirk Eddelbuettel
On 6 July 2023 at 08:14, Dirk Eddelbuettel wrote: | | On 6 July 2023 at 14:31, Vincent van Hees wrote: | | Thanks, in that case the REPLEX for the issue may need to be: | | | | > remember = Sys.getenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_") | |

Re: [R-pkg-devel] Warning 'as.data.frame.POSIXct()' is deprecated

2023-07-06 Thread Dirk Eddelbuettel
On 6 July 2023 at 14:31, Vincent van Hees wrote: | Thanks, in that case the REPLEX for the issue may need to be: | | > remember = Sys.getenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_") | > Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = TRUE) | > data.frame(time = Sys.time()) |

Bug#1040001: transition: r-base

2023-07-05 Thread Dirk Eddelbuettel
Paul, Graham, r-base 4.3.1-2 is now on its way. You will have to update / tweak the ben file as there is no 'r-api-4.3' tag as there is no such thing API change upstream in R itself. Filing the bug reports against the handful of packages testing the graphics engine version was the right thing

Bug#1040001: transition: r-base

2023-07-05 Thread Dirk Eddelbuettel
Paul, Graham, r-base 4.3.1-2 is now on its way. You will have to update / tweak the ben file as there is no 'r-api-4.3' tag as there is no such thing API change upstream in R itself. Filing the bug reports against the handful of packages testing the graphics engine version was the right thing

Bug#1039721: r-base: 4.3 causes many autopkgtests to fail

2023-07-05 Thread Dirk Eddelbuettel
Control: severity -1 normal I am changing this back because a) there is no general bug in R 4.3.1, and there newer was there were a few packages requiring an update to the new graphics engine version (as the packages choose to call R_GE_checkVersionOrDie, it is coming from

Bug#1039721: r-base: 4.3 causes many autopkgtests to fail

2023-07-05 Thread Dirk Eddelbuettel
Control: severity -1 normal I am changing this back because a) there is no general bug in R 4.3.1, and there newer was there were a few packages requiring an update to the new graphics engine version (as the packages choose to call R_GE_checkVersionOrDie, it is coming from

Bug#1040341: r-base: please drop libpcre3-dev dependencies

2023-07-04 Thread Dirk Eddelbuettel
On 4 July 2023 at 16:00, Graham Inggs wrote: | Source: r-base | Version: 4.3.1-1 | Tags: patch | | Hi Maintainer | | r-base has a build-dependency, and r-base-dev has a dependency, on the | ancient libpcre3-dev package. I believe these are no longer required | since the dependencies on the

Bug#1040038: r-base-core: Please provide r-graphics-api-*

2023-07-01 Thread Dirk Eddelbuettel
On 1 July 2023 at 15:26, Graham Inggs wrote: | Your patch has 'rgraphicsapiversion' and 'r-graphics-api-4.3'. | | Upstream [1] refer to it as follows: | | The graphics engine version, R_GE_version, has been bumped to 16 | and so packages that provide graphics devices should be |

Bug#1040001: transition: r-base

2023-07-01 Thread Dirk Eddelbuettel
This is not a bug in r-base, and does not warrant a transition. I have written at some length about it, and (if I find some time) will expand on it in blog post. I will also try to coordinate with upstream. In short, R header GraphicsEngine.h [1] defines an integer constant declaring the

Bug#1040001: transition: r-base

2023-07-01 Thread Dirk Eddelbuettel
This is not a bug in r-base, and does not warrant a transition. I have written at some length about it, and (if I find some time) will expand on it in blog post. I will also try to coordinate with upstream. In short, R header GraphicsEngine.h [1] defines an integer constant declaring the

Bug#1039926: svglite requires rebuild under R 4.3.*

2023-06-29 Thread Dirk Eddelbuettel
On 29 June 2023 at 10:22, Dirk Eddelbuettel wrote: | | Package: r-cran-svglite | Version: 2.1.1-1 | Severity: normal | | R 4.3.0 brought (once again) a new graphics API which requires a rebuild for | functionality that involves creating graphics device. Once rebuilt the | following will again

Bug#1039953: tikzDevice requires rebuild under R 4.3.*

2023-06-29 Thread Dirk Eddelbuettel
Package: r-cran-tikzdevice Version: 0.12.4-1 Severity: normal R 4.3.0 brought (once again) a new graphics API which requires a rebuild for functionality that involves creating graphics device. Once rebuilt the following will again work: > getRversion() [1] ‘4.3.1’ >

Bug#1039721: r-base: 4.3 causes many autopkgtests to fail

2023-06-29 Thread Dirk Eddelbuettel
On 28 June 2023 at 17:39, Jeremy Bícha wrote: | Control: severity -1 serious | | On Wed, Jun 28, 2023 at 5:29 PM Dirk Eddelbuettel wrote: | > Feel free to change the severity back if you truly think it is that serious. | | Done. | | Feel free to close the bug once r-base is ready to migr

Bug#1039721: r-base: 4.3 causes many autopkgtests to fail

2023-06-29 Thread Dirk Eddelbuettel
On 28 June 2023 at 17:39, Jeremy Bícha wrote: | Control: severity -1 serious | | On Wed, Jun 28, 2023 at 5:29 PM Dirk Eddelbuettel wrote: | > Feel free to change the severity back if you truly think it is that serious. | | Done. | | Feel free to close the bug once r-base is ready to migr

Bug#1039925: ragg requires rebuild under R 4.3.*

2023-06-29 Thread Dirk Eddelbuettel
Package: r-cran-ragg Version: 1.2.5-1 Severity: normal R 4.3.0 brought (once again) a new graphics API which requires a rebuild for functionality that involves creating graphics device. Once rebuilt the following will again work: > getRversion() [1] ‘4.3.1’ >

Bug#1039926: svglite requires rebuild under R 4.3.*

2023-06-29 Thread Dirk Eddelbuettel
Package: r-cran-svglite Version: 2.1.1-1 Severity: normal R 4.3.0 brought (once again) a new graphics API which requires a rebuild for functionality that involves creating graphics device. Once rebuilt the following will again work: > getRversion() [1] ‘4.3.1’ >

Bug#1039721: r-base: 4.3 causes many autopkgtests to fail

2023-06-28 Thread Dirk Eddelbuettel
Feel free to change the severity back if you truly think it is that serious. Some of the autopkgtests may be stumbling about the graphics API change and may need a rebuild of packages interfacing it: svglite, ggplot2, ragg, tikzdevice. As some of these are widely used the rest may be

Bug#1039721: r-base: 4.3 causes many autopkgtests to fail

2023-06-28 Thread Dirk Eddelbuettel
severity 1039721 normal thanks Hi Jeremy, That is a false positive (more below) and a duplicate of #1039510; the discussion of the latter now continues on the debian-r list. On 28 June 2023 at 12:31, Jeremy Bícha wrote: | Source: r-base | Version: 4.3.1-1 | Severity: serious | | I'm copying

Bug#1039721: r-base: 4.3 causes many autopkgtests to fail

2023-06-28 Thread Dirk Eddelbuettel
severity 1039721 normal thanks Hi Jeremy, That is a false positive (more below) and a duplicate of #1039510; the discussion of the latter now continues on the debian-r list. On 28 June 2023 at 12:31, Jeremy Bícha wrote: | Source: r-base | Version: 4.3.1-1 | Severity: serious | | I'm copying

Bug#1039645: Seems we need a transition for r-base instead of lots of single bugs against single packages (Was: Bug#1039645: r-cran-epi: autopkgtest failure with r-base (4.3.1-1))

2023-06-28 Thread Dirk Eddelbuettel
On 28 June 2023 at 14:03, Andreas Tille wrote: | Am Wed, Jun 28, 2023 at 08:11:05AM +0200 schrieb Bas Couwenberg: | > 189s DLL requires the use of native symbols | | I wonder, whether all those bugs against single r-* packages are | sensible. Yes they are. Those are bugs in the packages

Bug#1039645: Seems we need a transition for r-base instead of lots of single bugs against single packages (Was: Bug#1039645: r-cran-epi: autopkgtest failure with r-base (4.3.1-1))

2023-06-28 Thread Dirk Eddelbuettel
On 28 June 2023 at 14:03, Andreas Tille wrote: | Am Wed, Jun 28, 2023 at 08:11:05AM +0200 schrieb Bas Couwenberg: | > 189s DLL requires the use of native symbols | | I wonder, whether all those bugs against single r-* packages are | sensible. Yes they are. Those are bugs in the packages

Re: [ESS] Working with Roxygen2

2023-06-27 Thread Dirk Eddelbuettel via ESS-help
nce _forever_. Invoking it adds this header above ##' .. content for \description{} (no empty lines) .. ##' ##' .. content for \details{} .. ##' @title ##' @param x ##' @param y ##' @return ##' @author Dirk Eddelbuettel pyth <- function(x, y) { sq

Re: [Rd] Correct use of tools::R_user_dir() in packages?

2023-06-27 Thread Dirk Eddelbuettel
On 27 June 2023 at 15:36, Carl Boettiger wrote: | tools::R_user_dir() provides configurable directories for R packages | to write persistent information consistent with standard best | practices relative to each supported operating systems for | applications to store data, config, and cache

Bug#1039105: I can confirm this bug, fix works for me

2023-06-27 Thread Dirk Eddelbuettel
Hi Thomas, On 27 June 2023 at 22:05, Thomas Lange wrote: | Hi Dirk, | | I'm a vm user for reading my mail. So there's two of us! :-) | Thanks a lot for this bug report and fix. It also works for me. | Patching /etc/emacs/site-start.d/50vm-init.el still compiles vm-vars | and vm-version, but

Bug#1039510: mvtnorm breaks r-cran-pammtools autopkgtest: missing Breaks and/or versioned (test) Depends?

2023-06-27 Thread Dirk Eddelbuettel
Hi Paul, On 27 June 2023 at 20:08, Paul Gevers wrote: | Hi Dirk, | | On 26-06-2023 22:21, Dirk Eddelbuettel wrote: | > I really appreciate the diligence and detail you put into this. | > | > But I would like to offer a simple shortcut. I am also CCing debian-r again | > as this

Bug#1039510: mvtnorm breaks r-cran-pammtools autopkgtest: missing Breaks and/or versioned (test) Depends?

2023-06-27 Thread Dirk Eddelbuettel
Hi Paul, On 27 June 2023 at 20:08, Paul Gevers wrote: | Hi Dirk, | | On 26-06-2023 22:21, Dirk Eddelbuettel wrote: | > I really appreciate the diligence and detail you put into this. | > | > But I would like to offer a simple shortcut. I am also CCing debian-r again | > as this

Bug#1039510: mvtnorm breaks r-cran-pammtools autopkgtest: missing Breaks and/or versioned (test) Depends?

2023-06-26 Thread Dirk Eddelbuettel
Hi Paul, I really appreciate the diligence and detail you put into this. But I would like to offer a simple shortcut. I am also CCing debian-r again as this has come up time and time again, is guaranteed to come up again for as long as combine autopkgtests with letting packages go stake.

Bug#1039510: mvtnorm breaks r-cran-pammtools autopkgtest: missing Breaks and/or versioned (test) Depends?

2023-06-26 Thread Dirk Eddelbuettel
Hi Paul, I really appreciate the diligence and detail you put into this. But I would like to offer a simple shortcut. I am also CCing debian-r again as this has come up time and time again, is guaranteed to come up again for as long as combine autopkgtests with letting packages go stake.

Re: [R-pkg-devel] Questions regarding a new (seperated package) and how to submit them to cran

2023-06-26 Thread Dirk Eddelbuettel
On 26 June 2023 at 21:03, Uwe Ligges wrote: | On 26.06.2023 02:52, Bernd.Gruber wrote: | > Thanks, just to make sure: | > | > In the policy I find the entry: | > | > Additional_repositories: | | You can use this for CRAN-style repositories. Not for other inds of | storage. In that case you

Re: [Rd] restoring LANGUAGE env variable within an R session

2023-06-26 Thread Dirk Eddelbuettel
Ben, POSIX level / glibc level variables are set at process start and AGAIK cannot really be altered after start. They clearly work when set _before_ calling sqrt(-1): $ LANGUAGE=es Rscript -e 'sqrt(-1)' [1] NaN Warning message: In sqrt(-1) : Se han producido NaNs $

Bug#1039105: Fails to start with Emacs 28

2023-06-25 Thread Dirk Eddelbuettel
Package: vm Version: 8.2.0b-8 Severity: normal Ian, After updating my main machine (and the only one running vm along and exim4, dovecot, spamassassin and whatnot) to Ubuntu 23.04 with its Emacs 28.2 (in an upgrade from 22.10 with Emacs 27.*), I found that vm (which I have been using all

Re: [Vm] [Question #707095]: Emacs 28.2 does not start vm 8.2.0b-8

2023-06-24 Thread Dirk Eddelbuettel
Question #707095 on VM changed: https://answers.launchpad.net/vm/+question/707095 Dirk Eddelbuettel gave more information on the question: Uninstalling and re-installing the package worked. That should of course have been doing the upgrade -- somehow it didn't remake the .elc fine. So still

[Vm] [Question #707095]: Emacs 28.2 does not start vm 8.2.0b-8

2023-06-24 Thread Dirk Eddelbuettel
New question #707095 on VM: https://answers.launchpad.net/vm/+question/707095 After upgrading from Ubuntu 22.10 to 23.04, I cannot launch `vm`. It results in an error Wrong number of arguments: #, 0 from either the `(require 'vm)` or a simple `M-x vm`. The emacs version is

Re: [R-pkg-devel] Convention or standards for using header library (e.g. Eigen)

2023-06-24 Thread Dirk Eddelbuettel
On 24 June 2023 at 21:35, Stephen Wade wrote: | Doesnt seem like the system package is worth it. Should the convention | simply be to bundle the headers in the package then? What about package | size - is there some limit to the size of included libraries/headers to | consider for CRAN? Here is

Bug#1037439: Opinions about removal of 32bit architecture for r-cran-rstan (Was: Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74)

2023-06-22 Thread Dirk Eddelbuettel
Nilesh, But nobody suggested to turn 32bit builds for R off so it was not a question that needed adressing. Or did I miss something here? We do have _a_ package failing. My first suggestion always is to talk to upstream (and I did so on June 13 in my first post on this bug report). Has

Bug#1034683: r-base: new upstream release unintentionally uploaded to unstable

2023-06-21 Thread Dirk Eddelbuettel
Hi Philip, On 21 June 2023 at 20:15, Philip Rinn wrote: | Hi, | | could we please close this bug? We released bookworm some days ago and | propagating to testing should be fine now. [It blocks R packages to propagate to | testing currently.] Thanks for the reminder. I think we had informal

Bug#1034683: r-base: new upstream release unintentionally uploaded to unstable

2023-06-21 Thread Dirk Eddelbuettel
Hi Philip, On 21 June 2023 at 20:15, Philip Rinn wrote: | Hi, | | could we please close this bug? We released bookworm some days ago and | propagating to testing should be fine now. [It blocks R packages to propagate to | testing currently.] Thanks for the reminder. I think we had informal

Re: [R-sig-Debian] R 4.3.1 on Debian bullseye-cran40 repository

2023-06-21 Thread Dirk Eddelbuettel
On 21 June 2023 at 07:48, Iago Giné Vázquez wrote: | Although R 4.3.1 has been released some days ago, and in http://cloud.r-project.org/bin/linux/debian/ it is claimed that | | | Debian bullseye has been released with R 4.0.4. If you want to upgrade to R 4.3.1 on bullseye, you can use the

Re: [R-pkg-devel] Change package name

2023-06-20 Thread Dirk Eddelbuettel
Hi William, On 20 June 2023 at 16:06, William Becker wrote: | I am the maintainer of a package which is unfortunately involved in a complicated dispute regarding its intellectual property (since the package was partly built under a contract with an organisation), but also the "branding" of

Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74

2023-06-19 Thread Dirk Eddelbuettel
On 19 June 2023 at 16:37, Adrian Bunk wrote: | On Tue, Jun 13, 2023 at 03:30:18PM -0500, Dirk Eddelbuettel wrote: | > | > On 13 June 2023 at 13:15, Steve Langasek wrote: | > | Control: reassign -1 r-cran-rstan r-cran-bh | > | Control: found -1 r-cran-rstan/2.21.8-1 | > | | &g

Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74

2023-06-13 Thread Dirk Eddelbuettel
On 13 June 2023 at 13:15, Steve Langasek wrote: | Control: reassign -1 r-cran-rstan r-cran-bh | Control: found -1 r-cran-rstan/2.21.8-1 | | Unfortunately, at least in Ubuntu it appears the r-cran-rstan build still | exhausts the 32-bit memory space even with boost 1.81. | |

Bug#1037113: Should not be in /usr/games

2023-06-13 Thread Dirk Eddelbuettel
On 13 June 2023 at 00:46, Josh Triplett wrote: | On Mon, Jun 12, 2023 at 05:03:01PM -0500, Dirk Eddelbuettel wrote: | > | > reassign 1037113 screen-message | > thanks | > | > Binary package 'sm' is from source package 'screen-message' | > | > Binary package 'r-cran-sm' i

Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74, works with boost 1.81

2023-06-12 Thread Dirk Eddelbuettel
On 12 June 2023 at 16:08, Steve Langasek wrote: | On Mon, Jun 12, 2023 at 05:22:39PM -0500, Dirk Eddelbuettel wrote: | > edd@rob:~$ cat deb/bh/debian/control | > Source: r-cran-bh | > Section: gnu-r | > Priority: optional | > Maintainer: Dirk Eddelbuettel | &g

Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74, works with boost 1.81

2023-06-12 Thread Dirk Eddelbuettel
th discussing.) So for the last few years _Debian's_ r-cran-bh was an empty virtual package dependending on what Debian has as libboost* (particularly the headers only): edd@rob:~$ cat deb/bh/debian/control Source: r-cran-bh Section: gnu-r Priority: optional Maintainer: Dirk Eddelbuett

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