Re: [R-pkg-devel] new maintainer for CRAN package XML

Dear Uwe, Did CRAN ever reach a decision here with a suitable volunteer (or group of volunteers) ? The state of XML came up again recently on mastodon, and it might be helpful to share an update if there is one. Thanks, as always, for all you and the rest of the team do for CRAN. Cheers,

[Rd] RSS Feed of NEWS needs a hand

Years ago Duncan set up a nightly job to feed RSS based off changes to NEWS, borrowing some setup parts from CRANberries as for example the RSS 'compiler'. That job is currently showing the new \I{...} curly protection in an unfavourable light. Copying from the RSS reader I had pointed at this

Bug#1066403: R packages failing to build with missing -ltirpc are actually an issue in r-base

-Depends to fix build issue from side effects of t64 transition (Closes: #1065216) -- Dirk Eddelbuettel Mon, 04 Mar 2024 08:54:45 -0600 I will take care of it in -3. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1066403: R packages failing to build with missing -ltirpc are actually an issue in r-base

-Depends to fix build issue from side effects of t64 transition (Closes: #1065216) -- Dirk Eddelbuettel Mon, 04 Mar 2024 08:54:45 -0600 I will take care of it in -3. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 15:12, Duncan Murdoch wrote: | On 05/03/2024 2:26 p.m., Dirk Eddelbuettel wrote: | > The default behaviour is to build after every commit to the main branch. But | > there are options. On the repo I mentioned we use | > | > "branch": "*rele

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 13:28, Duncan Murdoch wrote: | What I'm seeing is that the tags are ignored, and it is distributing the | HEAD of the main branch. I don't think most users should be using that | version: in my packages it won't have had full reverse dependency | checks, I only do that

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 11:56, Duncan Murdoch wrote: | I have mixed feelings about r-universe. On the one hand, it is really | nicely put together, and it offers the service described above. On the | other, it's probably a bad idea to follow its advice and use | install.packages() with `repos`

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 06:25, Duncan Murdoch wrote: | You could make a compatible version of `survivalmodels` available on a | non-CRAN website, and refer to that website in the | Additional_repositories field of DESCRIPTION. Every r-universe sub-site fits that requirement. For this package

Bug#1065216: r-base: recent libc6-dev change causes the xdr feature to be dropped

On 1 March 2024 at 23:36, Aurelien Jarno wrote: | Source: r-base | Version: 4.3.3-1 | Severity: serious | Tags: ftbfs | Justification: fails to build from source (but built successfully in the past) | User: debian-gl...@lists.debian.org | Usertags: libtirpc-dev | | Dear maintainer, | |

Bug#1065216: r-base: recent libc6-dev change causes the xdr feature to be dropped

On 1 March 2024 at 23:36, Aurelien Jarno wrote: | Source: r-base | Version: 4.3.3-1 | Severity: serious | Tags: ftbfs | Justification: fails to build from source (but built successfully in the past) | User: debian-gl...@lists.debian.org | Usertags: libtirpc-dev | | Dear maintainer, | |

Re: [Rcpp-devel] segfault on exit CRAN+Intel only

Hi Murray, On 4 March 2024 at 07:03, Murray Efford wrote: | Dirk | Thanks for a very helpful reply. I'll simplify my return values. | | I mentioned Intel with rhub2 in my earlier post here, but I'm sorry | that was somewhat buried. Debugging is somewhere between painful and | impossible when

Re: [Rcpp-devel] segfault on exit CRAN+Intel only

And "beauty" (ahem) of discussion scattered over two mailing lists: I now see you have a testbed via rhub2 (good) even though it does not reproduce (hm...). So you could still try the suggested simplication. Cheers, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: [Rcpp-devel] segfault on exit CRAN+Intel only

On 3 March 2024 at 20:47, Murray Efford wrote: | A couple of days ago I posted on R-package-devel about a mysterious | segfault from R CMD checks of my package secrdesign (see | https://CRAN.R-project.org/package=secrdesign, and | https://github.com/MurrayEfford/secrdesign) The issue rises only

Re: [Rcpp-devel] RcppArmadillo with -fopenmp: Not using all available cores

the following: | | > extSoftVersion()["BLAS"] Ah yes -- I keep forgetting about that one. Good reminder! | Thanks for your help! Always a pleasure. Glad you are all set. Dirk | On Sat, Feb 24, 2024 at 9:17 AM Dirk Eddelbuettel wrote: | | | On 24 February 2024 at 11:44, Ro

Re: [Rcpp-devel] Segfault in wrapping code in Rcpp

Hi Nikhil, Don't post images. I read in a text-based reader. The mailing list software also scrubs html (I think). I would simplify. Start with the simplest Rcpp Modules setup. Then add. Check checking. Eventually on your way towards what you are doing now you may spot the error. Hope this

Bug#1063320: gretl: NMU diff for 64-bit time_t transition

On 29 February 2024 at 00:20, Steve Langasek wrote: | Dear maintainer, | | Please find attached a final version of this patch for the time_t | transition. This patch is being uploaded to unstable. | | Note that this adds a versioned build-dependency on dpkg-dev, to guard | against accidental

Bug#1063320: gretl: NMU diff for 64-bit time_t transition

On 29 February 2024 at 00:20, Steve Langasek wrote: | Dear maintainer, | | Please find attached a final version of this patch for the time_t | transition. This patch is being uploaded to unstable. | | Note that this adds a versioned build-dependency on dpkg-dev, to guard | against accidental

Bug#1062364: dieharder: NMU diff for 64-bit time_t transition

On 28 February 2024 at 21:28, mwhud...@fastmail.fm wrote: | Dear maintainer, | | Please find attached a final version of this patch for the time_t | transition. This patch is being uploaded to unstable. | | Note that this adds a versioned build-dependency on dpkg-dev, to guard | against

Bug#1062364: dieharder: NMU diff for 64-bit time_t transition

On 28 February 2024 at 21:28, mwhud...@fastmail.fm wrote: | Dear maintainer, | | Please find attached a final version of this patch for the time_t | transition. This patch is being uploaded to unstable. | | Note that this adds a versioned build-dependency on dpkg-dev, to guard | against

Bug#1064388: ess: New version 24.1.1

On 28 February 2024 at 10:17, Sébastien Villemot wrote: | Salut Dirk, | | Le mercredi 21 février 2024 à 06:54 -0600, Dirk Eddelbuettel a écrit : | > Source: ess | > Version: 24.01.0-1 | > Severity: minor | > | > Salut Seb -- and thanks for packaging the recent 24.1.0 which in

Re: [R-pkg-devel] Unable to access log operator in C

On 28 February 2024 at 19:05, Avraham Adler wrote: | I am hoping the solution to this question is simple, but I have not | been able to find one. I am building a routine in C to be called from | R. I am including Rmath.h. However, when I have a call to "log", I get | the error "called object

CRAN Package Matrix update and a possible transition or not

A couple of days ago, the (effective) Maintainer and rather active developer of the Matrix package Mikael Jagan (CC'ed) posted on the r-package-devel list (the primary list for R package development) that the upcoming change of Matrix 1.7-0, planned for March 11, will be _very midly disruptive_

CRAN Package Matrix update and a possible transition or not

A couple of days ago, the (effective) Maintainer and rather active developer of the Matrix package Mikael Jagan (CC'ed) posted on the r-package-devel list (the primary list for R package development) that the upcoming change of Matrix 1.7-0, planned for March 11, will be _very midly disruptive_

Re: [R-pkg-devel] Package required but not available: ‘arrow’

On 26 February 2024 at 09:19, Simon Urbanek wrote: | [requiring increased is] best way [..] and certainly the only good practice. No, not really. Another viewpoint, which is implemented in another project I contribute to, is where a version + build_revision tuple exists if, and only if, the

Re: [Rcpp-devel] RcppArmadillo with -fopenmp: Not using all available cores

rn arma::eig_sym(M); | })" | | size <- 1 | m <- matrix(rnorm(size^2), size, size) | m <- m * t(m) | | # This line compiles the above code with the -fopenmp flag. | sourceCpp(code = src, verbose = TRUE, rebuild = TRUE) | result <- getEigenValues(m) | print(result[1:10]) | | On Fri, Feb 23,

Re: [Rcpp-devel] RcppArmadillo with -fopenmp: Not using all available cores

On 23 February 2024 at 09:35, Robin Liu wrote: | Hi all, | | Here is an R script that uses Armadillo to decompose a large matrix and print | the first 10 eigenvalues. | | library(RcppArmadillo) | library(Rcpp) | | src <- | r"(#include | | // [[Rcpp::depends(RcppArmadillo)]] | | //

Re: [R-pkg-devel] Package required but not available: ‘arrow’

On 23 February 2024 at 15:53, Leo Mada wrote: | Dear Dirk & R-Members, | | It seems that the version number is not incremented: | # Archived | arrow_14.0.2.1.tar.gz   2024-02-08 11:57  3.9M | # Pending | arrow_14.0.2.1.tar.gz   2024-02-08 18:24  3.9M | | Maybe this is the reason why it got

Re: [R-pkg-devel] Package required but not available:‘arrow’

On 22 February 2024 at 04:01, Duncan Murdoch wrote: | For you to deal with this, you should make arrow into a suggested | package, For what it is worth, that is exactly what package tiledb does. Yet the Suggests: still lead to a NOTE requiring a human to override which did not happen until I

Bug#1064388: ess: New version 24.1.1

Source: ess Version: 24.01.0-1 Severity: minor Salut Seb -- and thanks for packaging the recent 24.1.0 which installs fine. There is by now a follow-up 24.1.1 which would be nice to have too. Amities, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: [Rcpp-devel] Wrapping a c++ class with singleton using RCPP Module

On 21 February 2024 at 09:21, Iñaki Ucar wrote: | Could you please provide more details about what you tried so far and what are | the issues you found? A link to a public repo with a test case would be even | better. Seconded! I think I also did something like that 'way early' and 'way

Re: [Rd] Compiling libR as a standalone C library for java+jni (-fPIC)

Salut Pierre, On 20 February 2024 at 10:33, Pierre Lindenbaum wrote: | (cross-posted on SO: https://stackoverflow.com/questions/78022766) | | Hi all, | | I'm trying to compile R as a static library with the -fPIC flag so I can use it within java+JNI (is it only possible ?), but I cannot find

Re: [Rd] Tcl socket server (tcltk) does not work any more on R 4.3.2

On 20 February 2024 at 12:27, webmail.gandi.net wrote: | Dear list, | | It seems that something changed between R 4.2.3 and R 4.3 (tested with 4.3.2) that broke the Tcl socket server. Here is a reproducible example: | | - R process #1 (Tcl socket server): | | library(tcltk) | cmd <- r"( |

Re: [ESS] FW: [GNU ELPA] ESS version 24.1.1

On 18 February 2024 at 20:54, Brett Presnell via ESS-help wrote: | | Forgot to mention that you may need to uninstall and reinstall the ess | package after putting the :pin in place, but I'm not sure about that. | Restarting emacs is maybe needed too, but not sure about that either. The pin,

Re: [ESS] FW: [GNU ELPA] ESS version 24.1.1

Rodney et al, Thanks for the update(s)! Alas, I also seem to see ess20240131.1041 installed Emacs Speaks Statistics which seems to win over ess24.1.1 obsolete Emacs Speaks Statistics What is the

Re: [R-sig-Debian] Error building and installing with GCC ASAN in a Docker container

Hi Brent, On 15 February 2024 at 10:14, Brent G Ewing wrote: | Hi, | | I want to build a Docker container with R and various R packages built and | installed with the gcc address sanitizer enabled. I am working on a Debian | Bookworm system running on an x86_64 architecture. | | I start with

Re: [R-pkg-devel] CRAN uses an old version of clang

On 9 February 2024 at 08:59, Marcin Jurek wrote: | I recently submitted an update to my package. It previous version relied on | Boost for Bessel and gamma functions but a colleague pointed out to me that | they are included in the standard library beginning with the C++17 | standard. There is

Re: [R-pkg-devel] failing CRAN checks due to problems with dependencies

On 8 February 2024 at 13:28, Marcin Jurek wrote: | Ok, this makes sense! I saw that Rcpp was failing the checks too but I | wasn't sure if I should resubmit or wait. Thanks! For completeness, it was not caused by Rcpp but rather by a mix on new clang and gcc versions which somehow got into each

Bug#1063320: gretl: NMU diff for 64-bit time_t transition

On 6 February 2024 at 06:43, Steve Langasek wrote: | Source: gretl | Version: 2023c-2 | Severity: serious | Tags: patch pending sid trixie | Justification: library ABI skew on upgrade | User: debian-...@lists.debian.org | Usertags: time-t | | NOTICE: these changes must not be uploaded to

Bug#1063320: gretl: NMU diff for 64-bit time_t transition

On 6 February 2024 at 06:43, Steve Langasek wrote: | Source: gretl | Version: 2023c-2 | Severity: serious | Tags: patch pending sid trixie | Justification: library ABI skew on upgrade | User: debian-...@lists.debian.org | Usertags: time-t | | NOTICE: these changes must not be uploaded to

Bug#1062364: dieharder: NMU diff for 64-bit time_t transition

On 1 February 2024 at 07:21, mwhud...@debian.org wrote: | Source: dieharder | Version: 3.31.1.4-1 | Severity: serious | Tags: patch pending | Justification: library ABI skew on upgrade | User: debian-...@lists.debian.org | Usertags: time-t | | Dear maintainer, | | As part of the 64-bit time_t

Re: [R-pkg-devel] r-oldrel-linux- not in CRAN checks?

On 7 February 2024 at 09:15, Vincent van Hees wrote: | Thanks Ivan, In that case I will conclude that it is time to upgrade my | Ubuntu 18 machine. I just wasn't sure whether there is still a need for | keeping my own package Ubuntu 18 compatible, but if dependencies like Rfast | do not do it

Re: [Rd] Advice debugging M1Mac check errors

On 4 February 2024 at 20:41, Holger Hoefling wrote: | I wanted to ask if people have good advice on how to debug M1Mac package | check errors when you don´t have a Mac? Is a cloud machine the best option | or is there something else? a) Use the 'mac builder' CRAN offers:

Bug#1063047: Unable to run R CMD Rserve

Appears to work based on a quick check in Docker: root@8d41067e72ce:/work# dpkg -i r-cran-rserve_1.8-13-2_amd64.deb Selecting previously unselected package r-cran-rserve. (Reading database ... 17542 files and directories currently installed.) Preparing to unpack

Bug#1063047: Unable to run R CMD Rserve

On 4 February 2024 at 18:12, Jerome Charaoui wrote: | Package: r-cran-rserve | Version: 1.8-13-1 | Severity: important | | Hello, | | Running the command "R CMD Rserve" doesn't work because of missing | symlinks in the package. The error message shown is: | | /usr/lib/R/bin/Rcmd: 64: exec:

Re: [R-pkg-devel] Bioconductor reverse dependency checks for a CRAN package

Ivan, On 30 January 2024 at 18:56, Ivan Krylov via R-package-devel wrote: | Hello R-package-devel, | | What would you recommend in order to run reverse dependency checks for | a package with 182 direct strong dependencies from CRAN and 66 from | Bioconductor (plus 3 more from annotations and

Re: [R-pkg-devel] lost braces note on CRAN pretest related to \itemize

On 23 January 2024 at 19:39, Patrick Giraudoux wrote: | Has anyone an idea about what is going wrong ? \item has no braces following it. From a package I submitted today and for which I still have NEWS.Rd in the editor (indented here): \section{Changes in version 0.0.22 (2024-01-23)}{

Re: [R-pkg-devel] New Package Removal because Shared Library Too Large from Debugging Symbols

Johann, On 20 January 2024 at 14:38, Johann Gaebler wrote: | Hi everyone, | | I received the following message regarding `rar` , a package that I put up on CRAN two days ago: | | > Dear maintainer, | > | > Please see the problems shown on | >

Bug#1060101: Boost 1.81 removal

On 14 January 2024 at 06:49, Dirk Eddelbuettel wrote: | | FYI two days before you filed #1060101 I actually happened to have updated | r-cran-bh to 1.84.0 (upstream, which is me, went to the 1.84.0 version | released in December as Boost releases every four months) using 1.83: | |r-cran-bh

Bug#1060101: Boost 1.81 removal

On 14 January 2024 at 06:49, Dirk Eddelbuettel wrote: | | FYI two days before you filed #1060101 I actually happened to have updated | r-cran-bh to 1.84.0 (upstream, which is me, went to the 1.84.0 version | released in December as Boost releases every four months) using 1.83: | |r-cran-bh

Re: [R-pkg-devel] current docker image for ASAN

On 16 January 2024 at 15:54, Steven Scott wrote: | Greetings everyone, though I expect this message is mainly for Dirk. | | CRAN checks of my bsts/Boom package generate an ASAN error that the CRAN | maintainers have asked me to look into. I recall doing this before (this | error has been there

Re: [R-pkg-devel] checking CRAN incoming feasibility

On 17 January 2024 at 09:42, Simon Urbanek wrote: | that check always hangs for me (I don't think it likes NZ ;)), so I just use | | _R_CHECK_CRAN_INCOMING_REMOTE_=0 R CMD check --as-cran ... You can also set it in Renviron files consulted just for checks: $ grep INCOMING_=

Re: [R-pkg-devel] test failure: oldrel

done 4.3.2 2024-01-16 America/Chicago 4.2.2 2024-01-15 18:00:00 America/Chicago edd@rob:~$ Thanks to Seb for the cluebat wave. Dirk | | | On Tue, Jan 16, 2024 at 9:59 AM Dirk Eddelbuettel wrote: | | | Doesn't seem to be the case as it moderately easy to check (especially when | y

[R-pkg-devel] test failure: oldrel

Doesn't seem to be the case as it moderately easy to check (especially when you happen to have local images of r-base around anyway): edd@rob:~$ for v in 4.3.2 4.2.2 4.1.3 4.0.5 3.6.3 3.5.3 3.4.4 3.3.3; do echo -n "R ${v}: "; docker run --rm -ti r-base:${v} Rscript -e 'as.POSIXct(Sys.Date(),

Re: [R-sig-Debian] R

Hi, Can you please resend, but this time not in html format? The mailing list manager software swallows html; your email did not contain any plain text so there is nothing for us to read and (hopefully) help you with. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1060101: Boost 1.81 removal

+b2 * debian/control: Set Build-Depends: to current R version * debian/control: Switch to virtual debhelper-compat (= 13) -- Dirk Eddelbuettel Wed, 10 Jan 2024 07:20:09 -0600 So this should sort itself out by itself in a matter of days. r-cran-bh is healthy: https

Bug#1060101: Boost 1.81 removal

+b2 * debian/control: Set Build-Depends: to current R version * debian/control: Switch to virtual debhelper-compat (= 13) -- Dirk Eddelbuettel Wed, 10 Jan 2024 07:20:09 -0600 So this should sort itself out by itself in a matter of days. r-cran-bh is healthy: https

Bug#1059875: RM: rJava [i386] -- RoM: FTBFS as i386 builds no longer maintained upstream

( Resending to now correctly-typed package r-cran-rcdklibs -- Dirk ) On 11 January 2024 at 07:09, Dirk Eddelbuettel wrote: | | Package: ftp.debian.org | Severity: normal | | The rJava package (source package 'rjava', binary package r-cran-rjava) no | longer builds on i386 as most

Bug#1059875: RM: rJava [i386] -- RoM: FTBFS as i386 builds no longer maintained upstream

( Resending to now correctly-typed package r-cran-rcdklibs -- Dirk ) On 11 January 2024 at 07:09, Dirk Eddelbuettel wrote: | | Package: ftp.debian.org | Severity: normal | | The rJava package (source package 'rjava', binary package r-cran-rjava) no | longer builds on i386 as most

Bug#1059875: RM: rJava [i386] -- RoM: FTBFS as i386 builds no longer maintained upstream

1 | source rjava | 1.0-10-1 | source Maintainer: Dirk Eddelbuettel --- Reason --- -- Checking reverse dependencies... # Broken Depends: libgoby-java: goby-java r-cran-rcdk: r-cran-rcdk r-cran-rcdklibs: r-cra

Bug#1060441: RM: rJava [i386] -- RoM: FTBFS as i386 builds no longer maintained upstream

1 | source rjava | 1.0-10-1 | source Maintainer: Dirk Eddelbuettel --- Reason --- -- Checking reverse dependencies... # Broken Depends: libgoby-java: goby-java r-cran-rcdk: r-cran-rcdk r-cran-rcdklibs: r-cra

Re: [R-pkg-devel] Suggests with non-CRAN packages

On 10 January 2024 at 16:25, Uwe Ligges wrote: | | | On 10.01.2024 15:35, Josiah Parry wrote: | > Thanks, all. As it goes, the package submission failed. The package that | > is suggested is available at https://r.esri.com/bin/ | > and as such provided

Re: [Rcpp-devel] Numerical precision in rotations with Eigen

On 10 January 2024 at 09:52, Rafael Ayala Hernandez wrote: | Hi, | | I have implemented a function to rotate a 3D vector a given angle around a given axis (basically wrapping the functionality provided by Eigen::AngleAxis) as an Rcpp function. | Below is an extract from the source file: | |

Re: [R-sig-Debian] SOLVED- Re: help installing R on Linux Mint 21.2

Luben, We all have different types of learning and how we approach this, let alone how we decompose things. With that, sorry you found this frustrating. Many of us put volunteer time into this trying to make things 'possible' and preferably 'easy' but we don't always get there. That said, I

Bug#1059875: src:rjava: fails to migrate to testing for too long: FTBFS on i386

(Adrian: Added you to CCs per suggestion of Paul.) Hi Paul, On 2 January 2024 at 21:00, Paul Gevers wrote: | Hi Dirk, | | On 02-01-2024 20:42, Dirk Eddelbuettel wrote: | > | The Release Team considers packages that are out-of-sync between testing | > | and unstable for more than 3

Bug#1059875: src:rjava: fails to migrate to testing for too long: FTBFS on i386

(Adrian: Added you to CCs per suggestion of Paul.) Hi Paul, On 2 January 2024 at 21:00, Paul Gevers wrote: | Hi Dirk, | | On 02-01-2024 20:42, Dirk Eddelbuettel wrote: | > | The Release Team considers packages that are out-of-sync between testing | > | and unstable for more than 3

Bug#1059875: src:rjava: fails to migrate to testing for too long: FTBFS on i386

On 2 January 2024 at 20:07, Paul Gevers wrote: | Source: rjava | Version: 1.0-6-1 | Severity: serious | Control: close -1 1.0-10-1 | Tags: sid trixie ftbfs | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The Release Team considers packages

Bug#1059875: src:rjava: fails to migrate to testing for too long: FTBFS on i386

On 2 January 2024 at 20:07, Paul Gevers wrote: | Source: rjava | Version: 1.0-6-1 | Severity: serious | Control: close -1 1.0-10-1 | Tags: sid trixie ftbfs | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The Release Team considers packages

Re: [R-sig-Debian] installing tydiverse on Linux Mint

Ivan, On 2 January 2024 at 10:15, Ivan Krylov wrote: | I've just read both scripts and I don't see them using sudo (the | comments say it has to be run as root). Have you edited the script? [...] | You need to find this line in /etc/apt/sources.list* and replace | victoria-cran40 with

Re: [R-sig-Debian] installing tydiverse on Linux Mint

Luben, r2u instructions are at the site; there are two scripts for Ubuntu focal and jammy. I tested those repeatedly. Many people used them. We also support Docker installationsl; the docker images are also rebuilt frequently. r2u is also used around the clock on CI, likely most often 'from

[R-sig-Debian] SOLVED- Re: help installing R on Linux Mint 21.2

Luben, I am glad to hear you sorted it out. As far as I can tell there are two or three issues here: - you are on Mint which is not 'officially' support by posit (Debian/Ubuntu are) - the installation instructions have said for a decade+ to download the .deb and then install it with gdebi

Re: [R-sig-Debian] custom built R will not change BLAS/LAPACK with update-alternatives

On 30 December 2023 at 23:49, Ramon Diaz-Uriarte wrote: | All is good. (Just for the sake of curiosity, and if you have the time: why did you find those incantations suspicious?) Memory is fuzzy and no ECC in my wetware :) but as I seem to recall it had to do with my fears over filenames not

Re: [R-sig-Debian] custom built R will not change BLAS/LAPACK with update-alternatives

What blas/lapack -dev libraries do you installed when you build? I varied this over the two+ decades for the Debian build but any consistent pair of LAPACK and BLAS should work. From the aforementioned build log: Get: 150 http://ftp.us.debian.org/debian sid/main amd64 libblas3 amd64 3.11.0-2

Re: [R-sig-Debian] custom built R will not change BLAS/LAPACK with update-alternatives

On 30 December 2023 at 21:57, Ivan Krylov wrote: | On Sat, 30 Dec 2023 18:37:06 +0100 | Ramon Diaz-Uriarte wrote: | | > configure: searching for an external BLAS | > configure: searching for BLAS in default libraries | > checking for dgemm_... no | > configure: searching for OpenBLAS | | The

Re: [R-sig-Debian] custom built R will not change BLAS/LAPACK with update-alternatives

If you match the exact build-deps I use and the exact options from debian/rules you should end up with the exact same output. As that is whay you desire but do not get we need to drill down into where it deviates. FWIW last time I build the Debian the (relevant) part (of the large) configure log

Re: [Rd] eval(parse()) within mutate() returning same value for all rows

On 29 December 2023 at 22:31, Mateo Obregón wrote: | Thanks Gabor, I like your solution that splits the args into separate columns, | in turn making the sprintf() call more interpretable . Well you may also like `tstrsplit()`, a gem inside data.table: > suppressMessages(library(data.table))

Re: [Rd] eval(parse()) within mutate() returning same value for all rows

On 29 December 2023 at 14:13, Mateo Obregón wrote: | Hi all- | | Looking through stackoverflow for R string combining examples, I found the | following from 3 years ago: | | | | The top

Re: [R-pkg-devel] portability question

The point of my email was that if [ `uname -s` = 'Darwin' ]; then ... allows for a clean branch between the (new here) macOS behaviour and (old, prior) behavior removing all concerns about 'portability' (per the Subject:). You missed 100% of that. Dirk -- dirk.eddelbuettel.com |

Re: [R-pkg-devel] portability question

On 20 December 2023 at 11:10, Steven Scott wrote: | The Boom package builds a library against which other packages link. The | library is built using the Makevars mechanism using the line | | ${AR} rc $@ $^ | | A user has asked me to change 'rc' to 'rcs' so that 'ranlib' will be run on | the

Re: [R-pkg-devel] CRAN submission struggle

Emailing 10mb blobs to every list subscriber is not ideal. Dirk PS Fortunes has that covered too > fortunes::fortune("mind read") There are actual error messages, and until you show them, we can not help as the mind reading machine is currently off for repairs. -- D

Re: [R-pkg-devel] Wrong mailing list: Could the 100 byte path length limit be lifted?

On 13 December 2023 at 16:02, Tomas Kalibera wrote: | | On 12/13/23 15:59, Dirk Eddelbuettel wrote: | > On 13 December 2023 at 15:32, Tomas Kalibera wrote: | > | Please don't forget about what has been correctly mentioned on this | > | thread already: there is essentially a 260 charac

Re: [R-pkg-devel] Wrong mailing list: Could the 100 byte path length limit be lifted?

On 13 December 2023 at 15:32, Tomas Kalibera wrote: | Please don't forget about what has been correctly mentioned on this | thread already: there is essentially a 260 character limit on Windows | (see | https://blog.r-project.org/2023/03/07/path-length-limit-on-windows/index.html | for

Re: [R-pkg-devel] Status of -mmacosx-version-min

PS One aspect I didn't mention clearly (my bad) that this does not affect all or even most packages: in most cases the src/Makevars should indeed be as simple as possible. But in _some_ cases we need to cooperate with external libraries and in some of these cases the switch has been seen to be

Re: [R-pkg-devel] Status of -mmacosx-version-min

On 10 December 2023 at 17:07, Simon Urbanek wrote: | As discussed here before packages should *never* set -mmacosx-version-min | or similar flags by hand. a) That is in conflict with what was said in the past; we have used an explicit min version of 10.14 for the C++17 we were using then (and

[R-pkg-devel] Status of -mmacosx-version-min

Last month, I had asked about the setting '-mmacosx-version-min' here. The setting can be used to specify what macOS version one builds for. It is, oddly enough, not mentioned in Writing R Extension but for both r-release and r-devel the R Administration manual states • Current CRAN macOS

Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)

On 9 December 2023 at 01:06, Charles Plessy wrote: | I do not know for r-bioc-netsam, but for r-bioc-org.hs.eg.db and similar | packages, it is because it is an "annotation package" made of data and | therefore not managed the same way as the other Bioconductor packages. | | This is why it

Bug#1054657: Transition seems to be blocked (Was: Bug#1054657: transition: r-bioc-biocgenerics)

On 9 December 2023 at 01:06, Charles Plessy wrote: | I do not know for r-bioc-netsam, but for r-bioc-org.hs.eg.db and similar | packages, it is because it is an "annotation package" made of data and | therefore not managed the same way as the other Bioconductor packages. | | This is why it

Re: [R-pkg-devel] problems with Maintainers in DESCRIPTION file

On 7 December 2023 at 20:58, María Olga Viedma Sillero wrote: | I receive the same note after fixing it, removing it, and checking Authors@R. I think the rejection is a false positive. | | Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64 | Check: CRAN incoming feasibility,

Re: [R] Convert character date time to R date-time variable.

`anytime` was written for this: > anytime::anytime("2020-09-17_00:00:00") [1] "2020-09-17 CDT" > class(anytime::anytime("2020-09-17_00:00:00")) [1] "POSIXct" "POSIXt" > Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: [R-pkg-devel] macos x86 oldrel backups?

Hi Simon, On 5 December 2023 at 23:17, Simon Urbanek wrote: | The high-sierra build packages are currently not built due to hardware issues. The macOS version is so long out of support by Apple (over 6 years) that it is hard to maintain it. Only big-sur builds are supported at this point.

Re: [R] Unable to add the CRAN apt repository

Steve, The better list for such questions is r-sig-debian. On 4 December 2023 at 13:41, Steve Gutreuter wrote: | I just upgraded from Linux Mint 20 to 21 and am no longer able to add the CRAN | Ubuntu repository to my list of repositories.  I am getting: | | $> sudo

Re: [ESS] [R-win] Difficulty installing R packages under Windows 11 / Cygwin

On 2 December 2023 at 22:06, Tomas Kalibera via ESS-help wrote: | R is not being tested under WSL. (From several arm lengths away:) WSL2 appears to be very solid. I had an early alpha tester of my (then brand-new) r2u [1] using and stressing it, it appears to work a like regular Ubuntu system

Re: [R-pkg-devel] URL woes at CRAN: Anaconda edition

Thank you all -- expecially Aron and Ivan for the deep dive on the underlying aspect of the hosting of that web property. And of course to Uwe for approving the package manually. For my taste, life is too short for all this. So users be damned, and I have now removed the badge. At the end of

[R-pkg-devel] URL woes at CRAN: Anaconda edition

I added a badge to point to Conda builds for the work repo: [](https://anaconda.org/conda-forge/r-tiledb) And as it goes with all good intentions I immediately got punished on the next upload: Found the following

Bug#1055922: rmatrix: ABI change in Matrix 1.6-2

Hi Graham On 30 November 2023 at 07:54, Graham Inggs wrote: | Hi Dirk | | On Thu, 30 Nov 2023 at 00:51, Dirk Eddelbuettel wrote: | > Ping squared. | > | > If I don't hear from you I may just close this. I believe this (non-, to me) | > issue has been taken care of. If you thin

Bug#1055922: rmatrix: ABI change in Matrix 1.6-2

Hi Graham On 30 November 2023 at 07:54, Graham Inggs wrote: | Hi Dirk | | On Thu, 30 Nov 2023 at 00:51, Dirk Eddelbuettel wrote: | > Ping squared. | > | > If I don't hear from you I may just close this. I believe this (non-, to me) | > issue has been taken care of. If you thin

Bug#1055922: rmatrix: ABI change in Matrix 1.6-2

On 27 November 2023 at 08:27, Dirk Eddelbuettel wrote: | | Graham, | | Quick ping to ask where we are we on this? Matrix is in testing so can this | be closed? Ping squared. If I don't hear from you I may just close this. I believe this (non-, to me) issue has been taken care of. If you

Bug#1055922: rmatrix: ABI change in Matrix 1.6-2

On 27 November 2023 at 08:27, Dirk Eddelbuettel wrote: | | Graham, | | Quick ping to ask where we are we on this? Matrix is in testing so can this | be closed? Ping squared. If I don't hear from you I may just close this. I believe this (non-, to me) issue has been taken care of. If you

Re: [Rcpp-devel] Rf_error() format string

Sorry for being slow to respond (very busy morning at work and play, got five such emails myself) but as Inaki and Georgi helpfully pointed out already the issue is _known_ and has a _fix_ at either the default branch of the Rcpp repo, or, if you prefer, via the Rcpp drat repo as detailed in

Bug#1055922: rmatrix: ABI change in Matrix 1.6-2

Graham, Quick ping to ask where we are we on this? Matrix is in testing so can this be closed? Cheers, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1055922: rmatrix: ABI change in Matrix 1.6-2

Graham, Quick ping to ask where we are we on this? Matrix is in testing so can this be closed? Cheers, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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