Bug#1054921: Build error for quantlib-swig on mips64el

2023-10-29 Thread Dirk Eddelbuettel
The Debian package fails to build now on mipsel, a log is at [1]. The gist seems to be a relocation error: g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -O0 -g0 -mxgot --param ggc-min-expand=20 -DBOOST_NO_AUTO_PTR build/temp.linux-mips64-cpython-311/QuantLib/quantlib_wrap.o

Bug#1054921: Build error for quantlib-swig on mips64el

2023-10-29 Thread Dirk Eddelbuettel
The Debian package fails to build now on mipsel, a log is at [1]. The gist seems to be a relocation error: g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -O0 -g0 -mxgot --param ggc-min-expand=20 -DBOOST_NO_AUTO_PTR build/temp.linux-mips64-cpython-311/QuantLib/quantlib_wrap.o

Bug#1054921: quantlib-swig: FTBFS on mips64el

2023-10-28 Thread Dirk Eddelbuettel
On 28 October 2023 at 22:53, Sebastian Ramacher wrote: | Source: quantlib-swig | Version: 1.32-1 | Severity: serious | Tags: ftbfs | Justification: fails to build from source (but built successfully in the past) | X-Debbugs-Cc: sramac...@debian.org | |

Bug#1054921: quantlib-swig: FTBFS on mips64el

2023-10-28 Thread Dirk Eddelbuettel
On 28 October 2023 at 22:53, Sebastian Ramacher wrote: | Source: quantlib-swig | Version: 1.32-1 | Severity: serious | Tags: ftbfs | Justification: fails to build from source (but built successfully in the past) | X-Debbugs-Cc: sramac...@debian.org | |

Bug#1054657: transition: r-bioc-biocgenerics

2023-10-27 Thread Dirk Eddelbuettel
On 27 October 2023 at 16:43, Andreas Tille wrote: | Am Fri, Oct 27, 2023 at 09:19:22AM -0500 schrieb Dirk Eddelbuettel: | > | > | BioConductor has just released version 3.17. Since the next r-base | > | > Typo: 3.18 | | Yes. Thanks for pointing this out. | | > | release is

Bug#1054657: transition: r-bioc-biocgenerics

2023-10-27 Thread Dirk Eddelbuettel
On 27 October 2023 at 16:43, Andreas Tille wrote: | Am Fri, Oct 27, 2023 at 09:19:22AM -0500 schrieb Dirk Eddelbuettel: | > | > | BioConductor has just released version 3.17. Since the next r-base | > | > Typo: 3.18 | | Yes. Thanks for pointing this out. | | > | release is

Bug#1054657: transition: r-bioc-biocgenerics

2023-10-27 Thread Dirk Eddelbuettel
On 27 October 2023 at 16:00, Andreas Tille wrote: | Package: release.debian.org | Severity: normal | User: release.debian@packages.debian.org | Usertags: transition | X-Debbugs-Cc: r-bioc-biocgener...@packages.debian.org, debia...@lists.debian.org | Control: affects -1 +

Bug#1054657: transition: r-bioc-biocgenerics

2023-10-27 Thread Dirk Eddelbuettel
On 27 October 2023 at 16:00, Andreas Tille wrote: | Package: release.debian.org | Severity: normal | User: release.debian@packages.debian.org | Usertags: transition | X-Debbugs-Cc: r-bioc-biocgener...@packages.debian.org, debia...@lists.debian.org | Control: affects -1 +

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

2023-10-27 Thread Dirk Eddelbuettel
Hi Jouni, On 27 October 2023 at 13:02, Helske, Jouni wrote: | Actually, the OMP_NUM_THREADS worked for vignettes and testthat tests, but | didn't help with the examples. However, I just wrapped the problematic example Now I am confused. What is your understanding of why it helps in one place

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

2023-10-27 Thread Dirk Eddelbuettel
Jouni, My CRANberriesFeed reports a new bssm package at CRAN, congratulations for sorting this out. [1,2] The OMP_NUM_THREADS setting is indeed all it takes, and it _does_ seem to be read even from a running session: i.e. you can set this inside an R session and the OpenMP code considers it in

Re: [R-sig-Debian] Error in ragg... Graphics API version mismatch

2023-10-27 Thread Dirk Eddelbuettel
On 27 October 2023 at 13:00, Johan Andresen wrote: | I am sorry yet delighted to announce that the problem has been resolved. | ragg didn't install successfully in the first place. When it was, there was | no graphics API mismatch. Apologies for the spam; this entry may be | deleted. Johan Yes.

Re: [R-pkg-devel] API client package failing due to API authentication

2023-10-26 Thread Dirk Eddelbuettel
On 26 October 2023 at 11:14, Cole Johanson wrote: | My package https://github.com/cole-johanson/smartsheetr requires an | environment variable, the API access token, to run most of the functions. | The steps for setting this are documented in the README, but my package is | being auto-rejected

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

2023-10-25 Thread Dirk Eddelbuettel
On 24 October 2023 at 08:15, Dirk Eddelbuettel wrote: | | On 24 October 2023 at 15:55, Ivan Krylov wrote: | | В Tue, 24 Oct 2023 10:37:48 + | | "Helske, Jouni" пишет: | | | | > Examples with CPU time > 2.5 times elapsed time | | > user system elapsed ratio |

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

2023-10-24 Thread Dirk Eddelbuettel
On 24 October 2023 at 15:55, Ivan Krylov wrote: | В Tue, 24 Oct 2023 10:37:48 + | "Helske, Jouni" пишет: | | > Examples with CPU time > 2.5 times elapsed time | > user system elapsed ratio | > exchange 1.196 0.04 0.159 7.774 | | I've downloaded the archived copy of the

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

2023-10-20 Thread Dirk Eddelbuettel
On 19 October 2023 at 05:57, Helske, Jouni wrote: | I am having difficulties in getting the latest version of the bssm (https://github.com/helske/bssm) package to CRAN, as the pretest issues a NOTE that the package uses too many cores in some of the examples ("Examples with CPU time > 2.5

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

2023-10-17 Thread Dirk Eddelbuettel
else, specifically using R.rsp. | > | > Best, | > John | > | > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: | >> Caution: External email. | >> On 16 October 2023 at 10:42, Kevin R Coombes wrote: | >> | Produce a PDF file yourself, then use the "as.is" feat

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

2023-10-17 Thread Dirk Eddelbuettel
is not accessible. Loading a precomputed set is similar. I may be doing that in the much older never quite finished gcbd package and its vignette. Hope this helps, maybe more once I am back home. Cheers, Dirk | Best, | John | | On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: | > Caution: Exter

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

2023-10-17 Thread Dirk Eddelbuettel
On 16 October 2023 at 10:42, Kevin R Coombes wrote: | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | package. For completeness, that approach also works directly with Sweave. Described in a blog post by Mark van der Loo in 2019, and used in a number of packages

Bug#1037439: Unlikely to be a bug in r-base

2023-10-16 Thread Dirk Eddelbuettel
On 16 October 2023 at 11:41, Andreas Beckmann wrote: | On 05/10/2023 17.05, Dirk Eddelbuettel wrote: | > | > Andreas, | > | > This looks like an error: | > | > > reassign 1037439 src:r-base | > Bug #1037439 {Done: Dirk Eddelbuettel } [r-cran-rstan] r-cran-

Bug#1037439: Unlikely to be a bug in r-base

2023-10-05 Thread Dirk Eddelbuettel
Andreas, This looks like an error: > reassign 1037439 src:r-base Bug #1037439 {Done: Dirk Eddelbuettel } [r-cran-rstan] r-cran-rstan/armhf FTBFS with r-cran-bh 1.74, works with boost 1.81 Bug reassigned from package 'r-cran-rstan' to 'src:r-base'. No longer marked as fo

Re: [ESS] run R code upon starting each ESS session

2023-10-03 Thread Dirk Eddelbuettel via ESS-help
On 3 October 2023 at 18:52, Manuel Teodoro via ESS-help wrote: | Is there a way to run R code upon starting each ESS session? | | Something like Rprofile but I'd like to make it more dependent to emacs. | | What I want is to have a few options settings in my R sessions by default. | Since I

Bug#1052655: gsl: CVE-2020-35357

2023-09-26 Thread Dirk Eddelbuettel
Hi Salvatore, Looks like we emailed concurrently :) (or concurrently enough for my batched mail setup). On 26 September 2023 at 14:19, Salvatore Bonaccorso wrote: | Hi Dirk, | | On Tue, Sep 26, 2023 at 06:54:31AM -0500, Dirk Eddelbuettel wrote: | > | > On 25 September 2023 at

Bug#1052655: gsl: CVE-2020-35357

2023-09-26 Thread Dirk Eddelbuettel
Fix made, built, uploaded and committed to the package's salsa repo. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1052655: gsl: CVE-2020-35357

2023-09-26 Thread Dirk Eddelbuettel
On 25 September 2023 at 20:58, Salvatore Bonaccorso wrote: | Source: gsl | Version: 2.7.1+dfsg-5 | Severity: important | Tags: security upstream | Forwarded: https://savannah.gnu.org/bugs/?59624 | X-Debbugs-Cc: car...@debian.org, Debian Security Team | Control: found -1

Re: [ESS] How to Duplicate Previous Functionality/Workflow

2023-09-23 Thread Dirk Eddelbuettel via ESS-help
On 22 September 2023 at 07:04, Stephen J. Eglen via ESS-help wrote: | 2. A non-answer to the original question, but I prefer writing Makefiles | to build my documents, rather than using Emacs functionality. Emacs has | a good interface to running make (e.g. through M-x compile). Use | whatever

Re: [Rcpp-devel] Life-cycle of Rcpp::XPtr

2023-09-23 Thread Dirk Eddelbuettel
PS There is another neat use case where a shared_ptr is allocated. Now we cannot wrap a shared_ptr in an XPtr but ... we can stick the shared_ptr into a struct, and allocate that with new and then make_xptr. You are then back to well-understood C++ semantics. Dirk -- dirk.eddelbuettel.com |

Re: [Rcpp-devel] Life-cycle of Rcpp::XPtr

2023-09-23 Thread Dirk Eddelbuettel
Hi Ralf, On 23 September 2023 at 08:28, Ralf Stubner wrote: | I have a question concerning the file-cycle of Rcpp::XPtr: Consider a | XPtr with the default delete finalizer wrapping some pointer. If I use | the copy constructor to create another XPtr, this is pointing at the | same underlying

Bug#1052291: ITP: r-cran-writexl -- GNU R package for export Excel xlsx format

2023-09-19 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-writexl Version : 1.4.2 Upstream Author : Jeroen Ooms * URL or Web page : https://cran.r-project.org/package=writexl * License : BSD-2 Description : GNU R package to write xlsx file

Bug#1052291: ITP: r-cran-writexl -- GNU R package for export Excel xlsx format

2023-09-19 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-writexl Version : 1.4.2 Upstream Author : Jeroen Ooms * URL or Web page : https://cran.r-project.org/package=writexl * License : BSD-2 Description : GNU R package to write xlsx file

Bug#1052291: ITP: r-cran-writexl -- GNU R package for export Excel xlsx format

2023-09-19 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-writexl Version : 1.4.2 Upstream Author : Jeroen Ooms * URL or Web page : https://cran.r-project.org/package=writexl * License : BSD-2 Description : GNU R package to write xlsx file

[R-pkg-devel] Cadence of macOS builds at CRAN

2023-09-14 Thread Dirk Eddelbuettel
Simon, A new package of mine [1] appeared on CRAN on Sep 5. Respecting the one week gap, I made a small update on Sep 12. Today is Sep 14. There are still no builds for macOS r-release (arm64) macOS r-oldrel (arm64) macOS r-release (x86_64) but we do have two oldrel releases. Weirder

Bug#1050955: rpy2: please make the build reproducible

2023-08-31 Thread Dirk Eddelbuettel
On 31 August 2023 at 11:37, Chris Lamb wrote: | Source: rpy2 | Version: 3.5.13-5 | Severity: normal | Tags: patch | User: reproducible-bui...@lists.alioth.debian.org | Usertags: timestamps | X-Debbugs-Cc: reproducible-b...@lists.alioth.debian.org | | Hi, | | Whilst working on the Reproducible

Re: [R-pkg-devel] What to do when a package is archived from CRAN

2023-08-31 Thread Dirk Eddelbuettel
On 31 August 2023 at 07:32, SHIMA Tatsuya wrote: | I submitted prqlr 0.5.1 yesterday, which is almost identical to prqlr | 0.5.0, and prqlr is now available again on CRAN. | Thanks to the CRAN reviewers for their quick reaction. And it is gone again (per CRANberries). Never a dull moment with

Bug#1050432: rpy2: FTBFS on mips64el

2023-08-27 Thread Dirk Eddelbuettel
On 27 August 2023 at 18:44, YunQiang Su wrote: | Maybe there is something wrong with ffi. (In fact the complex support of mips | was added by me. ;) Hah. | I am looking for a way to use debug to debug the extensions. | If you have any documents, can you point it to me. I can help you with R,

Bug#1050432: rpy2: FTBFS on mips64el

2023-08-27 Thread Dirk Eddelbuettel
On 27 August 2023 at 18:44, YunQiang Su wrote: | Maybe there is something wrong with ffi. (In fact the complex support of mips | was added by me. ;) Hah. | I am looking for a way to use debug to debug the extensions. | If you have any documents, can you point it to me. I can help you with R,

Re: Bug#1050432: rpy2: FTBFS on mips64el

2023-08-27 Thread Dirk Eddelbuettel
On 27 August 2023 at 18:44, YunQiang Su wrote: | Maybe there is something wrong with ffi. (In fact the complex support of mips | was added by me. ;) Hah. | I am looking for a way to use debug to debug the extensions. | If you have any documents, can you point it to me. I can help you with R,

Bug#1050432: rpy2: FTBFS on mips64el

2023-08-27 Thread Dirk Eddelbuettel
On 27 August 2023 at 14:09, YunQiang Su wrote: | Dirk Eddelbuettel 于2023年8月27日周日 00:15写道: | > | > | > Hi all, | > | > As the test failures for complex valued variables appeared to be systemic on | > the 'mips64el' platform, I buckled down, taught myself some Python ==:-) a

Bug#1050432: rpy2: FTBFS on mips64el

2023-08-27 Thread Dirk Eddelbuettel
On 27 August 2023 at 14:09, YunQiang Su wrote: | Dirk Eddelbuettel 于2023年8月27日周日 00:15写道: | > | > | > Hi all, | > | > As the test failures for complex valued variables appeared to be systemic on | > the 'mips64el' platform, I buckled down, taught myself some Python ==:-) a

Re: Bug#1050432: rpy2: FTBFS on mips64el

2023-08-27 Thread Dirk Eddelbuettel
On 27 August 2023 at 14:09, YunQiang Su wrote: | Dirk Eddelbuettel 于2023年8月27日周日 00:15写道: | > | > | > Hi all, | > | > As the test failures for complex valued variables appeared to be systemic on | > the 'mips64el' platform, I buckled down, taught myself some Python ==:-) a

Bug#1050432: rpy2: FTBFS on mips64el

2023-08-26 Thread Dirk Eddelbuettel
Hi all, As the test failures for complex valued variables appeared to be systemic on the 'mips64el' platform, I buckled down, taught myself some Python ==:-) and conditioned the number of failing tests away via @pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==

Bug#1050432: rpy2: FTBFS on mips64el

2023-08-26 Thread Dirk Eddelbuettel
Hi all, As the test failures for complex valued variables appeared to be systemic on the 'mips64el' platform, I buckled down, taught myself some Python ==:-) and conditioned the number of failing tests away via @pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==

Re: Bug#1050432: rpy2: FTBFS on mips64el

2023-08-26 Thread Dirk Eddelbuettel
Hi all, As the test failures for complex valued variables appeared to be systemic on the 'mips64el' platform, I buckled down, taught myself some Python ==:-) and conditioned the number of failing tests away via @pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

2023-08-25 Thread Dirk Eddelbuettel
On 25 August 2023 at 18:48, Jeff Newmiller wrote: | You have a really bizarre way of twisting what others are saying, Dirk. I have seen no-one here saying 'limit R to 2 threads' except for you, as a way to paint opposing views to be absurd. That's too cute. Nobody needs to repeat it, and

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

2023-08-25 Thread Dirk Eddelbuettel
On 26 August 2023 at 12:05, Simon Urbanek wrote: | In reality it's more people running R on their laptops vs the rest of the world. My point was that we also have 'single user on really Yuge workstation'. Plus we all know that those users are often not sysadmins, and do not have our levels

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

2023-08-25 Thread Dirk Eddelbuettel
On 25 August 2023 at 18:45, Duncan Murdoch wrote: | The real problem is that there are two stubborn groups opposing each | other: the data.table developers and the CRAN maintainers. The former | think users should by default dedicate their whole machine to | data.table. The latter think

Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server

2023-08-25 Thread Dirk Eddelbuettel
On 25 August 2023 at 15:37, Uwe Ligges wrote: | | | On 23.08.2023 16:00, Scott Ritchie wrote: | > Hi Uwe, | > | > I agree and have also been burnt myself by programs occupying the | > maximum number of cores available. | > | > My understanding is that in the absence of explicit

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

2023-08-25 Thread Dirk Eddelbuettel
On 24 August 2023 at 07:42, Fred Viole wrote: | Hi, I am receiving a NOTE upon submission regarding the re-building of | vignettes for CPU time for the Debian check. | | I am unable to find any documented instances or solutions to this issue. | The vignettes currently build in 1m 54.3s locally

Bug#1050432: rpy2: FTBFS on mips64el

2023-08-24 Thread Dirk Eddelbuettel
Paul, Thanks for the hint. I was aware and had been meaning to bring this up with Laurent (upstream, now CCed). Laurent: I should have access to a 'porterbox' running mips64el if you have an idea about what may be going on here / have a branch to test. Paul: While I have you here, and as all

Bug#1050432: rpy2: FTBFS on mips64el

2023-08-24 Thread Dirk Eddelbuettel
Paul, Thanks for the hint. I was aware and had been meaning to bring this up with Laurent (upstream, now CCed). Laurent: I should have access to a 'porterbox' running mips64el if you have an idea about what may be going on here / have a branch to test. Paul: While I have you here, and as all

Re: [R-sig-Debian] Is r2u at 3.4.1? [branch about handling package collisions under Ubuntu/Debian]

2023-08-24 Thread Dirk Eddelbuettel
My thanks to Ivan for catching that it was of course a legit Ubuntu mirror, which I had missed. Can we (ever so briefly, no need for long posts) get back to the issue at hand: was there a package you wanted to install from r2u, but could not because of another repo or build infelicity. If so,

Re: [R-sig-Debian] Is r2u at 3.4.1? [branch about handling package collisions under Ubuntu/Debian]

2023-08-23 Thread Dirk Eddelbuettel
Chris, This got a little long so I'll chop a few things down. On 22 August 2023 at 19:38, Chris Evans wrote: | On 16/08/2023 00:06, Dirk Eddelbuettel wrote: | > | > That can happen, and pinning can help. I would suggest to look at 'apt-cache | > polict nameofthepackagehere'. (

Re: [R-pkg-devel] Setting valgrind options when running R CMD check --use-valgrind

2023-08-23 Thread Dirk Eddelbuettel
On 23 August 2023 at 16:49, Duncan Murdoch wrote: | On 23/08/2023 2:54 p.m., Dirk Eddelbuettel wrote: | > | > When I invoke valgrind via | > R -d valgrind -e '...' | > the options in the file ~/.valgrindrc are being picked up. Good. | > | > When I invok valgrind via |

[R-pkg-devel] Setting valgrind options when running R CMD check --use-valgrind

2023-08-23 Thread Dirk Eddelbuettel
When I invoke valgrind via R -d valgrind -e '...' the options in the file ~/.valgrindrc are being picked up. Good. When I invok valgrind via R CMD check --use-valgrind ... the options in the file ~/.valgrindrc are NOT being picked up. Bad. And valgrind complains. How can I add the

Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server

2023-08-21 Thread Dirk Eddelbuettel
' @param ncores A numeric or character variable with the desired ##' count of threads to use ##' @param verbose A logical value with a default of \sQuote{FALSE} to ##' operate more verbosely ##' @return The return value of the \pkg{data.table} function ##' \code{setDTthreads} which is called as a side

Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server

2023-08-21 Thread Dirk Eddelbuettel
On 21 August 2023 at 15:16, Ivan Krylov wrote: | On Mon, 21 Aug 2023 12:02:55 +0100 | Scott Ritchie wrote: | | > remotes::install_github("sritchie73/ukbnmr") | > library(ukbnmr) | > system.time({ remove_technical_variation(test_data) }) | | data.tables, you say? Can you show us the NOTE

Re: [R-pkg-devel] possible solution to package-documentation-alias problem

2023-08-20 Thread Dirk Eddelbuettel
On 20 August 2023 at 09:22, Duncan Murdoch wrote: | That seems like a bug that should be reported to the Roxygen authors. Seb did so in June: https://github.com/r-lib/roxygen2/issues/1491 There has not been a response (but given the CRAN email to many maintainers it has now been referenced

Bug#1049438: r-cran-rgdal: autopkgtest needs update for new version of r-cran-sp

2023-08-18 Thread Dirk Eddelbuettel
On 18 August 2023 at 13:58, Andreas Tille wrote: | Control: tags -1 upstream | Control: forwarded -1 Roger Bivand | | Hi Roger, | | the CI tests in Debian uncovered some conflict between recent rgdal and | version 2.0 of sp. As you either can see in the bug report that was | filed[1] or in a

Bug#1049438: r-cran-rgdal: autopkgtest needs update for new version of r-cran-sp

2023-08-18 Thread Dirk Eddelbuettel
On 18 August 2023 at 13:58, Andreas Tille wrote: | Control: tags -1 upstream | Control: forwarded -1 Roger Bivand | | Hi Roger, | | the CI tests in Debian uncovered some conflict between recent rgdal and | version 2.0 of sp. As you either can see in the bug report that was | filed[1] or in a

Bug#1041556: What is the architecture name in R what we call armel/armhf

2023-08-17 Thread Dirk Eddelbuettel
On 17 August 2023 at 07:24, Graham Inggs wrote: | On Thu, 17 Aug 2023 at 05:52, Andreas Tille wrote: | > I tried to skip two tests in r-cran-checkmate with this patch[1] | > which is based on | > | > arch <- R.version$arch | > identical(arch, "i386") || identical(arch, "i686") ||

Bug#1041556: What is the architecture name in R what we call armel/armhf

2023-08-17 Thread Dirk Eddelbuettel
On 17 August 2023 at 07:24, Graham Inggs wrote: | On Thu, 17 Aug 2023 at 05:52, Andreas Tille wrote: | > I tried to skip two tests in r-cran-checkmate with this patch[1] | > which is based on | > | > arch <- R.version$arch | > identical(arch, "i386") || identical(arch, "i686") ||

Re: [R-sig-Debian] Is r2u at 4.3.1 [edited]?

2023-08-16 Thread Dirk Eddelbuettel
Chris, I edited the README.md for r2u (also the main page at https://eddelbuettel.github.io/r2u) in a few places, that should hopefully address a few of the snafus you found. As for your question 'is r2u running R version x.y.z' there are few way to find out - if you have docker: docker run

Re: [R-sig-Debian] Is r2u at 3.4.1?

2023-08-15 Thread Dirk Eddelbuettel
Hi Chris, Thanks for posting here, and sorry I missed it for two days due to sorting mailing list traffic into folders and clearly not glancing at all of them. On 13 August 2023 at 09:12, Chris Evans wrote: | I am putting this here as it may be of general and not just my own | interest.  I am

Re: [R-pkg-devel] Suppressing compiler warnings?

2023-08-14 Thread Dirk Eddelbuettel
On 14 August 2023 at 11:51, Mark Padgham wrote: | An update of a package of mine got immediately kicked off CRAN because | an externally-bundled file which had not been changed for years, and | which included "pragma clang system_header" to suppress warnings. The | concern is fair enough.

Bug#1044299: ggobi: Fails to build source after successful build

2023-08-13 Thread Dirk Eddelbuettel
e distribution unstable | > dpkg-buildpackage: info: source changed by Dirk Eddelbuettel | > dpkg-source --before-build . | > fakeroot debian/rules clean | > dh_testdir | > dh_testroot | > dh_autoreconf_clean | > rm -f build-stamp configure-stamp install-stamp | > [ ! -f Mak

Bug#1028111: r-cran-clock: autopkgtest failure on 32bit

2023-08-12 Thread Dirk Eddelbuettel
The 'bug fix' applied to the _previous_ version of CRAN package clock, namely a somewhat 'wild' sed patching of a single ie # Ignore single test for i386 architecture. This is a workaround for bug #1024828 of r-cran-igraph if [ "$hostarch" = "i386" -o "$hostarch" = "armel" -o "$hostarch" =

Bug#1028111: r-cran-clock: autopkgtest failure on 32bit

2023-08-12 Thread Dirk Eddelbuettel
The 'bug fix' applied to the _previous_ version of CRAN package clock, namely a somewhat 'wild' sed patching of a single ie # Ignore single test for i386 architecture. This is a workaround for bug #1024828 of r-cran-igraph if [ "$hostarch" = "i386" -o "$hostarch" = "armel" -o "$hostarch" =

Re: [R-pkg-devel] gdb availability on r-devel-linux-x86_64-fedora-gcc

2023-08-12 Thread Dirk Eddelbuettel
On 12 August 2023 at 18:12, Uwe Ligges wrote: | On 12.08.2023 15:10, Jamie Lentin wrote: | > The system call in question is done by the TMB package[2], and not ours | > to tinker with: | > | >   cmd <- paste("R --vanilla < ",file," -d gdb --debugger-args=\"-x", | >   

Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04

2023-08-11 Thread Dirk Eddelbuettel
On 11 August 2023 at 07:54, Thomas Petzoldt wrote: | After moving this discussion to R-SIG-Debian | (https://stat.ethz.ch/pipermail/r-sig-debian/2023-August/thread.html), | Dirk Eddelbuettel suggested five different approaches. | | I made indeed a snapshot (a local copy) of the complete "

Re: [R-sig-Debian] pinning of binary r-cran-* packages from c2d4u / r2u on Ubuntu 22.04

2023-08-09 Thread Dirk Eddelbuettel
On 9 August 2023 at 21:59, Thomas Petzoldt wrote: | On 09.08.2023 at 19:18 Dirk Eddelbuettel wrote: | > There is a fifth option I just realized. | > | > I use a variant of that to keep for example an old version of roxygen2 I | > prefer available. Recall that R packages a

Re: [R-sig-Debian] pinning of binary r-cran-* packages from c2d4u / r2u on Ubuntu 22.04

2023-08-09 Thread Dirk Eddelbuettel
ronemnt". On 9 August 2023 at 18:58, Thomas Petzoldt wrote: | Am 09.08.2023 um 18:17 schrieb Dirk Eddelbuettel: | > Yes. If and when that happens, it is a bug! | | Not necessarily. Breaking code can also be due to an incompatible | feature update. We know that R has both, conservative a

Re: [R-sig-Debian] pinning of binary r-cran-* packages from c2d4u / r2u on Ubuntu 22.04

2023-08-09 Thread Dirk Eddelbuettel
Hi Thomas, Thanks a lot for bringing this over from r-package-devel! As for your question, "there is a lot of meat on these bones" and I really think we should discuss this here. Quick comments inline, more recap at the bottom. On 9 August 2023 at 17:29, Thomas Petzoldt wrote: | Hi, | | I

Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04

2023-08-09 Thread Dirk Eddelbuettel
Hi Thomas, On 9 August 2023 at 17:00, Thomas Petzoldt wrote: | thank you very much dirk for the quick response. I was aware that | r-package-devel may not be the optimal place ;-) but hoped to address | the right audience between r-devel and r-help. | | Many thanks also for the suggestions,

Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04

2023-08-09 Thread Dirk Eddelbuettel
On 9 August 2023 at 16:26, Thomas Petzoldt wrote: | I am running a couple of  shiny servers with several apps that are based | around own CRAN packages. It worked stable for years, but due to the | growing number of packages, the compile time for regular manual package | installation and

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

2023-08-08 Thread Dirk Eddelbuettel
Hi Hadley, On 8 August 2023 at 08:34, Hadley Wickham wrote: | Do you think it's worth also/instead considering a fix to S4 to avoid | this caching issue in future R versions? That is somewhat orthogonal to my point of "'some uses' of the 20 year old S4 system (which as we know is fairly widely

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

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