Re: [Rcpp-devel] Rcpp shared libraries (?)

2022-06-23 Thread Dirk Eddelbuettel
One belated follow-up: one can in general control visibility so - a function can be in C(++) and used by other C(++) functions (and we have examples) - a function can be exported to R easily via [[Rcpp::export()]] thanks to magic of Rcpp::compileAttributes() - a function can also be

Re: [Rcpp-devel] Help reading libzma file

2022-06-23 Thread Dirk Eddelbuettel
On 23 June 2022 at 10:05, Serguei Sokol wrote: | Le 23/06/2022 à 04:07, Roberto Spadim a écrit : | > Hi folks | > | > I have a .xz file and need to read it and "convert" to a DataFrame using | > Rcpp if possible. | > | > But... I'm with a problem (first time testing this) using liblzma with |

Bug#1013235: RM: fexoticoptions -- RoM: Retired upstream

2022-06-19 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The fexoticoptions package (binary: r-cran-fexoticoptions) is no longer on CRAN and can be removed from unstable as well. If needed, old versions remain at https://cran.r-project.org/web/packages/fExoticOptions/index.html Dirk -- dirk.eddelbuettel.com

Bug#1013234: RM: fasionoptions -- RoM: Retired upstream

2022-06-19 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The fasianoptions package (binary: r-cran-fasianoptions) is no longer on CRAN and can be removed from unstable as well. If needed, old versions remain at https://cran.r-project.org/web/packages/fAsianOptions/index.html Dirk -- dirk.eddelbuettel.com |

Re: [R-sig-Debian] How to open an access mdb using the rodbc package under Ubuntu 22.04

2022-06-17 Thread Dirk Eddelbuettel
Postscriptum: We absolutely don't mind helping here, use on Ubuntu is *very much* on charter for r-sig-deb (which is, loosely, for help with any .deb-based OS and R). However, the question really had little to do with the OS and a lot with 'how do I do OBDC' which Ivan answered admirably. Next

Re: [Rcpp-devel] Assertion error in ud_ep.c, when running with MPI

2022-06-14 Thread Dirk Eddelbuettel
On 14 June 2022 at 09:38, Serguei Sokol wrote: | Hi, | | Probably, this issue would be better posted here | https://github.com/openucx/ucx/issues Seconded. I don't have much to add: these MPI examples are ten years old, worked all the time as far as we know, and haven't changed. Maybe some

Re: [Rcpp-devel] [R-pkg-devel] moving from C to C++ with Rcpp in R package

2022-06-03 Thread Dirk Eddelbuettel
rcppsimdjson/src/simdjson_example.cpp:// [[Rcpp::export(.cppVersion)]] rcppsimdjson/src/simdjson_example.cpp:// [[Rcpp::export(.unsupportedArchitecture)]] edd@rob:~/git$ Hope this helps, Dirk | Thanks | Jean | | | > Le 2 juin 2022 à 15:49, Dirk Eddelbuettel a écrit : | >

Re: [Rcpp-devel] [R-pkg-devel] moving from C to C++ with Rcpp in R package

2022-06-02 Thread Dirk Eddelbuettel
On 2 June 2022 at 08:32, Dirk Eddelbuettel wrote: | | (Removed CC to r-package-devel) | | On 2 June 2022 at 16:24, Ivan Krylov wrote: | | Unfortunately, this means editing RcppExports.R, which (I think) | | prevents you from enjoying the way Rcpp::compileAttributes() sets | | everything up

Re: [Rcpp-devel] [R-pkg-devel] moving from C to C++ with Rcpp in R package

2022-06-02 Thread Dirk Eddelbuettel
(Removed CC to r-package-devel) On 2 June 2022 at 16:24, Ivan Krylov wrote: | Unfortunately, this means editing RcppExports.R, which (I think) | prevents you from enjoying the way Rcpp::compileAttributes() sets | everything up for you. Yes. I think that is the best I came up with once too in a

Re: [Rd] How to access to internal header files

2022-05-24 Thread Dirk Eddelbuettel
On 24 May 2022 at 15:23, Martin Maechler wrote: | Well, if you want to explore how R is written ... and that's the | only good reason for looking into such private header files ... | then get the sources of R and explore... | | The official sources (and even daily snapshots from both |

Bug#1011476: beancounter: Please drop alternative dependency on libdbd-sqlite2-perl

2022-05-23 Thread Dirk Eddelbuettel
Hi Gregor, On 23 May 2022 at 21:05, gregor herrmann wrote: | Package: beancounter | Severity: minor | X-Debbugs-Cc: 998...@bugs.debian.org | | beancounter has "libdbd-pg-perl | libdbd-mysql-perl | | libdbd-odbc-perl | libdbd-sqlite3-perl | libdbd-sqlite2-perl" in | Depends, as it apparantly

Re: [Rd] CRAN webserver down

2022-05-23 Thread Dirk Eddelbuettel
On 23 May 2022 at 10:29, peter dalgaard wrote: | Apparently resurrected now. As another maintainer told me, the submission page appears to be down. Going to https://cran.r-project.org/submit.html (and then refreshing over the stale iframe) gets me The webpage at

Re: [R-sig-Debian] Ubuntu Impish (21.10) repository complains about weak security information

2022-05-16 Thread Dirk Eddelbuettel
On 16 May 2022 at 22:24, Lennart C. Karssen wrote: | Thanks Dirk, that gets me one step further. However, there is still a | hurdle. It seems that (at least at the time of writing) the | impish-cran40/ repo is broken. You are correct, sorry. I rushed earlier to help you on the key issue, and

Bug#1011044: libtiledb2.8 needs Breaks+Replaces: libtiledb2.7

2022-05-15 Thread Dirk Eddelbuettel
On 16 May 2022 at 04:48, Adrian Bunk wrote: | Package: libtiledb2.8 | Version: 2.8.3-2 | Severity: serious | | Unpacking libtiledb2.8:amd64 (2.8.3-2) ... | dpkg: error processing archive /var/cache/apt/archives/libtiledb2.8_2.8.3-2_amd64.deb (--unpack): | trying to overwrite

Bug#1011044: libtiledb2.8 needs Breaks+Replaces: libtiledb2.7

2022-05-15 Thread Dirk Eddelbuettel
On 16 May 2022 at 04:48, Adrian Bunk wrote: | Package: libtiledb2.8 | Version: 2.8.3-2 | Severity: serious | | Unpacking libtiledb2.8:amd64 (2.8.3-2) ... | dpkg: error processing archive /var/cache/apt/archives/libtiledb2.8_2.8.3-2_amd64.deb (--unpack): | trying to overwrite

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-15 Thread Dirk Eddelbuettel
Hi Nilesh, On 15 May 2022 at 07:48, Dirk Eddelbuettel wrote: | On 15 May 2022 at 14:10, Nilesh Patra wrote: | | Can I ask you to please take a look at my changes once? | | I will try that a little later. They look good. They are even more minimal than what I attempted (i.e. you knew to only

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-15 Thread Dirk Eddelbuettel
Hi Nilesh, On 15 May 2022 at 07:48, Dirk Eddelbuettel wrote: | On 15 May 2022 at 14:10, Nilesh Patra wrote: | | Can I ask you to please take a look at my changes once? | | I will try that a little later. They look good. They are even more minimal than what I attempted (i.e. you knew to only

Bug#1011012: tiledb-r FTBFS with tiledb 2.8.3

2022-05-15 Thread Dirk Eddelbuettel
Adrian, On 15 May 2022 at 13:38, Adrian Bunk wrote: | Source: tiledb-r | Version: 0.12.0-1 | Severity: serious | Tags: ftbfs | | https://buildd.debian.org/status/logs.php?pkg=tiledb-r=0.12.0-1%2Bb1 | | ... | g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/

Bug#1011012: tiledb-r FTBFS with tiledb 2.8.3

2022-05-15 Thread Dirk Eddelbuettel
Adrian, On 15 May 2022 at 13:38, Adrian Bunk wrote: | Source: tiledb-r | Version: 0.12.0-1 | Severity: serious | Tags: ftbfs | | https://buildd.debian.org/status/logs.php?pkg=tiledb-r=0.12.0-1%2Bb1 | | ... | g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-15 Thread Dirk Eddelbuettel
Hi Nilesh, On 15 May 2022 at 14:10, Nilesh Patra wrote: | | Hi Dirk, | | On Fri, 13 May 2022 19:57:11 -0500 Dirk Eddelbuettel wrote: | > As noted in a mail to debian-python [1], the tiledb-py package is creating a | > few issues I do not currently have time to work through. | | I sa

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-15 Thread Dirk Eddelbuettel
Hi Nilesh, On 15 May 2022 at 14:10, Nilesh Patra wrote: | | Hi Dirk, | | On Fri, 13 May 2022 19:57:11 -0500 Dirk Eddelbuettel wrote: | > As noted in a mail to debian-python [1], the tiledb-py package is creating a | > few issues I do not currently have time to work through. | | I sa

Re: Need a hand with tiledb-python

2022-05-13 Thread Dirk Eddelbuettel
I have now orphaned the package [1] as this one needs more attention that I can currently give it due to 180+ other packages I have, and other work and open source commitments. Dirk [1] https://bugs.debian.org/1010953 -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-13 Thread Dirk Eddelbuettel
Package: wnpp Severity: normal As noted in a mail to debian-python [1], the tiledb-py package is creating a few issues I do not currently have time to work through. I will continue to look after the tiledb package, and after the R bindings in package tiledb-r. If someone can devote some time to

Bug#1010953: O: tiledb-py -- TileDB Python bindings

2022-05-13 Thread Dirk Eddelbuettel
Package: wnpp Severity: normal As noted in a mail to debian-python [1], the tiledb-py package is creating a few issues I do not currently have time to work through. I will continue to look after the tiledb package, and after the R bindings in package tiledb-r. If someone can devote some time to

Re: [R-pkg-devel] advice on a rejected package (I think, because time was 13min, in excess of 10min limit)

2022-05-11 Thread Dirk Eddelbuettel
On 11 May 2022 at 19:07, Daniel Kelley wrote: | Today I tried to update the CRAN oce package to version 1.7-3, to address a problem with 1.7-2 on one of the CRAN build platforms. I used devtools::release() to submit it. I just received the text I've pasted at the bottom of this email. I've

Need a hand with tiledb-python

2022-05-10 Thread Dirk Eddelbuettel
Hi all, I look after the 'tiledb' (a C++ library) package and the 'tiledb-r' package. I also effectively maintain 'tiledb-python' but I am running into some issues there. I do know a little bit of Python and have (co-)maintained two or three packages there for decades but this one stumps me.

[ESS] [Rather ancient] ESS documentation on 'script is the truth' ?

2022-05-07 Thread Dirk Eddelbuettel via ESS-help
Many moons ago the ESS documentation contained a short write-up by (IIRC) Tony which detailed the workflow common for many of us: write in a script, execute lines or regions, possibly save a transcript buffer. Every now and then I want to refer people to this as it was a very clear expression

Re: [Rd] R-devel tarball at ETH is zero

2022-05-04 Thread Dirk Eddelbuettel
On 4 May 2022 at 11:32, Martin Maechler wrote: | I'm really sorry for this experience. Stuff happens -- thanks for fixing it. The weekly build for the rocker/drd container of r-devel (and r-patched) worked fine now that you restored the mirror, so big thanks! Dirk -- dirk.eddelbuettel.com |

[Rd] R-devel tarball at ETH is zero

2022-05-03 Thread Dirk Eddelbuettel
Dear Martin as our trusted ETH point person, I have some automated builders fall over as the tarball of R-devel is currently empty: edd@rob:/tmp$ wget https://stat.ethz.ch/R/daily/R-devel.tar.bz2 --2022-05-03 06:52:20-- https://stat.ethz.ch/R/daily/R-devel.tar.bz2 Resolving stat.ethz.ch

Re: [Rcpp-devel] Doubt about best pratices

2022-05-01 Thread Dirk Eddelbuettel
This is not a well-posed Rcpp question as - matrix and data.frame are _fundamentally_ two different data types - matrix being _one_ and only one storage type, or class, stored as one vector with dimension attribute of size two for rows and cols; this makes it _efficient_ and you will see a

Re: [Rcpp-devel] help with data.frame and numericvector

2022-04-27 Thread Dirk Eddelbuettel
On 27 April 2022 at 20:58, Roberto Spadim wrote: | Hello folks, | I'm converting some R functions to RCpp at | https://github.com/OVVO-Financial/NNS/ | | My problem is with a R "cast" function | |

Re: [R-pkg-devel] Should the LaTeX package pdfpages be available for use in vignettes?

2022-04-23 Thread Dirk Eddelbuettel
On 23 April 2022 at 18:05, Greg Hunt wrote: | I want to incorporate a static PDF (created from LaTeX source separately | from the R package) into an R package as a vignette. I do that in several vignettes via a zero-depends approach described by Mark in this blog post:

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

2022-04-14 Thread Dirk Eddelbuettel
Two (related) questions: 1. Could pandoc be installed on the macoOS machines CRAN uses? If not, could R Core devise a way to have a registered vignette builder fail gracefully? 2. Could CRAN define and publish a minimal set of external applications available on each build + test machine?

Bug#1009224: Using different R versions in parallel with Debian

2022-04-11 Thread Dirk Eddelbuettel
On 11 April 2022 at 18:40, Paul Menzel wrote: | I think, I see the misunderstanding. I thought the single quotes meant, | that *simpler* and *fancier* are commands for the mentioned purposes – | which made sense to me, as the end both on *r* (simpleR and fancieR). | Now I think they are just

Bug#1009224: Using different R versions in parallel with Debian

2022-04-09 Thread Dirk Eddelbuettel
On 9 April 2022 at 17:30, Charles Plessy wrote: | Le Sat, Apr 09, 2022 at 10:19:17AM +0200, Paul Menzel a écrit : | > | > Thank you very much for packaging and maintaining R and related software in | > Debian. Some of our scientists use Debian and its R packages. Sometimes | > they’d like to

Bug#1009224: Using different R versions in parallel with Debian

2022-04-09 Thread Dirk Eddelbuettel
Hallo Paul, On 9 April 2022 at 10:19, Paul Menzel wrote: | Package: r-base-core | Version: 4.1.3.20220324-1 | Severity: wishlist | | Dear Debian R maintainer, | | Thank you very much for packaging and maintaining R and related software | in Debian. Some of our scientists use Debian and its R

Bug#1009212: date does not respect timezone format

2022-04-08 Thread Dirk Eddelbuettel
reassign 1009212 coreutils thanks You reporeted this against source package 'date' which is CRAN package date at https://cran.r-project.org/package=date. You likely meant the command 'date' from source package coreutils. Dirk On 8 April 2022 at 23:43, mastrboy wrote: | Source: date |

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

2022-03-23 Thread Dirk Eddelbuettel
It was a mirage. The system is still locking up, something that did not happen with an older kernel, and also not with other systems booting off USB. -- You received this bug notification because you are a member of Kernel Packages, which is subscribed to linux in Ubuntu.

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

2022-03-23 Thread Dirk Eddelbuettel
It was a mirage. The system is still locking up, something that did not happen with an older kernel, and also not with other systems booting off USB. -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu.

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

2022-03-20 Thread Dirk Eddelbuettel
Update. And I don't want to jinx it but ... it seems like 22.04 (to be) has this fixed. Updated to it two days ago, and it seems fine with its kernel 5.15.0-23-generic. -- You received this bug notification because you are a member of Kernel Packages, which is subscribed to linux in Ubuntu.

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

2022-03-20 Thread Dirk Eddelbuettel
Update. And I don't want to jinx it but ... it seems like 22.04 (to be) has this fixed. Updated to it two days ago, and it seems fine with its kernel 5.15.0-23-generic. -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu.

Re: [R-pkg-devel] Ensuring permanence and SHA consistency of released CRAN packages for validated software

2022-03-16 Thread Dirk Eddelbuettel
On 16 March 2022 at 14:01, Henrik Bengtsson wrote: | Related to this, there's also been discussion (here or on R-devel), of | having `R CMD build` produce identical tarballs when the input doesn't | change, but the injection of `Packaged: ; ` to the | `DESCRIPTION` file prevents this. If I

Bug#1007032: r-cran-minqa: please consider upgrading to 3.0 source format

2022-03-12 Thread Dirk Eddelbuettel
-Browser: and Vcs-Git: * debian/compat: Removed * debian/control: Switch from cdbs to dh-r * debian/rules: Idem * debian/watch: Update to https -- Dirk Eddelbuettel Sat, 12 Mar 2022 21:03:53 -0600 r-cran-minqa (1.2.4-1) unstable; urgency=low * New upstream release

Re: [R-pkg-devel] Failing Valgrind Passing R CMD check

2022-03-08 Thread Dirk Eddelbuettel
On 8 March 2022 at 18:01, Sebastian Meyer wrote: | Not an expert here, but that does seem to be possible, according to WRE | (Section 4.3.2): | | > It is possible to run all the examples, tests and vignettes covered by R CMD check under valgrind by using the option --use-valgrind. If you do

Re: PROJ 9.0.0

2022-03-08 Thread Dirk Eddelbuettel
On 8 March 2022 at 21:17, Sebastiaan Couwenberg wrote: | On 3/8/22 21:07, Dirk Eddelbuettel wrote: | > Would you consider adding tiledb? | | No, because TileDB is not a dependency of PROJ. Ah yes my bad. | > We already added tiledb-py as well and I | > have been updating both

Re: PROJ 9.0.0

2022-03-08 Thread Dirk Eddelbuettel
On 8 March 2022 at 18:15, Sebastiaan Couwenberg wrote: | PROJ 9.0.0 has been released, it removed support for Autotools which | required the package to be updated to use CMake instead. | | It also bumped the SONAME requiring a transition. | | With the fix for SQLite 3.38.0 included, all

Bug#1006652: ITP: r-cran-tiledb -- R Interface to the TileDB Storage Engine

2022-03-01 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-tiledb Version : 0.11.0 Upstream Author : TileDB Inc * URL or Web page : https://github.com/TileDB-Inc/TileDB-R * License : MIT Description : R Interface to the TileDB Storage Engine

Bug#1006652: ITP: r-cran-tiledb -- R Interface to the TileDB Storage Engine

2022-03-01 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-tiledb Version : 0.11.0 Upstream Author : TileDB Inc * URL or Web page : https://github.com/TileDB-Inc/TileDB-R * License : MIT Description : R Interface to the TileDB Storage Engine

Bug#1006652: ITP: r-cran-tiledb -- R Interface to the TileDB Storage Engine

2022-03-01 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-tiledb Version : 0.11.0 Upstream Author : TileDB Inc * URL or Web page : https://github.com/TileDB-Inc/TileDB-R * License : MIT Description : R Interface to the TileDB Storage Engine

Bug#1006415: FTBFS with capnproto 0.9.1

2022-02-26 Thread Dirk Eddelbuettel
On 25 February 2022 at 18:39, Tom Lee wrote: | So the tiledb upstream sources include *pre-generated *capnproto sources | that were generated using 0.8.0. The *update-serialization* target will Indeed! I forgot about that. TileDB has a habit of (strongly) enforcing third-party dependencies,

Bug#1006415: FTBFS with capnproto 0.9.1

2022-02-26 Thread Dirk Eddelbuettel
Hi Tom, On 25 February 2022 at 13:14, Tom Lee wrote: | Thanks for giving it a shot. Surprised to hear the patch didn't apply | cleanly, believe I worked directly from the source pulled via | | dget -a http://deb.debian.org/debian/pool/main/t/tiledb/tiledb_2.6.2-2.dsc Would it be possible for

Bug#1006415: FTBFS with capnproto 0.9.1

2022-02-25 Thread Dirk Eddelbuettel
Tom, Sad news. The build fails for me in unstable as is (using an updated pbuilder chroot). I log these to file and what I see is cd /build/tiledb-2.6.2/obj-x86_64-linux-gnu/tiledb/tiledb && /usr/bin/cc -DFMT_LOCALE -DFMT_SHARED -DSPDLOG_COMPILED_LIB -DSPDLOG_FMT_EXTERNAL

Bug#1006415: FTBFS with capnproto 0.9.1

2022-02-25 Thread Dirk Eddelbuettel
Tom, The patch does not apply cleanly to the sources. It is also not unified. A bit weird. Will patch by hand, and regenerate with dpkg-source --commit. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1006415: FTBFS with capnproto 0.9.1

2022-02-25 Thread Dirk Eddelbuettel
Hi Tom, On 24 February 2022 at 20:49, Tom Lee wrote: | Source: tiledb | Version: 2.6.2 | Severity: important | Tags: bookworm sid | X-Debbugs-CC: tmanc...@debian.org | | Hi there, | | tiledb fails to build against capnproto 0.9.1, largely because of the | hard-coded version number in the

Re: Salsa python-team write access for tiledb-py ?

2022-02-18 Thread Dirk Eddelbuettel
On 18 February 2022 at 21:41, Nilesh Patra wrote: | On 2/18/22 9:33 PM, Dirk Eddelbuettel wrote: | > | > Hi debian-python, | > [...] | > I cannot write to https://salsa.debian.org/python-team/packages/tiledb-py so | > I created a (temporary ?) copy at https://salsa.debian.or

Salsa python-team write access for tiledb-py ?

2022-02-18 Thread Dirk Eddelbuettel
Hi debian-python, Recently I had packaged tiledb for Debian, based on earlier work by Adam (CC'ed), and we now followed up with tiledb-py which I just sent to NEW following up on an older ITP/WNPP from almost two years ago. (TileDB is a 'universal' data storage engine:

Re: [Rcpp-devel] RCPP_USE_UNWIND_PROTECT by default

2022-02-06 Thread Dirk Eddelbuettel
On 7 February 2022 at 00:12, Jeroen Ooms wrote: | I have pushed a new version of V8 to CRAN that wraps the R callbacks | in another tryCatch() such that we do not make any assumptions on the | sort of exception handing provided by Rcpp. This should unblock you if | you want to move forward on

Re: [Rcpp-devel] RCPP_USE_UNWIND_PROTECT by default

2022-02-06 Thread Dirk Eddelbuettel
To sum up: ¯\_(ツ)_/¯ I have no bone in this fight. Leaving it as is works for me too. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org

Re: [Rcpp-devel] RCPP_USE_UNWIND_PROTECT by default

2022-02-06 Thread Dirk Eddelbuettel
On 6 February 2022 at 18:18, Jeroen Ooms wrote: | Well not really, this kind of misses my point that it the | unwind-protect makes it impossible to meaningfully catch the R error | in C++, handle it, and continue running the C++ code, without aborting | the entire mission and throwing the user

Re: [Rcpp-devel] RCPP_USE_UNWIND_PROTECT by default

2022-02-06 Thread Dirk Eddelbuettel
On 6 February 2022 at 17:40, Jeroen Ooms wrote: | We can try to take V8 out of the equation, and see what actually | causes the change. V8 uses (and tests!) the Rcpp feature to call an R | function from C++. This behaves quite differently when using | RCPP_UNWIND_PROTECT. | | Here is a dummy

Bug#1001589: I'm stuck too

2022-02-02 Thread Dirk Eddelbuettel
On 2 February 2022 at 08:53, Emmanuel Charpentier wrote: | For information : this bug has bitten me too : | | I run testing, R (from testing), a bucketfull of R packages (mostly | from R repositories) and sagemath (installed from source). | | Recently, the "energy" R packages started to be

Re: [Rcpp-devel] RCPP_USE_UNWIND_PROTECT by default

2022-02-01 Thread Dirk Eddelbuettel
Lionel, Thanks a bunch for the prompt and detailed reply. CCing Jeroen now, I think I had poked him over DM on this but not followed. Easy for us to delegate to V8 :) That is of course a complicated (and toolchain-dependent) package too so we shall see what we can do there. But the good news on

Re: [Rcpp-devel] Detecting Singular Matrices in RcppArmadillo

2022-01-31 Thread Dirk Eddelbuettel
On 31 January 2022 at 11:25, Alex Ilich wrote: | Thank you Zé and Dirk! That helped clarify exactly what solve is doing | which I was having trouble tracking down in just the standard docs page. The `solve()` function in Armadillo does exactly what it sets out to do. Yet what Prof Bates has

Re: [Rcpp-devel] Detecting Singular Matrices in RcppArmadillo

2022-01-30 Thread Dirk Eddelbuettel
On 31 January 2022 at 09:13, Zé Vinícius wrote: | Yes, quoting the paper on which ‘solve’ is based on ( | http://arma.sourceforge.net/armadillo_solver_2020.pdf): | | “The SVD-based solver uses the xGELSD set of functions, which find a | minimum-norm solution to a linear least squares problem.”

Bug#1004591: ITP: r-cran-simplermarkdown -- GNU R package with simple engine for generating reports

2022-01-30 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-simplermarkdown Version : 0.0.4 Upstream Author : Jan van der Laan * URL or Web page : https://cran.r-project.org/package=simplermarkdown * License : GPL (>= 3) Description : GN

Bug#1004591: ITP: r-cran-simplermarkdown -- GNU R package with simple engine for generating reports

2022-01-30 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-simplermarkdown Version : 0.0.4 Upstream Author : Jan van der Laan * URL or Web page : https://cran.r-project.org/package=simplermarkdown * License : GPL (>= 3) Description : GN

Bug#1004591: ITP: r-cran-simplermarkdown -- GNU R package with simple engine for generating reports

2022-01-30 Thread Dirk Eddelbuettel
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-simplermarkdown Version : 0.0.4 Upstream Author : Jan van der Laan * URL or Web page : https://cran.r-project.org/package=simplermarkdown * License : GPL (>= 3) Description : GN

Bug#931519: 931519 resolved

2022-01-28 Thread Dirk Eddelbuettel
On 29 January 2022 at 10:38, Paul Wise wrote: | Control: fixed -1 4.0.3 | | On Fri, 2022-01-28 at 20:07 -0600, Dirk Eddelbuettel wrote: | | > Per email by Graham from 14 Nov 2020 this has been resolved. | | Resolved upstream in 2020 but not in Debian until 2021. Correct. Graham (as aut

Bug#931519: 931519 resolved

2022-01-28 Thread Dirk Eddelbuettel
On 29 January 2022 at 10:38, Paul Wise wrote: | Control: fixed -1 4.0.3 | | On Fri, 2022-01-28 at 20:07 -0600, Dirk Eddelbuettel wrote: | | > Per email by Graham from 14 Nov 2020 this has been resolved. | | Resolved upstream in 2020 but not in Debian until 2021. Correct. Graham (as aut

Re: [Rcpp-devel] Detecting Singular Matrices in RcppArmadillo

2022-01-28 Thread Dirk Eddelbuettel
On 28 January 2022 at 13:25, Alex Ilich wrote: | Thank you Neal and Dirk. Based on these comments I think using arma::rcond Ah, yes, of course. Should have remembered arma::rcond. | to get the reciprocal of the condition factor, and checking if that is zero | rather than the determinant may be

Re: [Rcpp-devel] Detecting Singular Matrices in RcppArmadillo

2022-01-28 Thread Dirk Eddelbuettel
On 28 January 2022 at 09:16, Neal Fultz wrote: | There's an R object that has the machine precision, which could be a | reasonable threshold. | | .Machine$double.eps | | I believe there is a similar constant in the C++ standard library. | | You might also try checking the condition of the

Re: [R-pkg-devel] Is using global assignment in package tests allowed?

2022-01-27 Thread Dirk Eddelbuettel
On 27 January 2022 at 11:18, Ben Bolker wrote: |I have spent hours trying to understand the scoping behaviour of | testthat, mostly without success. It may bear repeating that use of a test runner package is NOT required by CRAN Repo Policy, Writing R Extensions, or any other official

Re: [Rcpp-devel] violates the C++ One Definition Rule ?

2022-01-25 Thread Dirk Eddelbuettel
Jan 24, 2022 at 1:14 PM Dirk Eddelbuettel wrote: | | > | > On 24 January 2022 at 12:55, Toby Hocking wrote: | > | Hi Rcpp Devs, | > | Does anyone know how to fix this warning in a package with LinkingTo: | > | RcppArmadillo? My package plotHMM | > | https://www.stats.ox.ac.uk/pu

Re: [Rcpp-devel] violates the C++ One Definition Rule ?

2022-01-24 Thread Dirk Eddelbuettel
On 24 January 2022 at 12:55, Toby Hocking wrote: | Hi Rcpp Devs, | Does anyone know how to fix this warning in a package with LinkingTo: | RcppArmadillo? My package plotHMM | https://www.stats.ox.ac.uk/pub/bdr/LTO/plotHMM.out got this message on CRAN Worth stressing that this happens under

Re: Adding tiledb to gdal and pdal ? (And help with tiledb-py ?)

2022-01-21 Thread Dirk Eddelbuettel
On 21 January 2022 at 07:19, Sebastiaan Couwenberg wrote: | Because I'm skeptical of fads. TileDB is the latest shiny new thing | which hasn't been time tested yet and proven to last. Beg to differ, and think you will come around. Time will tell. | As said before I don't use TileDB, and no

Re: Adding tiledb to gdal and pdal ? (And help with tiledb-py ?)

2022-01-20 Thread Dirk Eddelbuettel
On 20 January 2022 at 20:14, Sebastiaan Couwenberg wrote: | On 1/20/22 15:59, Dirk Eddelbuettel wrote: | > The tiledb package is now in testing [1] which means gdal and pdal could | > configure with it. I tested this over the holiday break with earlier | > (informal) packages from launc

Adding tiledb to gdal and pdal ? (And help with tiledb-py ?)

2022-01-20 Thread Dirk Eddelbuettel
The tiledb package is now in testing [1] which means gdal and pdal could configure with it. I tested this over the holiday break with earlier (informal) packages from launchpad -- I still have the repos and could file bug reports with patches if that helped but I think it really is just

Re: [R-pkg-devel] Fix JFM package problem

2022-01-14 Thread Dirk Eddelbuettel
On 11 January 2022 at 18:44, riccardo wrote: | Hallo, | | I wish to submit the following error rising running an example in a rcpp | function *only *in Debian check: | | > ### Name: least_square_plane_rcpp | > ### Title: returns the coefficients of the least square plane and the | > ###

Re: WNPP/ITP/... for Amazon SDK for C++ ?

2022-01-13 Thread Dirk Eddelbuettel
On 13 January 2022 at 19:18, Ross Vandegrift wrote: | On Sat, Jan 08, 2022 at 10:31:03AM -0600, Dirk Eddelbuettel wrote: | > You have a large set there which covers three of the ones I'd need. Could | > you upload these: | > | > https://salsa.debian.org/rvandegrift/aws-c-common

Bug#1003540: gsl-doc: please update to 2.7.1

2022-01-12 Thread Dirk Eddelbuettel
On 13 January 2022 at 02:29, Andreas Beckmann wrote: | On 11/01/2022 17.54, Dirk Eddelbuettel wrote: | > On 11 January 2022 at 17:31, Andreas Beckmann wrote: | > | Package: gsl-doc | > | Version: 2.6-2 | > | Severity: serious | > | > Why would that be a serious bug rather no

Bug#1003540: gsl-doc: please update to 2.7.1

2022-01-12 Thread Dirk Eddelbuettel
On 13 January 2022 at 02:29, Andreas Beckmann wrote: | On 11/01/2022 17.54, Dirk Eddelbuettel wrote: | > On 11 January 2022 at 17:31, Andreas Beckmann wrote: | > | Package: gsl-doc | > | Version: 2.6-2 | > | Severity: serious | > | > Why would that be a serious bug rather no

Bug#1003540: gsl-doc: please update to 2.7.1

2022-01-11 Thread Dirk Eddelbuettel
On 11 January 2022 at 17:31, Andreas Beckmann wrote: | Package: gsl-doc | Version: 2.6-2 | Severity: serious Why would that be a serious bug rather normal or even minor? It's a bit of a manual process becuase of the dfsg dance and manual ops. And there generally is not that much that changes

Bug#1003540: gsl-doc: please update to 2.7.1

2022-01-11 Thread Dirk Eddelbuettel
On 11 January 2022 at 17:31, Andreas Beckmann wrote: | Package: gsl-doc | Version: 2.6-2 | Severity: serious Why would that be a serious bug rather normal or even minor? It's a bit of a manual process becuase of the dfsg dance and manual ops. And there generally is not that much that changes

Re: [R-sig-Debian] Segfault from c2d4u binary of RandomFields

2022-01-08 Thread Dirk Eddelbuettel
On 8 January 2022 at 20:40, Ege Rubak wrote: | Hi everyone, | | For some time the GitHub Action of spatstat.core has been failing due | to a segfault when calling RandomFields (which calls RandomFieldsUtils | which may be causing the acutal segfault): | |

Re: WNPP/ITP/... for Amazon SDK for C++ ?

2022-01-08 Thread Dirk Eddelbuettel
On 31 December 2021 at 07:51, Dirk Eddelbuettel wrote: | On 30 December 2021 at 22:17, Ross Vandegrift wrote: | | On Mon, Dec 27, 2021 at 08:10:50AM -0600, Dirk Eddelbuettel wrote: | | > My (very informal) packaging has always been in the open (but on GitHub). A | | > possible first step

Bug#1003193: Switch maintainer?

2022-01-06 Thread Dirk Eddelbuettel
On 6 January 2022 at 19:48, Adam Cécile wrote: | On 1/5/22 10:39 PM, Dirk Eddelbuettel wrote: | > Hi Adam, | > | > Would you be ok with me more formally adopting the package as maintainer? | | Hello, | | Absolutely no issue on my side. Who could be a better maintainer than | the

Bug#1003193: Switch maintainer?

2022-01-05 Thread Dirk Eddelbuettel
Package: tiledb Severity: normal Hi Adam, Would you be ok with me more formally adopting the package as maintainer? Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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

2022-01-04 Thread Dirk Eddelbuettel
Bump. This bug is still open AFAICT. And I just realized that the real cost to me on this machine (which otherwise runs great with the old 4.* kernel) is that I cannot launch Docker containers any more. Which stinks. Machine otherwise happy and stable under 21.10 *provided I run the ancient

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

2022-01-04 Thread Dirk Eddelbuettel
Bump. This bug is still open AFAICT. And I just realized that the real cost to me on this machine (which otherwise runs great with the old 4.* kernel) is that I cannot launch Docker containers any more. Which stinks. Machine otherwise happy and stable under 21.10 *provided I run the ancient

Bug#1003119: RM: rsprng -- RoM: Retired upstream years ago

2022-01-04 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The rsprng package (binary: r-cran-rsprng) was the first package for R offering a parallel RNG stream suitable for parallel simulation. We now have better ones, including in Debian, and this one which had been retired upstream years ago can now move

[Rcpp-devel] RcppArmadillo 0.10.8.0.0

2022-01-02 Thread Dirk Eddelbuettel
Happy New Year to all! Conrad released version 10.8 Armadillo (and I had prepared two pre-releases which passed reverse dependency checks just fine so not expecting surprises). Given that 0.10.7.5.0, the final RcppRelease for the 10.7.* series with his last release 10.7.5, only got to CRAN on

Bug#1002999: ftp.debian.org: RM: cairodevice -- ROM: Retired upstream

2022-01-02 Thread Dirk Eddelbuettel
retitle -1 RM: r-cran-cairodevice -- ROM: Retired upstream thanks Somehow I mess the form up more often than not with the emacs helper debian-bug being a little out of whack. Sorry about that. Dirk On 2 January 2022 at 09:00, Dirk Eddelbuettel wrote: | | Package: ftp.debian.org | Severity

Bug#1003000: RM: rgtk2 -- ROM: Retired upstream

2022-01-02 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The RGtk2 package (source rgtk2 for us, binary r-cran-rgtk2) was an important package in its day in bringing a modern and pretty UI framework to R across different OS, and I looked after it for 15 years. It never made the move to Gtk3 though, and usage

Bug#1002999: ftp.debian.org: RM: cairodevice -- ROM: Retired upstream

2022-01-02 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The cairoDevice package (source cairodevice for us, binary r-cran-cairodevice) was the first 'Cairo' device for R, it has been replaced by the actively maintained 'Cairo' package (r-cran-cairo for us). It was now retired at CRAN. We should remove it

Bug#1002837: tiledb: diff for NMU version 1.7.7-1.2

2021-12-31 Thread Dirk Eddelbuettel
Ok, we are now at a place where the package is tamed somewhat: - a lot of the smaller architectures did not build for 1.7.7-4 - five larger ones (all 64-bit based AFAICT) did - so I hard-wired these explicitly in Architecture: All green now for the ones attempted:

Bug#1002907: RM: r-cran-rggobi -- ROM: retired upstream

2021-12-31 Thread Dirk Eddelbuettel
Package: ftp.debian.org Severity: normal The `rggobi` package for R was a front-end to the `ggobi` interactive visualization tool (which we still have). But `rggobi` development ceased, and the package has been off CRAN since July of 2020. We should remove it too. There is only one

Re: WNPP/ITP/... for Amazon SDK for C++ ?

2021-12-31 Thread Dirk Eddelbuettel
(Dual reply to two emails) On 30 December 2021 at 23:32, Wookey wrote: | On 2021-12-26 18:08 -0600, Dirk Eddelbuettel wrote: | > | > Does anybody know where we are with respect to the WNPPs / ITPs / ... on the | > Amazon SDK for C++? | > | > I have a package that could

Bug#1002648: RM: r-cran-multicore -- ROM: retired upstream years ago

2021-12-30 Thread Dirk Eddelbuettel
: | | On Sun, 26 Dec 2021 10:20:51 -0600 Dirk Eddelbuettel wrote: | | > | | > Package: ftp.debian.org | | > Severity: normal | | > | | > The 'multicore' package for R was an early extension (during 2009 to 2011) | | to | | > support process-parallel work. Its key parts (especially

Bug#1002837: tiledb: diff for NMU version 1.7.7-1.2

2021-12-30 Thread Dirk Eddelbuettel
Hi Adam, On 30 December 2021 at 11:12, Adam Cécile wrote: | Sure, I was suggesting adding you directly to uploaders because the | package is maintained on Salsa, sadly I see we both missed each other there: | | https://salsa.debian.org/acecile-guest/tiledb |

Bug#1002837: tiledb: diff for NMU version 1.7.7-1.2

2021-12-29 Thread Dirk Eddelbuettel
Couldn't resist an attempt to send in an 1.7.7-3 attempt but still seeing too many unit test failures. Very strange as this works for me on amd64 :-/ Adam, how would you feel about an update to 2.5.3 and catch2 (and no more tbb-dev) ? Would you be ok with me sending that up as NMU? Dirk --

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