Bug#980809: Matrix package default tolerance on s390x (Re: Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x)

2021-02-17 Thread Dirk Eddelbuettel
wnloaded_packages$ (Obviously the if above could be indentented and all that.) Graham: What does that bigendian box say for Sys.info()[["machine"]] ? Should we test for endianness instead? And then maybe try to roll up to the cause of the difference? Dirk | Best, Martin |

Bug#980809: Matrix package default tolerance on s390x (Re: Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x)

2021-02-15 Thread Dirk Eddelbuettel
Martin, I have this long-running bug report against Matrix, triggered by glmmTMB on s390x. Graham has been chasing this patiently and we are now at the level of checking on a shell account on the appropriate hardware. We validated that everything does in fact "still break" with CRAN-current

Bug#980809: Matrix package default tolerance on s390x (Re: Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x)

2021-02-15 Thread Dirk Eddelbuettel
Martin, I have this long-running bug report against Matrix, triggered by glmmTMB on s390x. Graham has been chasing this patiently and we are now at the level of checking on a shell account on the appropriate hardware. We validated that everything does in fact "still break" with CRAN-current

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-02-14 Thread Dirk Eddelbuettel
On 14 February 2021 at 12:00, Graham Inggs wrote: | glmmTMB upstream came up with a minimal reproducer (see forwarded bug): | | stopifnot(require("testthat"), | require("glmmTMB"), | require("lme4")) | data("Orthodont", package="nlme") | fm1 <- glmmTMB(distance ~ age +

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-02-14 Thread Dirk Eddelbuettel
On 14 February 2021 at 12:00, Graham Inggs wrote: | glmmTMB upstream came up with a minimal reproducer (see forwarded bug): | | stopifnot(require("testthat"), | require("glmmTMB"), | require("lme4")) | data("Orthodont", package="nlme") | fm1 <- glmmTMB(distance ~ age +

Re: [R-pkg-devel] Subarchitectures

2021-02-12 Thread Dirk Eddelbuettel
On 11 February 2021 at 11:30, Balasubramanian Narasimhan wrote: | If GNU make is acceptable as a system requirement, you can get any R | configuration/runtime variable in Makevars, e.g. | | R_ARCH=$(shell $(R_HOME)/bin/Rscript -e 'cat(.Platform$r_arch)') You can switch to backticks to not

Bug#982465: Bug in r-base and r-cran-rcppparallel

2021-02-11 Thread Dirk Eddelbuettel
On 11 February 2021 at 16:06, Johannes Ranke wrote: | > | > The documentation does not list a search behaviour for bare library | > | > names on non-Windows systems. So completely ignoring the system library | > | > paths is kind of weird. | > | | > | I can see that it looks weird - but is it

Bug#982465: Bug in r-base and r-cran-rcppparallel

2021-02-11 Thread Dirk Eddelbuettel
On 11 February 2021 at 12:50, Johannes Ranke wrote: | Am Donnerstag, 11. Februar 2021, 12:20:33 CET schrieb Bastian Blank: | > Hi Johannes | | Hello Bastian! | | > On Thu, Feb 11, 2021 at 09:26:48AM +0100, Johannes Ranke wrote: | > > dyn.load is used in base R to load compiled code from R

Bug#982465: Bug in r-base and r-cran-rcppparallel

2021-02-10 Thread Dirk Eddelbuettel
On 10 February 2021 at 20:35, Bastian Blank wrote: | On Wed, Feb 10, 2021 at 01:30:10PM -0600, Dirk Eddelbuettel wrote: | > Thanks for the CVE. I am happy to discuss this with R Core and one fellow in | > particular. | > Before I do so can you clarify what you think the issue is? Loa

Bug#982465: Bug in r-base and r-cran-rcppparallel

2021-02-10 Thread Dirk Eddelbuettel
Hi Bastian, On 10 February 2021 at 20:03, Bastian Blank wrote: | Hi Dirk | | On Wed, Feb 10, 2021 at 12:18:04PM -0600, Dirk Eddelbuettel wrote: | > As for your suggested patch to R's own dynload.c: that is very well tested | > and robust system code I do not have any real int

Bug#982465: Bug in r-base and r-cran-rcppparallel

2021-02-10 Thread Dirk Eddelbuettel
Hi Bastian, Thanks for taking the time to propose a bug report. However (and please see below) I don't think this is the way forward. There have been a lot of recent changed in RcppParallel upstream (as I lurk on the GH repo which is part of our Rcpp org), and maybe some of these things will

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-02-08 Thread Dirk Eddelbuettel
Hi Graham, On 2 February 2021 at 11:32, Graham Inggs wrote: | Control: forwarded -1 https://github.com/glmmTMB/glmmTMB/issues/665 | | After another detour via #981623, r-cran-glmmtmb is now also rebuilt. | Even with the rebuilt r-cran-glmmtmb, I still see the "gradient | function must return a

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-02-08 Thread Dirk Eddelbuettel
Hi Graham, On 2 February 2021 at 11:32, Graham Inggs wrote: | Control: forwarded -1 https://github.com/glmmTMB/glmmTMB/issues/665 | | After another detour via #981623, r-cran-glmmtmb is now also rebuilt. | Even with the rebuilt r-cran-glmmtmb, I still see the "gradient | function must return a

[Rcpp-devel] Sorry about double and triple posts from me

2021-02-08 Thread Dirk Eddelbuettel
I am truly sorry about sending multiple posts. I did have an issue where my mail from this machine was blocked because as a Comcast host I pass mail too was a spam blacklist so I experimented sending via alternative setups, and as R-Forge email was apparently down too for a few days never got a

[Rcpp-devel] [ANN] More Micro Releases on Rcpp Drat Repo

2021-02-08 Thread Dirk Eddelbuettel
More micro-releases on the Rcpp-core drat: And once more new micro-releases on drat: - Rcpp 1.0.6.5 now with global Rcout and Rcerr object (if enabled at compiled), thanks once again to Inaki - RcppArmadillo 0.10.2.1.0 with upstream fixes in 10.2.1 Dirk --

Re: [Rcpp-devel] [ANN] Rcpp Micro Releases on Rcpp Drat Repo

2021-02-08 Thread Dirk Eddelbuettel
And once more new micro-releases on drat: - Rcpp 1.0.6.5 now with global Rcout and Rcerr object (if enabled at compiled), thanks once again to Inaki - RcppArmadillo 0.10.2.1.0 with upstream fixes in 10.2.1 Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: [Rcpp-devel] [ANN] Rcpp Micro Releases on Rcpp Drat Repo

2021-02-08 Thread Dirk Eddelbuettel
Another Rcpp release candidate for your testing pleasure: - Rcpp 1.0.6.5 with the next fine PR by Inaki allow global Rcout and Rcerr instances (using a compile-time #define to enable, so opt-in) Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#982069: /usr/local/lib/R owned by group staff even if /etc/staff-group-for-usr-local not present

2021-02-06 Thread Dirk Eddelbuettel
On 6 February 2021 at 15:17, Sébastien Villemot wrote: | Le samedi 06 février 2021 à 08:12 -0600, Dirk Eddelbuettel a écrit : | | > # edd 03 Apr 2003 cf Section 10.1.2 of Debian Policy | > # edd 06 Feb 2021 #982069, with a nod to Python's debian/PVER-minimal.posti

Bug#982069: /usr/local/lib/R owned by group staff even if /etc/staff-group-for-usr-local not present

2021-02-06 Thread Dirk Eddelbuettel
On 6 February 2021 at 14:57, Sébastien Villemot wrote: | Le samedi 06 février 2021 à 07:49 -0600, Dirk Eddelbuettel a écrit : | > So I now have this. Or do I need to protect /usr/local/lib/R/site- | > library too? | | You need to protect both. | | In order to simplify the code, you ca

Bug#982069: /usr/local/lib/R owned by group staff even if /etc/staff-group-for-usr-local not present

2021-02-06 Thread Dirk Eddelbuettel
So I now have this. Or do I need to protect /usr/local/lib/R/site-library too? # edd 03 Apr 2003 cf Section 10.1.2 of Debian Policy # edd 06 Feb 2021 #982069 if [ ! -e /usr/local/lib/R ]; then if [ -f /etc/staff-group-for-usr-local ]; then if mkdir /usr/local/lib/R

Bug#982069: /usr/local/lib/R owned by group staff even if /etc/staff-group-for-usr-local not present

2021-02-06 Thread Dirk Eddelbuettel
On 6 February 2021 at 10:04, Sébastien Villemot wrote: | Package: r-base-core | Version: 3.5.2-1 That is two+ years behind (3.5.0 released April 2018, 3.6.0 in April 2019, 4.0.0 last year -- and 4.1.0 soon). | Severity: normal | | Hi Dirk, | | The /usr/local/lib/R directory (and its

Re: [R-pkg-devel] Cache in vignette not working when checking a package

2021-02-01 Thread Dirk Eddelbuettel
On 1 February 2021 at 20:21, Jose Barrera wrote: | Many thanks for your help Thierry but unfortunately I can't see the link | between your first reply and my issue (of course, that's my fault). Thierry very gently (yet correctly) suggested to have the "cached" results as "precomputed"

Re: [R-sig-Debian] 32 bit 64 bit question, ELFCLASS32 error

2021-02-01 Thread Dirk Eddelbuettel
On 1 February 2021 at 10:20, semih ozlem wrote: | Hi everyone, | | On a usb with knoppix live uname -a gives the response Wow. Blast from the past. | Linux Microknoppix 5.3.5-64 #16 SMP PREEMPT Wed Oct 23 02:08:38 CEST 2019 | x86_64 GNU/Linux | | uname -i | | unknown | | I am trying to run

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-31 Thread Dirk Eddelbuettel
On 31 January 2021 at 20:09, Graham Inggs wrote: | Hi Dirk | | On Sun, 31 Jan 2021 at 16:13, Dirk Eddelbuettel wrote: | > This is a bug in glmmTMB. | | I don't see how you can be so sure. Experience around R. glmmTMB is a huge package with many dependencies, there will be a stale

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-31 Thread Dirk Eddelbuettel
On 31 January 2021 at 20:09, Graham Inggs wrote: | Hi Dirk | | On Sun, 31 Jan 2021 at 16:13, Dirk Eddelbuettel wrote: | > This is a bug in glmmTMB. | | I don't see how you can be so sure. Experience around R. glmmTMB is a huge package with many dependencies, there will be a stale

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-31 Thread Dirk Eddelbuettel
On 31 January 2021 at 09:20, Graham Inggs wrote: | Control: reopen -1 | | Hi Dirk | | Paul's test results showed that the run-unit-test autopkgtest still | fails with the same errors ( | Error: gradient function must return a numeric vector of length...) as | in my original report. | | | The

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-31 Thread Dirk Eddelbuettel
On 31 January 2021 at 09:20, Graham Inggs wrote: | Control: reopen -1 | | Hi Dirk | | Paul's test results showed that the run-unit-test autopkgtest still | fails with the same errors ( | Error: gradient function must return a numeric vector of length...) as | in my original report. | | | The

Re: [R-pkg-devel] Testing on old R versions

2021-01-28 Thread Dirk Eddelbuettel
On 28 January 2021 at 16:50, Duncan Murdoch wrote: | Thanks Dirk, Neal and Nathan. I ended up going with Dirk's suggestion. | | So far I haven't got it to work in 3.2.0; I probably won't put much | effort into supporting that old version. But it's fine in 3.4.0 and | 3.5.0, and I'm trying

Re: [R-pkg-devel] Testing on old R versions

2021-01-28 Thread Dirk Eddelbuettel
The Rocker Project provides both rocker/r-ver (with package snapshotting) as well as the (much smaller, just R) rocker/r-base images which are then passed on to the Docker team to become the official r-base image. These go back to 3.1.3 with (almost if not all) interim releases, see

Bug#980809: [R-pkg-team] Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-28 Thread Dirk Eddelbuettel
Hi Graham, On 28 January 2021 at 08:19, Graham Inggs wrote: | On Thu, 28 Jan 2021 at 01:12, Dirk Eddelbuettel wrote: | > Any update here? It still points at Matrix aka rmatrix aka r-cran-matrix, | > and I still think wrongly. | | I'm still waiting for the results of the autopkgtest a

Bug#980809: [R-pkg-team] Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-28 Thread Dirk Eddelbuettel
Hi Graham, On 28 January 2021 at 08:19, Graham Inggs wrote: | On Thu, 28 Jan 2021 at 01:12, Dirk Eddelbuettel wrote: | > Any update here? It still points at Matrix aka rmatrix aka r-cran-matrix, | > and I still think wrongly. | | I'm still waiting for the results of the autopkgtest a

Re: [ESS] unexpected behavior for Emacs-27.1-1-modified-1 for two MacBooks.

2021-01-27 Thread Dirk Eddelbuettel via ESS-help
On 26 January 2021 at 18:59, Dirk Eddelbuettel via ESS-help wrote: | | On 26 January 2021 at 22:07, Stephen Berman via ESS-help wrote: | | > I. Both machines report in *Messages* | | >Package cl is deprecated | | | | The NEWS file in Emacs 27 says: | | | | ** The 'cl' package

Bug#980809: [R-pkg-team] Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-27 Thread Dirk Eddelbuettel
Graham, Any update here? It still points at Matrix aka rmatrix aka r-cran-matrix, and I still think wrongly. Best, Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#980809: [R-pkg-team] Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-27 Thread Dirk Eddelbuettel
Graham, Any update here? It still points at Matrix aka rmatrix aka r-cran-matrix, and I still think wrongly. Best, Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: [Rcpp-devel] [ANN] Rcpp Micro Releases on Rcpp Drat Repo

2021-01-26 Thread Dirk Eddelbuettel
And more micro-releases on drat: - Rcpp 1.0.6.4 now with an additional 'echo' argument to evaluate R code in sourceCpp() silently, plus a removed unused variable - RcppArmadillo 0.10.2.0.0 with an upstream update, will go to CRAN once a month since last release passed Both had the usual

Re: [ESS] unexpected behavior for Emacs-27.1-1-modified-1 for two MacBooks.

2021-01-26 Thread Dirk Eddelbuettel via ESS-help
On 26 January 2021 at 22:07, Stephen Berman via ESS-help wrote: | > I. Both machines report in *Messages* | >Package cl is deprecated | | The NEWS file in Emacs 27 says: | | ** The 'cl' package is now officially deprecated in favor of 'cl-lib'. I know. What I do not know is which of the

Re: [ESS] unexpected behavior for Emacs-27.1-1-modified-1 for two MacBooks.

2021-01-26 Thread Dirk Eddelbuettel via ESS-help
On 26 January 2021 at 18:49, Richard M. Heiberger via ESS-help wrote: | I. Both machines report in *Messages* |Package cl is deprecated I have that too on the 27.1 build I use on Ubuntu (based on the current Debian source package I rebuilt). I'd love to get rid of that. | II. When I

Bug#981064: ITP: xrprof -- External sampling profiler for R

2021-01-25 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: xrprof Version : 0.3.1 Upstream Author : Aaron Jacobs * URL or Web page : https://github.com/atheriel/xrprof * License : GPL-2 Description : External sampling profiler for R This (still

Bug#981064: ITP: xrprof -- External sampling profiler for R

2021-01-25 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: xrprof Version : 0.3.1 Upstream Author : Aaron Jacobs * URL or Web page : https://github.com/atheriel/xrprof * License : GPL-2 Description : External sampling profiler for R This (still

Bug#981064: ITP: xrprof -- External sampling profiler for R

2021-01-25 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: xrprof Version : 0.3.1 Upstream Author : Aaron Jacobs * URL or Web page : https://github.com/atheriel/xrprof * License : GPL-2 Description : External sampling profiler for R This (still

Bug#980902: [R-pkg-team] Bug#980902: r-cran-tmb: prints warning when rmatrix is upgraded

2021-01-25 Thread Dirk Eddelbuettel
On 25 January 2021 at 21:39, Graham Inggs wrote: | Thanks again for your input on this issue! Always a pleasure :) Best, Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#980902: rmatrix: which reverse dependencies need rebuilds?

2021-01-25 Thread Dirk Eddelbuettel
On 25 January 2021 at 09:17, Graham Inggs wrote: | Hi | | On Sun, 24 Jan 2021 at 18:06, Graham Inggs wrote: | > I'm awaiting autopkgtest results on the binNMU'd r-cran-tmb. I will | > update this bug and #980809 when they are in. | | The autopkgtests for r-cran-tmb [1] and r-cran-glmmtmb [2]

Bug#980902: r-cran-tmb: prints warning when rmatrix is upgraded

2021-01-25 Thread Dirk Eddelbuettel
On 25 January 2021 at 10:21, Andreas Tille wrote: | Hi Graham, | | On Mon, Jan 25, 2021 at 10:31:36AM +0200, Graham Inggs wrote: | > Control: tags -1 + patch | > | > The attached patch upgrades the warning() to a stop(). | > This will cause r-cran-tmb's autopkgtests to fail whenever rmatrix is

Bug#980902: rmatrix: which reverse dependencies need rebuilds?

2021-01-24 Thread Dirk Eddelbuettel
Hi Graham, On 24 January 2021 at 18:06, Graham Inggs wrote: | Hi Dirk | | On Sun, 24 Jan 2021 at 14:47, Dirk Eddelbuettel wrote: | > R code can promote warnings to errors on a per-session basis: | | Thanks! This could be useful in the r-cran-tmb autopkgtest. | | > I am still not quit

Bug#980902: rmatrix: which reverse dependencies need rebuilds?

2021-01-24 Thread Dirk Eddelbuettel
Howdy, On 24 January 2021 at 18:01, Graham Inggs wrote: | Hi Andreas | | On Sun, 24 Jan 2021 at 09:55, Andreas Tille wrote: | > dh-r injects versioned dependencies if this is specified in the | > DESCRIPTION file of an r-* package. If this is not specified we | > need to add this manually

Bug#980902: rmatrix: which reverse dependencies need rebuilds?

2021-01-24 Thread Dirk Eddelbuettel
Hi Graham, On 24 January 2021 at 17:53, Graham Inggs wrote: | On Sun, 24 Jan 2021 at 07:10, Dirk Eddelbuettel wrote: | > There is a confusion here. You filed this again rmatrix (aka "Matrix"). | > Matrix does not impose dependencies -- dependent packages do. | | I filed

Bug#980902: rmatrix: which reverse dependencies need rebuilds?

2021-01-24 Thread Dirk Eddelbuettel
On 24 January 2021 at 06:08, Graham Inggs wrote: | The actual warning message is generated by r-base, is there a way to | make this an error instead of a warning? R code can promote warnings to errors on a per-session basis: > warning("I am just a warning") Warning message: I am just

Bug#980902: rmatrix: which reverse dependencies need rebuilds?

2021-01-23 Thread Dirk Eddelbuettel
Graham, On 24 January 2021 at 06:08, Graham Inggs wrote: | Source: rmatrix | Version: 1.3-2-1 | Severity: important | Control: affects -1 src:r-cran-tmb | X-Debbugs-CC: debia...@lists.debian.org | | Hi R Maintainers There is a confusion here. You filed this again rmatrix (aka "Matrix").

Bug#980809: [R-pkg-team] Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-23 Thread Dirk Eddelbuettel
Hi Graham, On 23 January 2021 at 00:21, Graham Inggs wrote: | On Fri, 22 Jan 2021 at 23:38, Dirk Eddelbuettel wrote: | > Can you still please talk to the corresponding Debian maintainer for glmmTMB | > so that he/she can walk it upstream? | | I have assigned this bug to both packages,

Bug#980809: [R-pkg-team] Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-23 Thread Dirk Eddelbuettel
Hi Graham, On 23 January 2021 at 00:21, Graham Inggs wrote: | On Fri, 22 Jan 2021 at 23:38, Dirk Eddelbuettel wrote: | > Can you still please talk to the corresponding Debian maintainer for glmmTMB | > so that he/she can walk it upstream? | | I have assigned this bug to both packages,

Re: [R-pkg-devel] Rdmacros as Suggests rather than Imports

2021-01-22 Thread Dirk Eddelbuettel
Hi James, On 22 January 2021 at 15:42, James Pustejovsky wrote: | Thanks very much for your input! By "patch it out" do you mean modify my | package description for the Debian distribution only? Would it work to And code / content! Can't just alter the DESCRIPTION if the Rd still call

Bug#980809: [R-pkg-team] Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-22 Thread Dirk Eddelbuettel
Hi Graham, On 22 January 2021 at 23:13, Graham Inggs wrote: | Hi Dirk | | On Fri, 22 Jan 2021 at 22:39, Dirk Eddelbuettel wrote: | > Matrix 1.3.0 from December has long been known to fail. Please use release 1.3.2. | | The test at [2], run at 2021-01-22 17:34:51 UTC was against | r-c

Bug#980809: [R-pkg-team] Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-22 Thread Dirk Eddelbuettel
Hi Graham, On 22 January 2021 at 23:13, Graham Inggs wrote: | Hi Dirk | | On Fri, 22 Jan 2021 at 22:39, Dirk Eddelbuettel wrote: | > Matrix 1.3.0 from December has long been known to fail. Please use release 1.3.2. | | The test at [2], run at 2021-01-22 17:34:51 UTC was against | r-c

Re: [Rd] Inconsistency of c.Date: non-commutativity and non-integer Value

2021-01-22 Thread Dirk Eddelbuettel
On 22 January 2021 at 21:35, Jens Heumann wrote: | Dear r-devel, | | Today I came across what I would call inconsistencies in the `c.Date` | method compared to what happens when concatenating other classes: 1. | Non-commutativity: The type in the arrangements of the elements does | matter

Re: [R-pkg-devel] Rdmacros as Suggests rather than Imports

2021-01-22 Thread Dirk Eddelbuettel
Hi James, On 22 January 2021 at 14:29, James Pustejovsky wrote: | I'm writing to see if anyone has suggestions for how to handle an issue I'm | facing with the clubSandwich package ( | https://CRAN.R-project.org/package=clubSandwich; Github repo: | https://github.com/jepusto/clubSandwich). The

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-22 Thread Dirk Eddelbuettel
On 22 January 2021 at 22:03, Graham Inggs wrote: | While investigating this failure, I noticed the following output in | the test log: | | | > library('glmmTMB') | Warning message: | In checkMatrixPackageVersion() : Package version inconsistency detected. | TMB was built with Matrix version

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-22 Thread Dirk Eddelbuettel
On 22 January 2021 at 22:03, Graham Inggs wrote: | While investigating this failure, I noticed the following output in | the test log: | | | > library('glmmTMB') | Warning message: | In checkMatrixPackageVersion() : Package version inconsistency detected. | TMB was built with Matrix version

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-22 Thread Dirk Eddelbuettel
On 22 January 2021 at 21:45, Graham Inggs wrote: | Source: rmatrix, r-cran-glmmtmb | Control: found -1 rmatrix/1.3-0-1 | Control: found -1 r-cran-glmmtmb/1.0.2.1-1 | Severity: serious | Tags: sid bullseye | X-Debbugs-CC: debian...@lists.debian.org | User: debian...@lists.debian.org | Usertags:

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-01-22 Thread Dirk Eddelbuettel
On 22 January 2021 at 21:45, Graham Inggs wrote: | Source: rmatrix, r-cran-glmmtmb | Control: found -1 rmatrix/1.3-0-1 | Control: found -1 r-cran-glmmtmb/1.0.2.1-1 | Severity: serious | Tags: sid bullseye | X-Debbugs-CC: debian...@lists.debian.org | User: debian...@lists.debian.org | Usertags:

[Rcpp-devel] [ANN] Rcpp Micro Releases on Rcpp Drat Repo

2021-01-20 Thread Dirk Eddelbuettel
Hi all, As for the last few years, we are placing minor increments marking Rcpp version snapshots into the drat repo at http://rcppcore.github.io/drat/ Following the 1.0.6 CRAN release of Rcpp, I first folded in a PR from a branch created right before the 1.0.6 allowing packages with dots

Re: [R-pkg-devel] BH windows compilation issues in R devel

2021-01-19 Thread Dirk Eddelbuettel
On 19 January 2021 at 21:51, Frantisek Bartos wrote: | I wanted to submit a new version of my package and I encountered issues | with boost when compiling it on R devel version for windows. (Please excuse | my stupidity, but I'm a complete noob in regards to compilers and C++) | | A full error

Re: [R-pkg-devel] Solaris x68 and C++17

2021-01-19 Thread Dirk Eddelbuettel
On 19 January 2021 at 17:45, Florian Rupprecht wrote: | Hello, | | the CRAN checks show an error for my newly released package 'httpgd' with | 'r-patched-solaris-x86': | | Error: C++17 standard requested but CXX17 is not defined | | It seems like 'rcppsimdjson' had the same problem ( |

Bug#980430: ITP: r-cran-nanotime -- nanosecond resolution date and time calculations for R

2021-01-18 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-nanotime Version : 0.3.2 Upstream Author : Dirk Eddelbuettel and Leonardo Silvestri * URL or Web page : https://github.com/eddelbuettel/nanotime * License : GPL-2+ Description

Bug#980430: ITP: r-cran-nanotime -- nanosecond resolution date and time calculations for R

2021-01-18 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-nanotime Version : 0.3.2 Upstream Author : Dirk Eddelbuettel and Leonardo Silvestri * URL or Web page : https://github.com/eddelbuettel/nanotime * License : GPL-2+ Description

Bug#980430: ITP: r-cran-nanotime -- nanosecond resolution date and time calculations for R

2021-01-18 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-nanotime Version : 0.3.2 Upstream Author : Dirk Eddelbuettel and Leonardo Silvestri * URL or Web page : https://github.com/eddelbuettel/nanotime * License : GPL-2+ Description

Bug#977919: vm: Mail quoting no longer works in emacs27

2021-01-18 Thread Dirk Eddelbuettel
On 18 January 2021 at 13:49, Ian Jackson wrote: | Control: tags -1 + confirmed | | Dirk Eddelbuettel writes ("Bug#977919: vm: Mail quoting no longer works in emacs27"): | > | > As per the previous bug report emacs27 and vm are having some issues. Another | > wart i

Bug#977919: vm: Mail quoting no longer works in emacs27

2021-01-18 Thread Dirk Eddelbuettel
On 18 January 2021 at 13:49, Ian Jackson wrote: | Control: tags -1 + confirmed | | Dirk Eddelbuettel writes ("Bug#977919: vm: Mail quoting no longer works in emacs27"): | > | > As per the previous bug report emacs27 and vm are having some issues. Another | > wart i

Bug#977918: vm: Package vm prevents clean emacs27 start

2021-01-18 Thread Dirk Eddelbuettel
On 18 January 2021 at 13:47, Ian Jackson wrote: | Control: priority -1 normal | | Dirk Eddelbuettel writes ("Bug#977918: vm: Package vm prevents clean emacs27 start"): | > And of course in a minimal container with just emacs27 and vm the issue does | > not reproduce. Wh

Re: [Rcpp-devel] Ranges and Casting

2021-01-15 Thread Dirk Eddelbuettel
On 16 January 2021 at 01:35, Francisco Bischoff wrote: | About the Range() function, I think it should handle decreasing ranges | too... | But, idk if using Matlabs approach or R approach: | | R's: | | a <- 1 | b <- 10 | | print(a:b) | 1 2 3 4 5 6 7 8 9 10 | print(b:a) | 10 9 8 7 6 5 4 3 2 1 |

[Rcpp-devel] [ANN] Rcpp 1.0.6 now on CRAN

2021-01-15 Thread Dirk Eddelbuettel
Rcpp 1.0.6 is now on CRAN, following the six months release cycle adopted in July. A brief blog post is at http://dirk.eddelbuettel.com/blog/2021/01/15#rcpp_1.0.6 and you know where to find it :) My thanks to Walter Somerville, Mattias Ellert and Benjamin Christoffersen for three fine PRs

Re: [R-pkg-devel] REAL(16) fails on M1 Macs

2021-01-14 Thread Dirk Eddelbuettel
On 14 January 2021 at 15:32, Rampal Etienne wrote: | I have a package with FORTRAN code using REAL(16) for accurate | computations. This package has been on CRAN for several years, but now | it suddenly fails on M1 Macs, apparently due to the use of REAL(16) - it | cannot handle higher

Re: [Rd] [External] brief update on the pipe operator in R-devel

2021-01-12 Thread Dirk Eddelbuettel
On 12 January 2021 at 20:38, Iñaki Ucar wrote: | On Tue, 12 Jan 2021 at 20:23, wrote: | > | > After some discussions we've settled on a syntax of the form | > | > mtcars |> subset(cyl == 4) |> d => lm(mpg ~ disp, data = d) | > | > to handle cases where the pipe lhs needs to be passed to an

Re: [Rcpp-devel] [ANN] Refined Matrix package bug fix release RcppArmadillo 0.10.1.2.2 on drat

2021-01-09 Thread Dirk Eddelbuettel
With Matrix 1.3.2 now on CRAN, and thanks to the hints by Martin and Binxiang (plus an unrelated upstream buglet fix from Conrad), a new and refined RcppArmadillo release 0.10.1.2.2 is now uploaded to CRAN. Where it has been stuck is incoming with an apparently frozen pretest queue. After which

Re: [Rd] URL checks

2021-01-09 Thread Dirk Eddelbuettel
The idea of 'white lists' to prevent known (and 'tolerated') issues, note, warnings, ... from needlessly reappearing is very powerful and general, and can go much further than just URL checks. I suggested several times in the past that we can look at the format Debian uses in its 'lintian'

Re: [R-pkg-devel] Package used unconditionally only in testing

2021-01-08 Thread Dirk Eddelbuettel
On 8 January 2021 at 11:32, Henrik Bengtsson wrote: | R CMD check --as-cran will give an ERROR if not all Suggest:ed | packages are installed and available when it runs. This can be overridden with R_CHECK_FORCE_SUGGESTS_=false which may be helpful if Suggests: has a long tail of dependencies,

Re: [R] seq.Date when date is the last date of the month

2021-01-07 Thread Dirk Eddelbuettel
Jeremie, As months have irregular number of dates, one needs to use a function that accounts for that (date libraries and packages have that, one of the earliest for R was my RcppBDT package using Boost Date_Time), or be otherwise clever. Here is a one-liner using the latter approach:

Re: [Rcpp-devel] Ranges and Casting

2021-01-05 Thread Dirk Eddelbuettel
Francisco, On 5 January 2021 at 13:58, Francisco Bischoff wrote: | First of all, let me thank all involved with the Rcpp package! | | I just have a (maybe silly) question, but I struggle with this frequently | in my codes: | | Range() vs IntegerVector | | One example is when I need a reverse

[ESS] Current Status of [OT] Best Practices Emacs / ESS Mini-Webinars

2021-01-05 Thread Dirk Eddelbuettel via ESS-help
1. There are now fourteen of us in a GitHub organization at https://github.com/ess-intro with an overall 'top-level' repo https://github.com/ess-intro/ess-intro Membership defaults to 'private' so unless you're (or a person makes it public) in you won't see membership, but

Bug#979353: rmatrix: Please package 1.3-2 to file errors

2021-01-05 Thread Dirk Eddelbuettel
On 6 January 2021 at 05:33, Peter Hickey wrote: | Thanks. I've been camping since Christmas without laptop/reception but I'll | be back next week and deal with these issues Ah the 'seasonal' advantages of being down under! Lovely. Take your time; we have to wait on Martin Maechler and CRAN to

Bug#979353: rmatrix: Please package 1.3-2 to file errors

2021-01-05 Thread Dirk Eddelbuettel
On 5 January 2021 at 19:20, Michael R. Crusoe wrote: | On Tue, 5 Jan 2021 at 19:12, Dirk Eddelbuettel wrote: | | > On 5 January 2021 at 18:41, Michael R. Crusoe wrote: | > | | | > | r-cran-matrix 1.3-0-1 causes a bug that is evidently fixed in version | > | 1.3-2 | &g

Bug#979353: rmatrix: Please package 1.3-2 to file errors

2021-01-05 Thread Dirk Eddelbuettel
On 5 January 2021 at 18:41, Michael R. Crusoe wrote: | Source: rmatrix | Version: 1.3-0-1 | Severity: important | | -BEGIN PGP SIGNED MESSAGE- | Hash: SHA512 | | Hello, | | r-cran-matrix 1.3-0-1 causes a bug that is evidently fixed in version | 1.3-2 |

Re: [ESS] Next steps [OT] Best Practices Emacs / ESS Mini-Webinars

2021-01-02 Thread Dirk Eddelbuettel via ESS-help
Happy New Year to all! Very exciting to see this take shape! The page at http://collabedit.com/537yq has been serving us really for the initial discussions and overview but I suggest to move it up a notch: - create a GitHub organization ess-intro to serve as an umbrella to - set up a

Re: [Rcpp-devel] [ANN] Matrix package bug fix release RcppArmadillo 0.10.1.2.1 on drat

2021-01-01 Thread Dirk Eddelbuettel
Happy New Year Martin and everybody! On 1 January 2021 at 12:32, Martin Maechler wrote: | I had wanted to send e-mail to all Matrix reverse dependent | packages affected, as one of the changes indeed was very much | on purpose and listed among the (very rare!!) user visible NEWS | of Matrix: |

[Rcpp-devel] [ANN] Matrix package bug fix release RcppArmadillo 0.10.1.2.1 on drat

2020-12-31 Thread Dirk Eddelbuettel
Binxiang and I indepedently noticed (and independently fixed, my bad for not committing earlier) that the very recent Matrix 1.3.0 (on CRAN) breaks one our (optional) unit tests related to sparse matrix conversion. So I made a fix release 0.10.1.2.1 which is now in the usual Rcpp drat repo from

Re: [ESS] Next steps [OT] Best Practices Emacs / ESS Mini-Webinars

2020-12-30 Thread Dirk Eddelbuettel via ESS-help
On 30 December 2020 at 17:27, Greg Minshall wrote: | i've never been involved in a multi-user gitlab/github thing (i'm pretty | much a loner), so i don't know how collaboration works best. but, it | might make sense to start all in the same repo. in ignorance, maybe | Dirk would be in charge

Re: [ESS] Next steps [OT] Best Practices Emacs / ESS Mini-Webinars

2020-12-30 Thread Dirk Eddelbuettel via ESS-help
Very nice to see all the energy and interest, so a big thank you to everybody for chipping in! The page at http://collabedit.com/537yq is very active. I feel we need now need to take this one level up and pick actual 'topics' for these 5-minute mini talks, as well as a possible sequence. I

Re: [ESS] [OT] Best Practices Emacs / ESS Mini-Webinars

2020-12-28 Thread Dirk Eddelbuettel via ESS-help
Hi Stephen, On 28 December 2020 at 16:23, Stephen Bond wrote: | I have been struggling with trying to follow the steps in | https://r-pkgs.org/ and the best thing would be to have a similar | online book showing the steps with ESS. the Hadley book is chained to | RStudio and they assume

Re: [ESS] [OT] Best Practices Emacs / ESS Mini-Webinars

2020-12-28 Thread Dirk Eddelbuettel via ESS-help
On 28 December 2020 at 18:48, Greg Minshall wrote: | i'm a fan. thanks. someone already added ESS and orgmode to the | collwhatever site. i'd mostly be extracting information, as i'm not an | expert (but might be able to chip in during a discussion). | | i'd prefer an e-mail list or

Re: [ESS] [OT] Best Practices Emacs / ESS Mini-Webinars

2020-12-28 Thread Dirk Eddelbuettel via ESS-help
On 28 December 2020 at 10:05, Tyler Smith via ESS-help wrote: | I could reframe my talk as "an overview of Blogdown" to more clearly articulate a single goal. Sorry to be stickler but to keep this focused I would still say no. _Blogdown per se_ has no relationship with ESS. And I say that as

Re: [ESS] [OT] Best Practices Emacs / ESS Mini-Webinars

2020-12-28 Thread Dirk Eddelbuettel via ESS-help
On 28 December 2020 at 14:26, Sparapani, Rodney via ESS-help wrote: | All great ideas. How about ESS and Roxygen? Good one, added! On 28 December 2020 at 09:40, Tyler Smith wrote: | I'd be happy to demo blogging with Emacs, RMarkdown, Blogdown, Hugo, ESS etc. Colour me sceptical. That is a

[ESS] [OT] Best Practices Emacs / ESS Mini-Webinars

2020-12-28 Thread Dirk Eddelbuettel via ESS-help
A few weeks ago a few of riffed about all the "known unknown" in using ESS and that teaching each other a few tricks would be cool. We really should do this. To kick it off, maybe we should spawn a quick one-off mailing list (I have used groups.io before) or Slack instance (if someone wants to

Bug#978483: r-cran-pbkrtest: not installable in sid

2020-12-27 Thread Dirk Eddelbuettel
On 28 December 2020 at 00:25, Aurelien Jarno wrote: | Package: r-cran-pbkrtest | Version: 0.5-0.1-1 | Severity: serious | | r-cran-pbkrtest is currently not installable in sid: | | # apt-get install r-cran-pbkrtest | Reading package lists... Done | Building dependency tree | Reading state

Bug#978483: r-cran-pbkrtest: not installable in sid

2020-12-27 Thread Dirk Eddelbuettel
On 28 December 2020 at 00:25, Aurelien Jarno wrote: | Package: r-cran-pbkrtest | Version: 0.5-0.1-1 | Severity: serious | | r-cran-pbkrtest is currently not installable in sid: | | # apt-get install r-cran-pbkrtest | Reading package lists... Done | Building dependency tree | Reading state

Bug#978136: RFP: r-cran-rcppdate -- R bindings of Date library

2020-12-26 Thread Dirk Eddelbuettel
Package: wnpp Severity: wishlist * Package name: r-cran-rcppdate Version : 0.0.1 Upstream Author : Dirk Eddelbuettel * URL or Web page : https://cran.r-project.org/package=RcppDate * License : GPL (>= 2) Description : R bindings of Date library This is the sec

Bug#978136: RFP: r-cran-rcppdate -- R bindings of Date library

2020-12-26 Thread Dirk Eddelbuettel
Package: wnpp Severity: wishlist * Package name: r-cran-rcppdate Version : 0.0.1 Upstream Author : Dirk Eddelbuettel * URL or Web page : https://cran.r-project.org/package=RcppDate * License : GPL (>= 2) Description : R bindings of Date library This is the sec

Bug#978134: RFP: r-cran-rcppcctz -- R binding for CCTZ

2020-12-26 Thread Dirk Eddelbuettel
Package: wnpp Severity: wishlist * Package name: r-cran-rcppcctz Version : 0.2.9-0 Upstream Author : Dirk Eddelbuettel * URL or Web page : https://cran.r-project.org/package=RcppCCTZ * License : GPL (>= 2) Description : R binding for CCTZ This is one of th

Bug#978134: RFP: r-cran-rcppcctz -- R binding for CCTZ

2020-12-26 Thread Dirk Eddelbuettel
Package: wnpp Severity: wishlist * Package name: r-cran-rcppcctz Version : 0.2.9-0 Upstream Author : Dirk Eddelbuettel * URL or Web page : https://cran.r-project.org/package=RcppCCTZ * License : GPL (>= 2) Description : R binding for CCTZ This is one of th

Bug#977918: vm: Package vm prevents clean emacs27 start

2020-12-22 Thread Dirk Eddelbuettel
Package: vm Version: 8.2.0b-6 Severity: serious Using the (awesome !!) newer emacs 27.1, I am having issues with package vm. One issue is that on startup, a message 'Package cl is deprecated' is shown. Startup appears to finish in interactive, but does not in daemon

Bug#977918: vm: Package vm prevents clean emacs27 start

2020-12-22 Thread Dirk Eddelbuettel
Package: vm Version: 8.2.0b-6 Severity: serious Using the (awesome !!) newer emacs 27.1, I am having issues with package vm. One issue is that on startup, a message 'Package cl is deprecated' is shown. Startup appears to finish in interactive, but does not in daemon

Bug#977919: vm: Mail quoting no longer works in emacs27

2020-12-22 Thread Dirk Eddelbuettel
Package: vm Version: 8.2.0b-6 Severity: serious As per the previous bug report emacs27 and vm are having some issues. Another wart is that mail replies no longer work. Hitting 'F' for a quoted reply inserts the full email including headers _unquoted_ and _unindented_ with an error message

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