Bug#1001892: ftp.debian.org: RM: r-cran-hdf5 -- ROM: retired upstream twelve years ago

2021-12-18 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal Winthin the R system, hdf5 packages have a difficult history. This package was one of the earlier ones (earliest?) and was maintained from 2000 to 2009. I packaged it in 2005, and it has served us well. These days the BioConductor package rhdf5 is a

Re: [R-sig-Debian] Open a text file with vi/vim in another Terminal

2021-12-17 Thread Dirk Eddelbuettel
On 17 December 2021 at 21:13, Patrice Kiener wrote: | Thank you for your suggestions. Let's give more details. The idea is to | insert the code in a function and then in a (private) package. We have | to rely on the default editors provided by the OS to R and cannot invent | a new editor, as

Re: [R-sig-Debian] Open a text file with vi/vim in another Terminal

2021-12-17 Thread Dirk Eddelbuettel
Patrice, Also: if you are on a terminal, have you discovered tmux / byobu yet to multiplex? It is fairly magic as you can just open as many 'sessions with the outer sessions', the sessions persist and many more advantages. I talked a little about this (with short videos) last year

Re: [R-sig-Debian] Open a text file with vi/vim in another Terminal

2021-12-17 Thread Dirk Eddelbuettel
On 17 December 2021 at 18:48, Patrice Kiener wrote: | | With Debian and macOS, the default editor (getenv("EDITOR") or | getOption("editor")) is "vi" which opens vi/vim. The following instruction: | |fileREP <- file.path(R.home("etc"), "repositories") |system2(getOption("editor"),

Re: [R-pkg-devel] pandoc missing on r-{release,oldrel}-macos-x86_64

2021-12-16 Thread Dirk Eddelbuettel
On 17 December 2021 at 09:51, Simon Urbanek wrote: | Sure, installed pandoc 2.16.2. Perfect, thank you! Dirk | Cheers, | Simon | | | > On Dec 17, 2021, at 9:21 AM, Dirk Eddelbuettel wrote: | > | > | > CRAN results flag NOTEs on the two platforms | > r-release-macos

[R-pkg-devel] pandoc missing on r-{release,oldrel}-macos-x86_64

2021-12-16 Thread Dirk Eddelbuettel
CRAN results flag NOTEs on the two platforms r-release-macos-x86_64 r-oldrel-macos-x86_64 because `pandoc` is apparently missing. These platforms being somewhat common, could pandoc be installed? Or are they running such a jurassic version that no premade pandoc is available _anywhere_ ?

Re: [Rcpp-devel] Limit of 20

2021-12-16 Thread Dirk Eddelbuettel
On 16 December 2021 at 06:38, Joseph Park wrote: | As R itself has no practical limit, and, large, ugly parameter lists are | sometimes unavoidable in API's, I respectfully request consideration to | relax the limit as design and resources allow. Please keep in mind that this project is provided

Re: [Rcpp-devel] R Session Sometimes Aborts

2021-12-15 Thread Dirk Eddelbuettel
On 15 December 2021 at 12:30, Robert J. Hijmans wrote: | Dirk thanks very much for the help. And sorry, Alex, I misspoke. I meant to | say that Rcpp will coerce a R "numeric" (vector) to an | "Rcpp::IntegerVector" if you ask it to do so (and that is what happened in | the context we were

Re: [Rcpp-devel] Limit of 20

2021-12-15 Thread Dirk Eddelbuettel
On 15 December 2021 at 20:10, Balamuta, James Joseph wrote: | For those interested, the few other instances can be found by looking under the inst/include/Rcpp/generated/ folder: | | https://github.com/RcppCore/Rcpp/tree/master/inst/include/Rcpp/generated Yup, I mentioned the dir, but thanks

Re: [Rcpp-devel] Limit of 20

2021-12-15 Thread Dirk Eddelbuettel
On 15 December 2021 at 10:19, Kevin Ushey wrote: | I assume we're talking about Vector::create()? Anyone curious poking at it | can start by looking here: | | https://github.com/RcppCore/Rcpp/blob/940fb23868bf442e587994451e85263baa302d9c/inst/include/Rcpp/vector/Vector.h#L1122-L1126 There is

Re: [Rcpp-devel] Limit of 20

2021-12-15 Thread Dirk Eddelbuettel
Joseph, Sorry, can't quote your message as whatever you used confused my mail handler. (Maybe try text-only next time if you remeber? I have had this before, albeit very rarely.) But it is a good idea. Someone with a bit of time should sit down and could do this as we now have C++11 / C++14 as

Re: [Rcpp-devel] R Session Sometimes Aborts

2021-12-15 Thread Dirk Eddelbuettel
--no-save --debugger=valgrind | >>> --debugger-args="--track-origins=yes --vgdb=full --vgdb-error=0" | >>> then in another window start a debugger process with | >>> $ gdb RHOME/bin/exec/R | >>> ... | >>>(gdb) target remote | vgdb |

Bug#996033: ftp.debian.org: ROM: its -- retired upstream five years ago

2021-12-15 Thread Dirk Eddelbuettel
retitle 996033 RM: its -- ROM: retired upstream five years ago quit Setting a better / correct title. Dirk On 18 November 2021 at 10:06, Dirk Eddelbuettel wrote: | | reassign 996033 ftp.debian.org | quit | | I must have been absent-minded when I filed this as I got the Subject: right

Re: [Rcpp-devel] R Session Sometimes Aborts

2021-12-13 Thread Dirk Eddelbuettel
On 13 December 2021 at 09:15, Bill Dunlap wrote: | I ran your example under valgrind on Linux (Ubuntu 20.04) Excellent call, as usual! Thanks for doing that. R actually makes is so easy to run with valgrind by calling R CMD check --use-valgrind somePkg_1.2-3.tar.gz that I started to add

Bug#1001589: libgsl25: Can't be upgraded to 2.7+dfsg-2

2021-12-13 Thread Dirk Eddelbuettel
Hi Tobias, Thanks for piping in! On 13 December 2021 at 16:42, Tobias Hansen wrote: | On 12/13/21 4:30 PM, Dirk Eddelbuettel wrote: | > Hi Alexandre, | > | > On 13 December 2021 at 09:08, Alexandre Lymberopoulos wrote: | > | Hi there, Dirk! | > | | > | I see that, libgslbl

Re: [Rcpp-devel] R Session Sometimes Aborts

2021-12-13 Thread Dirk Eddelbuettel
On 13 December 2021 at 11:14, Alexander Ilich wrote: | Hi, I'm upgrading one of my R packages to rely on the terra package instead | of the raster package for the handling of spatial raster data. Previously | when relying on the raster package I had to convert the data to a matrix | and send it

Bug#1001589: libgsl25: Can't be upgraded to 2.7+dfsg-2

2021-12-13 Thread Dirk Eddelbuettel
ple email to the maintainer. Cheers, Dirk | Best, Alexandre | | On Dec 12 2021, Dirk Eddelbuettel wrote: | > | > PS As a follow-up, it also looks like the Debian aggregation pages think | > everything should be fine: | > | > https://packages.debian.org/sid/libgslcblas0 | > |

Bug#1001589: libgsl25: Can't be upgraded to 2.7+dfsg-2

2021-12-12 Thread Dirk Eddelbuettel
PS As a follow-up, it also looks like the Debian aggregation pages think everything should be fine: https://packages.debian.org/sid/libgslcblas0 Maybe you just has bad luck with a mirror, or hit a mirro sync? Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1001589: libgsl25: Can't be upgraded to 2.7+dfsg-2

2021-12-12 Thread Dirk Eddelbuettel
Salut Alexandre, On 12 December 2021 at 14:47, Alexandre Lymberopoulos wrote: | Package: libgsl25 | Version: 2.6+dfsg-2 | Severity: normal | | Dear Maintainer, | | Trying to upgrade all packages here, I see myself in a dependence | conflict apparently without solution. Library libgsl25

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-08 Thread Dirk Eddelbuettel
On 8 December 2021 at 12:16, Sebastian Ramacher wrote: | gsl now migrated and libgsl25 got removed from testing. Fantastic! Thanks to you and to Patrick (CC'ed again) and we're back to where we once were (GSL updates upstream, I can update without fuss or formal transitions) but now we are

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-08 Thread Dirk Eddelbuettel
On 8 December 2021 at 12:16, Sebastian Ramacher wrote: | gsl now migrated and libgsl25 got removed from testing. Fantastic! Thanks to you and to Patrick (CC'ed again) and we're back to where we once were (GSL updates upstream, I can update without fuss or formal transitions) but now we are

Re: [Rd] string concatenation operator (revisited)

2021-12-07 Thread Dirk Eddelbuettel
On 8 December 2021 at 00:06, Simon Urbanek wrote: | Hence it's much easier to ban a package than to hack it out of R ;). Paging Achim for suggested `fortunes` inclusion. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-06 Thread Dirk Eddelbuettel
Hi Mattia and Sebastian, On 6 December 2021 at 22:44, Mattia Rizzolo wrote: | Yes! See https://wiki.debian.org/BuildProfileSpec for the | documentation. | | Unfortunately there have been a few troubles getting a formal and good | specifical text that was "good enough" for the Debian Policy.

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-06 Thread Dirk Eddelbuettel
Hi Mattia and Sebastian, On 6 December 2021 at 22:44, Mattia Rizzolo wrote: | Yes! See https://wiki.debian.org/BuildProfileSpec for the | documentation. | | Unfortunately there have been a few troubles getting a formal and good | specifical text that was "good enough" for the Debian Policy.

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-06 Thread Dirk Eddelbuettel
Hi Sebastian, On 6 December 2021 at 21:58, Sebastian Ramacher wrote: | gsl needs another upload. It currently lists libgsl-prof as package that | should be built, but it isn't. I've been told that in the past this has | been worked around by manually changing the .dsc before uploading. It has

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-06 Thread Dirk Eddelbuettel
Hi Sebastian, On 6 December 2021 at 21:58, Sebastian Ramacher wrote: | gsl needs another upload. It currently lists libgsl-prof as package that | should be built, but it isn't. I've been told that in the past this has | been worked around by manually changing the .dsc before uploading. It has

Re: [R-pkg-devel] CRAN no longer checking for solaris?

2021-12-05 Thread Dirk Eddelbuettel
On 5 December 2021 at 17:23, Travers Ching wrote: | I see that there doesn't exist a Solaris flavor on any CRAN check page. | However, I'm certain that Solaris was being checked up until very recently. | | Is this just temporary? | | Is there any information for the future of Solaris on CRAN?

Re: [Rcpp-devel] Rcpp::plugins - Unwinding protection

2021-12-03 Thread Dirk Eddelbuettel
On 3 December 2021 at 12:06, Kevin Ushey wrote: | I'm a fan. I think we could just have a single header RcppLite.h which | would turn off the "heaviest" pieces of Rcpp; that is, modules + sugar | + (maybe?) RTTI. Yep. That's where I started. I may make that a PR then. But I also still lean to

Re: [Rcpp-devel] Rcpp::plugins - Unwinding protection

2021-12-03 Thread Dirk Eddelbuettel
On 3 December 2021 at 19:47, Iñaki Ucar wrote: | Mmmh, no strong opinions here. I think it doesn't matter much whether | it's an include or a define. What matters most is whether this is | discoverable and the user understands what it does. That was my motivation -- by pointing to such a

Re: [Rcpp-devel] Rcpp::plugins - Unwinding protection

2021-12-03 Thread Dirk Eddelbuettel
On 3 December 2021 at 17:03, Iñaki Ucar wrote: | On Fri, 3 Dec 2021 at 15:44, Víthor Rosa wrote: | > | > Thank you for your response. Adding my functions to an R package and changing the Makevars file as suggested reduced the runtime by half. Excited for Rcpp 1.0.8! :) | | Excellent! Glad it

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-02 Thread Dirk Eddelbuettel
On 2 December 2021 at 15:57, Dirk Eddelbuettel wrote: | Yep. It's in the queue by now. I sometimes forget if an experimental -> | unstable passage does or does not need an orig.tar.gz to go along or not but | the bots will tell me if so :) And by now in unstable. Thanks so much for look

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-02 Thread Dirk Eddelbuettel
On 2 December 2021 at 15:57, Dirk Eddelbuettel wrote: | Yep. It's in the queue by now. I sometimes forget if an experimental -> | unstable passage does or does not need an orig.tar.gz to go along or not but | the bots will tell me if so :) And by now in unstable. Thanks so much for look

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-02 Thread Dirk Eddelbuettel
On 2 December 2021 at 22:39, Sebastian Ramacher wrote: | On 2021-12-02 15:11:20, Dirk Eddelbuettel wrote: | > | > On 2 December 2021 at 20:55, Sebastian Ramacher wrote: | > | gsl cleared NEW thanks to ta. So this should be good to go. | > | | > | Please go ahead with the upl

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-02 Thread Dirk Eddelbuettel
On 2 December 2021 at 22:39, Sebastian Ramacher wrote: | On 2021-12-02 15:11:20, Dirk Eddelbuettel wrote: | > | > On 2 December 2021 at 20:55, Sebastian Ramacher wrote: | > | gsl cleared NEW thanks to ta. So this should be good to go. | > | | > | Please go ahead with the upl

Re: [Rcpp-devel] Rcpp::plugins - Unwinding protection

2021-12-02 Thread Dirk Eddelbuettel
On 2 December 2021 at 17:48, Iñaki Ucar wrote: | My simulation package makes heavy use of calls to R user functions from a | C++ simulation loop, and therefore greatly benefits from this feature too, | which I think we should promote to default. I agree and believe I looked into it once before

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-02 Thread Dirk Eddelbuettel
On 2 December 2021 at 20:55, Sebastian Ramacher wrote: | gsl cleared NEW thanks to ta. So this should be good to go. | | Please go ahead with the upload to unstable. Will do. Without any other requirements, correct? I.e. standard upload which thanks to Patrick's work will be around a new

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-02 Thread Dirk Eddelbuettel
On 2 December 2021 at 20:55, Sebastian Ramacher wrote: | gsl cleared NEW thanks to ta. So this should be good to go. | | Please go ahead with the upload to unstable. Will do. Without any other requirements, correct? I.e. standard upload which thanks to Patrick's work will be around a new

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-02 Thread Dirk Eddelbuettel
On 1 December 2021 at 21:47, Patrick Alken wrote: | Ok please send along the patches. Sure thing. They are actually 'in the open' as we (== Debian devs) these days have most / all work in git(-lab via our instance at salsa.debian.org). See this directory and note that the 'series' file governs

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-02 Thread Dirk Eddelbuettel
On 1 December 2021 at 21:47, Patrick Alken wrote: | Ok please send along the patches. Sure thing. They are actually 'in the open' as we (== Debian devs) these days have most / all work in git(-lab via our instance at salsa.debian.org). See this directory and note that the 'series' file governs

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-01 Thread Dirk Eddelbuettel
On 1 December 2021 at 21:41, Sebastian Ramacher wrote: | Indeed, it will need a trip through NEW. So going via experimental would | be appreciated. But, once it passed NEW, you can then immediatly follow | up with the upload to unstable. I will take care of the binNMUs of the | reverse

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-01 Thread Dirk Eddelbuettel
On 1 December 2021 at 21:41, Sebastian Ramacher wrote: | Indeed, it will need a trip through NEW. So going via experimental would | be appreciated. But, once it passed NEW, you can then immediatly follow | up with the upload to unstable. I will take care of the binNMUs of the | reverse

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-01 Thread Dirk Eddelbuettel
On 1 December 2021 at 09:45, Sebastian Ramacher wrote: | On 2021-11-30 22:43:11 -0700, Patrick Alken wrote: | > All, I have uploaded a new GSL release (2.7.1) which I hope fixes the | > libtool version numbers Patrick, Big big thank you! (And I missed this email yesterday) | Thank you! | |

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-12-01 Thread Dirk Eddelbuettel
On 1 December 2021 at 09:45, Sebastian Ramacher wrote: | On 2021-11-30 22:43:11 -0700, Patrick Alken wrote: | > All, I have uploaded a new GSL release (2.7.1) which I hope fixes the | > libtool version numbers Patrick, Big big thank you! (And I missed this email yesterday) | Thank you! | |

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

2021-11-26 Thread Dirk Eddelbuettel
Hi Witold, On 26 November 2021 at 17:09, Witold E Wolski wrote: | We have been using the package at work since 2018. We made some | feature requests in 2019 to the maintainer and Author Amir B.K. | Foroushani and was so kind to | implement them for us and release a new version in 2019. But

Re: [R-pkg-devel] Best way to cache a dataframe available for all functions in a package

2021-11-26 Thread Dirk Eddelbuettel
Agreed. I have used `.pkgenv` in a few packages (digest, rpushbullet, ...), and usually added a comment that it is package-global. And so have a few others: https://github.com/search?l=R=org%3Acran+pkgenv=Code Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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

2021-11-26 Thread Dirk Eddelbuettel
On 26 November 2021 at 14:40, Witold E Wolski wrote: | I am submitting a package to CRAN and I am asked to fix 2 NOTE's | I am not sure how I should ask the following NOTE? | | | * this is package 'sigora' version '3.0.9' | * checking CRAN incoming feasibility ... NOTE | Maintainer: 'Witold

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

2021-11-23 Thread Dirk Eddelbuettel
On 23 November 2021 at 12:19, Hervé Pagès wrote: | But why would you need to check for anything in the first place? | | If you only use 2 cores in your examples, vignettes, and unit tests, 'R | CMD check' will run fine everywhere and not eat all the CPU power of the | machine where it's

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

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

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-11-23 Thread Dirk Eddelbuettel
On 22 November 2021 at 09:08, Patrick Alken wrote: | Hi all, sorry for all this trouble. I will try to make a new GSL release | with the correct numbers. Much appreciate it! Sebastian, we'll then run a new transition with gsl 2.8 (or whichever version number it will be) and its new somajor.

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-11-23 Thread Dirk Eddelbuettel
On 22 November 2021 at 09:08, Patrick Alken wrote: | Hi all, sorry for all this trouble. I will try to make a new GSL release | with the correct numbers. Much appreciate it! Sebastian, we'll then run a new transition with gsl 2.8 (or whichever version number it will be) and its new somajor.

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-11-21 Thread Dirk Eddelbuettel
Hi Patrick, Can you please chime in (as you did in the earlier exchanges when Sebastian explained to us how to set valus triplet for libtool via configure.ac) ? On 21 November 2021 at 23:00, Sebastian Ramacher wrote: | On 2021-11-09 12:54:44 -0600, Dirk Eddelbuettel wrote: | > | >

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-11-21 Thread Dirk Eddelbuettel
Hi Patrick, Can you please chime in (as you did in the earlier exchanges when Sebastian explained to us how to set valus triplet for libtool via configure.ac) ? On 21 November 2021 at 23:00, Sebastian Ramacher wrote: | On 2021-11-09 12:54:44 -0600, Dirk Eddelbuettel wrote: | > | >

Bug#996033: ftp.debian.org: ROM: its -- retired upstream five years ago

2021-11-18 Thread Dirk Eddelbuettel
reassign 996033 ftp.debian.org quit I must have been absent-minded when I filed this as I got the Subject: right but use the package itself instead of ftp.debian.org. My bad! Dirk On 10 October 2021 at 12:04, Dirk Eddelbuettel wrote: | | Severity: normal | Package: its | | The its

Bug#996033: ftp.debian.org: ROM: its -- retired upstream five years ago

2021-11-18 Thread Dirk Eddelbuettel
reassign ftp.debian.org quit I must have been absent-minded when I filed this as I got the Subject: right but use the package itself instead of ftp.debian.org. My bad! Dirk On 10 October 2021 at 12:04, Dirk Eddelbuettel wrote: | | Severity: normal | Package: its | | The its package

Re: [R-sig-Debian] singning key of repo expired

2021-11-16 Thread Dirk Eddelbuettel
On 16 November 2021 at 12:08, bodo riediger-klaus wrote: | Hello, | | i get a key-expired message when i try to update my repository | | root@merlot:/etc/apt/sources.list.d# cat rbase-stable.list | deb http://ftp.gwdg.de/pub/misc/cran/bin/linux/debian buster-cran40/ | | | W: GPG-Fehler:

Bug#999231: beancounter: missing required debian/rules targets build-arch and/or build-indep

2021-11-10 Thread Dirk Eddelbuettel
On 9 November 2021 at 22:28, Lucas Nussbaum wrote: | Source: beancounter | Version: 0.8.10 | Severity: important | Justification: Debian Policy section 4.9 | Tags: bookworm sid | User: debian...@lists.debian.org | Usertags: missing-build-arch-indep | | Dear maintainer, | | Your package does

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-11-09 Thread Dirk Eddelbuettel
On 8 November 2021 at 22:14, Sebastian Ramacher wrote: | Control: tags -1 moreinfo | Control: forwarded -1 https://release.debian.org/transitions/html/auto-gsl.html | | On 2021-10-31 14:29:40 -0500, Dirk Eddelbuettel wrote: | > | > Package: release.debian.org | > Severity: normal

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-11-09 Thread Dirk Eddelbuettel
On 8 November 2021 at 22:14, Sebastian Ramacher wrote: | Control: tags -1 moreinfo | Control: forwarded -1 https://release.debian.org/transitions/html/auto-gsl.html | | On 2021-10-31 14:29:40 -0500, Dirk Eddelbuettel wrote: | > | > Package: release.debian.org | > Severity: normal

Re: [Rcpp-devel] Package does not compile on MAC when running R-CMD-check github action

2021-11-07 Thread Dirk Eddelbuettel
Simon, Your Makevars [1] is very standard so I would suspect it may be the actions setup for macOS. Rcpp is still used by a large number of packages all of which appear to build just fine on macOS (as eg evidenced by the CRAN checks) if and when everything is setup correctly. Dirk [1]

Bug#998331: r-cran-tzdb: Embedded Howard Hinnant Date library

2021-11-02 Thread Dirk Eddelbuettel
On 2 November 2021 at 16:09, Andrea Pappacoda wrote: | Control: close -1 | | Thanks for your fast response. | | As you might have guessed I'm not really experienced in Debian | packaging, and I didn't know this was acceptable. | | I have no complaints then, I'm closing this :) | | Thanks

Bug#998331: r-cran-tzdb: Embedded Howard Hinnant Date library

2021-11-02 Thread Dirk Eddelbuettel
On 2 November 2021 at 15:43, Andrea Pappacoda wrote: | Source: r-cran-tzdb | Severity: normal | | -BEGIN PGP SIGNED MESSAGE- | Hash: SHA256 | | Dear Maintainer, | | I'm currently working to package the "date" library from Howard Hinnant, you | can see the ITP here:

Bug#998230: gsl-doc: LaTeX Error: File `tgtermes.sty' not found.

2021-11-01 Thread Dirk Eddelbuettel
On 1 November 2021 at 12:38, Andreas Beckmann wrote: | Source: gsl-doc | Version: 2.6-1 | Severity: serious | Tags: ftbfs sid bookworm | Justification: fails to build from source | | Hi, | | gsl-doc cannot be built any longer in sid: | | Latexmk: applying rule 'pdflatex'... | This is pdfTeX,

Bug#998230: gsl-doc: LaTeX Error: File `tgtermes.sty' not found.

2021-11-01 Thread Dirk Eddelbuettel
On 1 November 2021 at 12:38, Andreas Beckmann wrote: | Source: gsl-doc | Version: 2.6-1 | Severity: serious | Tags: ftbfs sid bookworm | Justification: fails to build from source | | Hi, | | gsl-doc cannot be built any longer in sid: | | Latexmk: applying rule 'pdflatex'... | This is pdfTeX,

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-10-31 Thread Dirk Eddelbuettel
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition GNU GSL 2.7 was release a few months ago, and we now realised (in the discussion of #993324 which also included upstream) that the upstream libtool instruction were in error by _not_

Bug#998192: release.debian.org: Transition for gsl-2.7 / libgsl26

2021-10-31 Thread Dirk Eddelbuettel
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition GNU GSL 2.7 was release a few months ago, and we now realised (in the discussion of #993324 which also included upstream) that the upstream libtool instruction were in error by _not_

[Bug 1948701] Re: Hard system lock under 5.* kernel on standard laptop

2021-10-31 Thread Dirk Eddelbuettel
If anybody has a hypothesis of what could be causing the lock, I would be game to trying different kernel builds (or parameterizations). So far I mostly glad I can run the machine again, even if it needs a 4.* kernel. Otherwise, is there a particular crash I could enable to diagnose? The

[Kernel-packages] [Bug 1948701] Re: Hard system lock under 5.* kernel on standard laptop

2021-10-31 Thread Dirk Eddelbuettel
If anybody has a hypothesis of what could be causing the lock, I would be game to trying different kernel builds (or parameterizations). So far I mostly glad I can run the machine again, even if it needs a 4.* kernel. Otherwise, is there a particular crash I could enable to diagnose? The

Bug#998064: sm: fails to display text containing letter 'e' due to errors in libfreetype after upgrade

2021-10-29 Thread Dirk Eddelbuettel
On 29 October 2021 at 18:14, Paul Wise wrote: | Package: sm, libfreetype6 | Version: 0.26-1, 2.11.0+dfsg-1 | Severity: important | File: /usr/games/sm | Usertags: regression Maintainer of _source package_ sm here: bad habit, 15 years ago binary packages like r-cran-sm used their upstream source

[Bug 1948701] [NEW] Hard system lock under 5.* kernel on standard laptop

2021-10-25 Thread Dirk Eddelbuettel
Public bug reported: This issue appeared first under 21.04, and I (wrongly) suspected a bug in the window manager or graphics stack. I posted on askubuntu at https://askubuntu.com/questions/1346317/ubuntu-21-04-and-21-10-lock- hard-with-basic-gui-redrawing-using-standard-intel-g and even

[Kernel-packages] [Bug 1948701] [NEW] Hard system lock under 5.* kernel on standard laptop

2021-10-25 Thread Dirk Eddelbuettel
Public bug reported: This issue appeared first under 21.04, and I (wrongly) suspected a bug in the window manager or graphics stack. I posted on askubuntu at https://askubuntu.com/questions/1346317/ubuntu-21-04-and-21-10-lock- hard-with-basic-gui-redrawing-using-standard-intel-g and even

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-24 Thread Dirk Eddelbuettel
On 24 October 2021 at 11:38, Sebastian Ramacher wrote: | On 2021-10-23 19:44:49 -0500, Dirk Eddelbuettel wrote: | > | > I have now 'patched' the upstream setting of GSL_AGE, this results (as kindly | > analysed by Sebastian) in new sonames '26' so I prepared a new version which | &g

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-24 Thread Dirk Eddelbuettel
On 24 October 2021 at 11:38, Sebastian Ramacher wrote: | On 2021-10-23 19:44:49 -0500, Dirk Eddelbuettel wrote: | > | > I have now 'patched' the upstream setting of GSL_AGE, this results (as kindly | > analysed by Sebastian) in new sonames '26' so I prepared a new version which | &g

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-23 Thread Dirk Eddelbuettel
I have now 'patched' the upstream setting of GSL_AGE, this results (as kindly analysed by Sebastian) in new sonames '26' so I prepared a new version which just went out to unstable. Unless I am mistaken, I need to get the release team on board for a proper transition. Correct? Dirk --

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-23 Thread Dirk Eddelbuettel
I have now 'patched' the upstream setting of GSL_AGE, this results (as kindly analysed by Sebastian) in new sonames '26' so I prepared a new version which just went out to unstable. Unless I am mistaken, I need to get the release team on board for a proper transition. Correct? Dirk --

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

2021-10-20 Thread Dirk Eddelbuettel
On 20 October 2021 at 09:31, Sebastian Meyer wrote: | If you set the environment variable inside a running R process, it will | only affect that process and child processes, but not an independent R | process launched from a shell like you seem to be doing here: Yes. That is somewhat common,

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-16 Thread Dirk Eddelbuettel
On 16 October 2021 at 17:50, Sebastian Ramacher wrote: | On 2021-10-15 13:54:07 -0500, Dirk Eddelbuettel wrote: | > | > On 15 October 2021 at 20:35, Sebastian Ramacher wrote: | > | On 2021-10-15 10:38:48 -0500, Dirk Eddelbuettel wrote: | > | > | > | > Turns out this was fu

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-16 Thread Dirk Eddelbuettel
On 16 October 2021 at 17:50, Sebastian Ramacher wrote: | On 2021-10-15 13:54:07 -0500, Dirk Eddelbuettel wrote: | > | > On 15 October 2021 at 20:35, Sebastian Ramacher wrote: | > | On 2021-10-15 10:38:48 -0500, Dirk Eddelbuettel wrote: | > | > | > | > Turns out this was fu

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-15 Thread Dirk Eddelbuettel
On 15 October 2021 at 20:35, Sebastian Ramacher wrote: | On 2021-10-15 10:38:48 -0500, Dirk Eddelbuettel wrote: | > | > Turns out this was fully my fault. The 2.7 release sets the SO number to 26, | > and I didn't use that. | | No, it doesn't. gsl 2.7 has current=26 and age=1

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-15 Thread Dirk Eddelbuettel
On 15 October 2021 at 20:35, Sebastian Ramacher wrote: | On 2021-10-15 10:38:48 -0500, Dirk Eddelbuettel wrote: | > | > Turns out this was fully my fault. The 2.7 release sets the SO number to 26, | > and I didn't use that. | | No, it doesn't. gsl 2.7 has current=26 and age=1

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-15 Thread Dirk Eddelbuettel
Turns out this was fully my fault. The 2.7 release sets the SO number to 26, and I didn't use that. So a new package will be forthcoming, and likely need a transition. That means I should upload to experimental first, right, to then request the transition? (I'll read up on it later today as a

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-15 Thread Dirk Eddelbuettel
Turns out this was fully my fault. The 2.7 release sets the SO number to 26, and I didn't use that. So a new package will be forthcoming, and likely need a transition. That means I should upload to experimental first, right, to then request the transition? (I'll read up on it later today as a

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-15 Thread Dirk Eddelbuettel
Graham, On 15 October 2021 at 13:34, Graham Inggs wrote: | > Yes. And I follow upstream. They didn't change :-/ | | Right, so please speak to your upstream. Dropping (or renaming) a Done. Looks like a 2.8 release is coming, so maybe the soname gets cleaned up there and we get to do (yet

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-15 Thread Dirk Eddelbuettel
Graham, On 15 October 2021 at 13:34, Graham Inggs wrote: | > Yes. And I follow upstream. They didn't change :-/ | | Right, so please speak to your upstream. Dropping (or renaming) a Done. Looks like a 2.8 release is coming, so maybe the soname gets cleaned up there and we get to do (yet

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-14 Thread Dirk Eddelbuettel
On 14 October 2021 at 23:20, Sebastian Ramacher wrote: | On 2021-10-14 15:52:03 -0500, Dirk Eddelbuettel wrote: | > | > Hi Sebastian, | > | > On 14 October 2021 at 22:46, Sebastian Ramacher wrote: | > | Hi Dirk | > | | > | On 2021-08-30 16:27:49 -0500, Di

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-14 Thread Dirk Eddelbuettel
On 14 October 2021 at 23:20, Sebastian Ramacher wrote: | On 2021-10-14 15:52:03 -0500, Dirk Eddelbuettel wrote: | > | > Hi Sebastian, | > | > On 14 October 2021 at 22:46, Sebastian Ramacher wrote: | > | Hi Dirk | > | | > | On 2021-08-30 16:27:49 -0500, Di

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-14 Thread Dirk Eddelbuettel
Hi Sebastian, On 14 October 2021 at 22:46, Sebastian Ramacher wrote: | Hi Dirk | | On 2021-08-30 16:27:49 -0500, Dirk Eddelbuettel wrote: | > | > On 30 August 2021 at 23:42, Niko Tyni wrote: | > | Package: libgsl25 | > | Version: 2.7+dfsg-2 | > | Control: affects -1 l

Bug#993324: libgsl25: ABI breakage: removed symbol gsl_linalg_QR_TR_decomp

2021-10-14 Thread Dirk Eddelbuettel
Hi Sebastian, On 14 October 2021 at 22:46, Sebastian Ramacher wrote: | Hi Dirk | | On 2021-08-30 16:27:49 -0500, Dirk Eddelbuettel wrote: | > | > On 30 August 2021 at 23:42, Niko Tyni wrote: | > | Package: libgsl25 | > | Version: 2.7+dfsg-2 | > | Control: affects -1 l

Bug#996451: src:gsl: fails to migrate to testing for too long: unresolved RC bug (found by autopkgtest breakage)

2021-10-14 Thread Dirk Eddelbuettel
On 14 October 2021 at 10:55, Paul Gevers wrote: | Source: gsl | Version: 2.6+dfsg-2 | Severity: serious | Control: close -1 2.7+dfsg-2 | Tags: sid bookworm | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The Release Team considers packages

Bug#996451: src:gsl: fails to migrate to testing for too long: unresolved RC bug (found by autopkgtest breakage)

2021-10-14 Thread Dirk Eddelbuettel
On 14 October 2021 at 10:55, Paul Gevers wrote: | Source: gsl | Version: 2.6+dfsg-2 | Severity: serious | Control: close -1 2.7+dfsg-2 | Tags: sid bookworm | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The Release Team considers packages

Bug#996033: ftp.debian.org: ROM: its -- retired upstream five years ago

2021-10-10 Thread Dirk Eddelbuettel
Severity: normal Package: its The its package was retired from CRAN five years ago [1] upon the request of its original author (who is a friend), but I kept it in Debian because it was generally useful. However, as time and packaging standards move on (while the package remains frozen) it is

Re: [R-pkg-devel] [Tagged] Re: multithreading in packages

2021-10-09 Thread Dirk Eddelbuettel
On 9 October 2021 at 12:08, Ben Bolker wrote: |FWIW there is some machinery in the glmmTMB package for querying, | setting, etc. the number of OpenMP threads. | | https://github.com/glmmTMB/glmmTMB/search?q=omp https://cloud.r-project.org/package=RhpcBLASctl Dirk --

Re: Bug#993750: rgtk2: FTBFS on s390x: smoke-test failure: caught segfault

2021-10-04 Thread Dirk Eddelbuettel
A new r-cran-rgtk2 build has been uploaded which no longer builds on s390x by default, so closing the bug report. If someone from the s390 team wants to try just add the arch to the Architecture line in debian/control. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: [Rcpp-devel] Any recent change that would remove Rcpp_precious_remove?

2021-10-01 Thread Dirk Eddelbuettel
Howdy, Somone (on r-help which I don't really follow for lack of time) called [3] this a 'quasi-FAQ': This problem is pratically a StackOverflow FAQ [1], with link to the Rcpp-devel mailing list [2]. [1]

Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files

2021-09-22 Thread Dirk Eddelbuettel via ESS-help
On 22 September 2021 at 15:15, Lionel Henry wrote: | We'd love to do a release but ESS is not in a good place right now. | Recent versions of Emacs interrupt background commands (essential to | completion and contextual help like eldoc) when the user starts | typing, which causes hard to solve

Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files

2021-09-22 Thread Dirk Eddelbuettel via ESS-help
On 20 September 2021 at 13:59, Sparapani, Rodney via ESS-help wrote: | Generally, this stuff should just work out-of-the-box. Understood. | And we are not a company like RStudio so this FOSS setup works for us as | developers and hopefully it still serves the users well. But legal structure

Re: [ESS] Advice on setting up ESS to edit and knit Rmarkdown files

2021-09-20 Thread Dirk Eddelbuettel via ESS-help
On 20 September 2021 at 13:59, Sparapani, Rodney via ESS-help wrote: | Over the last few years, we have moved away from having to set up features | with .emacs/etc. as much as possible. Generally, this stuff should just | work out-of-the-box. I completely concur and _love it_. I mostly just

Bug#991859: BioConductor MOFA2 needs basilisk - which installs a conda environment

2021-09-20 Thread Dirk Eddelbuettel
On 20 September 2021 at 07:50, Andreas Tille wrote: | On Sun, Sep 19, 2021 at 03:45:57PM -0500, Dirk Eddelbuettel wrote: | > | > | I'm thinking about a "fake-basilisk" like r-cran-bh or r-bioc-zlib. | > | > I had a similar thought. I am also f

Bug#991859: BioConductor MOFA2 needs basilisk - which installs a conda environment

2021-09-20 Thread Dirk Eddelbuettel
On 20 September 2021 at 07:50, Andreas Tille wrote: | On Sun, Sep 19, 2021 at 03:45:57PM -0500, Dirk Eddelbuettel wrote: | > | > | I'm thinking about a "fake-basilisk" like r-cran-bh or r-bioc-zlib. | > | > I had a similar thought. I am also f

Bug#991859: BioConductor MOFA2 needs basilisk - which installs a conda environment

2021-09-19 Thread Dirk Eddelbuettel
On 19 September 2021 at 16:09, Andreas Tille wrote: | On Sun, Sep 19, 2021 at 05:31:14PM +0530, Nilesh Patra wrote: | > | > But I do wonder if more packages in future might as well end up needing basilisk too. | | I'm thinking about a "fake-basilisk" like r-cran-bh or r-bioc-zlib. I had a

Bug#991859: BioConductor MOFA2 needs basilisk - which installs a conda environment

2021-09-19 Thread Dirk Eddelbuettel
On 19 September 2021 at 16:09, Andreas Tille wrote: | On Sun, Sep 19, 2021 at 05:31:14PM +0530, Nilesh Patra wrote: | > | > But I do wonder if more packages in future might as well end up needing basilisk too. | | I'm thinking about a "fake-basilisk" like r-cran-bh or r-bioc-zlib. I had a

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