Bug#1072979: beast-mcmc - build-dependencies unsatisfiable on i386.

2024-06-11 Thread Dirk Eddelbuettel
On 11 June 2024 at 10:05, Peter Green wrote: | Package: beast-mcmc | Version: 1.10.4+dfsg-5 | Severity: serious | x-debbugs-cc: r-cran-rj...@packages.debian.org | | beast-mcmc build-depends on r-cran-rjava, which is no longer available | on i386. It appears that the package failed to build, and

Bug#1072979: beast-mcmc - build-dependencies unsatisfiable on i386.

2024-06-11 Thread Dirk Eddelbuettel
On 11 June 2024 at 10:05, Peter Green wrote: | Package: beast-mcmc | Version: 1.10.4+dfsg-5 | Severity: serious | x-debbugs-cc: r-cran-rj...@packages.debian.org | | beast-mcmc build-depends on r-cran-rjava, which is no longer available | on i386. It appears that the package failed to build, and

Re: [R-pkg-devel] No email with confirmation link on resubmission of package

2024-06-07 Thread Dirk Eddelbuettel
On 6 June 2024 at 04:47, Paul Kabaila wrote: | When I resubmitted, I didn't realise that I needed to change the version number. As this comes up every now and then: This is still a _soft_ requirement. CRAN does not 'cache' what versions you used in uploads. I have often reiterated with the

Bug#1072648: src:survival: fails to migrate to testing for too long: triggers autopkgtest issues in r-cran-popepi which needs an update

2024-06-06 Thread Dirk Eddelbuettel
On 6 June 2024 at 08:22, Johannes Ranke wrote: | Am Mittwoch, 5. Juni 2024, 22:27:09 CEST schrieb Dirk Eddelbuettel: | > On 5 June 2024 at 21:55, Paul Gevers wrote: | > | Source: survival | > | Version: 3.5-8-1 | > | Severity: serious | > | Control: close -1 3.6-4-1 | >

Bug#1072648: src:survival: fails to migrate to testing for too long: triggers autopkgtest issues in r-cran-popepi which needs an update

2024-06-06 Thread Dirk Eddelbuettel
On 6 June 2024 at 08:22, Johannes Ranke wrote: | Am Mittwoch, 5. Juni 2024, 22:27:09 CEST schrieb Dirk Eddelbuettel: | > On 5 June 2024 at 21:55, Paul Gevers wrote: | > | Source: survival | > | Version: 3.5-8-1 | > | Severity: serious | > | Control: close -1 3.6-4-1 | >

Bug#1072661: r-cran-popepi: Please update to current version

2024-06-05 Thread Dirk Eddelbuettel
Source: r-cran-popepi Version: 0.4.11+dfsg-1 This package is holding CRAN package 'survival' (aka r-cran-survival, a package listed as part of the 'recommended' set by R Core and hence in r-recommended) back from migrating and is now threatening removal. See #1072648 for details. And that is

Bug#1072650: src:quantlib-swig: fails to migrate to testing for too long: FTBFS on armel, armhf, i386 and riscv64

2024-06-05 Thread Dirk Eddelbuettel
On 5 June 2024 at 21:57, Paul Gevers wrote: | Source: quantlib-swig | Version: 1.33-1 | Severity: serious | Control: close -1 1.34-1 | Tags: sid trixie ftbfs | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The Release Team considers packages

Bug#1072650: src:quantlib-swig: fails to migrate to testing for too long: FTBFS on armel, armhf, i386 and riscv64

2024-06-05 Thread Dirk Eddelbuettel
On 5 June 2024 at 21:57, Paul Gevers wrote: | Source: quantlib-swig | Version: 1.33-1 | Severity: serious | Control: close -1 1.34-1 | Tags: sid trixie ftbfs | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The Release Team considers packages

Bug#1072648: src:survival: fails to migrate to testing for too long: triggers autopkgtest issues

2024-06-05 Thread Dirk Eddelbuettel
On 5 June 2024 at 21:55, Paul Gevers wrote: | Source: survival | Version: 3.5-8-1 | Severity: serious | Control: close -1 3.6-4-1 | Tags: sid trixie | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The Release Team considers packages that are

Bug#1072648: src:survival: fails to migrate to testing for too long: triggers autopkgtest issues

2024-06-05 Thread Dirk Eddelbuettel
On 5 June 2024 at 21:55, Paul Gevers wrote: | Source: survival | Version: 3.5-8-1 | Severity: serious | Control: close -1 3.6-4-1 | Tags: sid trixie | User: release.debian@packages.debian.org | Usertags: out-of-sync | | Dear maintainer(s), | | The Release Team considers packages that are

Bug#1072322: r-cran-gdata: CVE-2023-7101 due to unpatched ParseExcel/Utility.pm

2024-05-31 Thread Dirk Eddelbuettel
Mark, On 31 May 2024 at 22:33, Voorhies, Mark wrote: | Package: r-cran-gdata | Version: 2.18.0.1-1 | Severity: normal | | Dear Maintainer, | | I believe r-cran-gdata 2.18.0.1-1 in Debian 12 is vulnerable to CVE-2023-7101 | due to shipping a copy of Utility.pm from Spreadsheet::ParseExcel that

Bug#1072036: release.debian.org: Transition for gsl-2.8 / libgsl28

2024-05-27 Thread Dirk Eddelbuettel
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition GNU GSL 2.8 was released a few days ago, and I uploaded a new version to experimental was has now cleared NEW. I checked my email folder, and the last time this happened (gsl 2.7,

Bug#1072036: release.debian.org: Transition for gsl-2.8 / libgsl28

2024-05-27 Thread Dirk Eddelbuettel
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition GNU GSL 2.8 was released a few days ago, and I uploaded a new version to experimental was has now cleared NEW. I checked my email folder, and the last time this happened (gsl 2.7,

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

2024-05-26 Thread Dirk Eddelbuettel
On 26 May 2024 at 13:31, Kurt Hornik wrote: | >>>>> Dirk Eddelbuettel writes: | | > Kurt, | | > Could you do me a favour and run on that clang18-using machine in question | > the following one-liner (provided your session has access to a .libPaths() | > inclu

Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault

2024-05-26 Thread Dirk Eddelbuettel
We are still having the open issue of rpy2 now segfaulting on the embedding tests which reproduces on my plain vanilla amd64 setup -- so I commented that test out too. Laurent: Any idea why R 4.4.0 and rpy2 do not get along on embedding? Cheers, Dirk -- dirk.eddelbuettel.com | @eddelbuettel

Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault

2024-05-26 Thread Dirk Eddelbuettel
We are still having the open issue of rpy2 now segfaulting on the embedding tests which reproduces on my plain vanilla amd64 setup -- so I commented that test out too. Laurent: Any idea why R 4.4.0 and rpy2 do not get along on embedding? Cheers, Dirk -- dirk.eddelbuettel.com | @eddelbuettel

Bug#1071940: r-cran-matrix: why depend on r-base instead of r-base-core?

2024-05-26 Thread Dirk Eddelbuettel
On 26 May 2024 at 11:41, Jörg-Volker Peetz wrote: | Package: r-cran-matrix | Version: 1.7-0-2 | Severity: wishlist | | Dear Dirk Eddelbuettel, | | shouldn't this package depend on r-base-core instead of r-base? | The description of r-base says it "eases the transition from the | pre-

Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault

2024-05-26 Thread Dirk Eddelbuettel
On 25 May 2024 at 12:35, Bo YU wrote: | Hi, | On Sat, May 18, 2024 at 06:41:53AM -0500, Dirk Eddelbuettel wrote: | > | >On 17 May 2024 at 23:05, Santiago Vila wrote: | >| Dirk Eddelbuettel wrote: | >| > Is there a chance this could be spurious? | >| | >| Unlikely because

Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault

2024-05-26 Thread Dirk Eddelbuettel
On 25 May 2024 at 12:35, Bo YU wrote: | Hi, | On Sat, May 18, 2024 at 06:41:53AM -0500, Dirk Eddelbuettel wrote: | > | >On 17 May 2024 at 23:05, Santiago Vila wrote: | >| Dirk Eddelbuettel wrote: | >| > Is there a chance this could be spurious? | >| | >| Unlikely because

Re: [R-pkg-devel] gcc14 checks on fedora

2024-05-24 Thread Dirk Eddelbuettel
On 24 May 2024 at 20:01, Brad Eck wrote: | I received a note that my package -- epanet2toolkit -- was showing a | warning in the fedora-gcc results on CRAN. | https://www.stats.ox.ac.uk/pub/bdr/gcc12/epanet2toolkit.out | | I'd like to reproduce the warning and fix it. Usually I'd do that with

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

2024-05-24 Thread Dirk Eddelbuettel
Kurt, Could you do me a favour and run on that clang18-using machine in question the following one-liner (provided your session has access to a .libPaths() including Rcpp) and, in the case of success, the resulting function? > Rcpp::cppFunction("int ompconfigtest() { return

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

2024-05-23 Thread Dirk Eddelbuettel
On 23 May 2024 at 20:02, Ivan Krylov wrote: | On Wed, 22 May 2024 09:18:13 -0500 | Dirk Eddelbuettel wrote: | | > Testing via 'nm' as you show is possible but not exactly 'portable'. | > So any suggestions as to what to condition on here? | | (My apologies if you already got an answe

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

2024-05-23 Thread Dirk Eddelbuettel
On 22 May 2024 at 14:03, Duncan Murdoch wrote: | On 2024-05-22 10:18 a.m., Dirk Eddelbuettel wrote: | > | > On 22 May 2024 at 13:54, Nixon, Michelle Pistner wrote: | > | Thank you both for your responses and help! Kurt-- your message makes a lot of | > | sense. I'll try t

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

2024-05-22 Thread Dirk Eddelbuettel
the Right Thing (TM) by 'borrowing' from the fairly mature check in RcppArmadillo. Dirk | | Thanks, | Michelle | ━━━ | From: Kurt Hornik | Sent: Wednesday, May 22, 2024 3:57 AM | To: Dirk Eddelbuettel | Cc: Nixon, Michelle

Re: [R-pkg-devel] handling documentation build tools

2024-05-21 Thread Dirk Eddelbuettel
As lyx is not listed in 'Writing R Extensions', the one (authorative) manual describing how to build packages for R, I would not assume it to be present on every CRAN machine building packages. Also note that several user recently had to ask here how to deal with less common fonts for style

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

2024-05-21 Thread Dirk Eddelbuettel
Hi Michelle, On 21 May 2024 at 13:46, Nixon, Michelle Pistner wrote: | Hi all, | | I'm running into build issues for my package (fido: https://github.com/jsilve24/fido) on the r-devel-linux-x86_64-debian-clang system on CRAN (full check log here:

Re: [R-sig-Debian] Default CXXFLAGS

2024-05-21 Thread Dirk Eddelbuettel
On 21 May 2024 at 15:59, Ivan Krylov wrote: | On Tue, 21 May 2024 14:48:48 +0200 | Kurt Hornik wrote: | | > I guess foer the CXXFLAGS we want dpkg-buildflags --get CXXFLAGS? Good catch, and expansion, by both of you. | It must be the case. It's both the documented option [1] and it |

Re: [R-sig-Debian] Default CXXFLAGS

2024-05-21 Thread Dirk Eddelbuettel
On 21 May 2024 at 13:01, Jeroen Ooms wrote: | Compiling packages with C++ code using the default r-base-dev | configuration on debian:sid shows a lot of: | |cc1plus: warning: '-Werror=' argument | '-Werror=implicit-function-declaration' is not valid for C++ | | Can this flag be removed

Bug#1071535: car: Please remove r-cran-maptools from (Build-)Depends

2024-05-20 Thread Dirk Eddelbuettel
On 20 May 2024 at 19:12, Andreas Tille wrote: | Source: car | Version: 3.1-2-2 | Severity: normal | | Hi, | | car mentions r-cran-maptools in (Build-)Depends which is not backed up | by the DESCRIPTION file. Since maptools is removed from CRAN I'd like Yes, we fail to build if 'added'

Bug#1071362: rpy2 segfaults in tests under Debian bulk rebuild

2024-05-18 Thread Dirk Eddelbuettel
On 18 May 2024 at 07:59, Dirk Eddelbuettel wrote: | | Hi Laurent, | | We a build issue in Debian found via bulk rebuilds. Which everything current | in 'unstable', rpy2 (version 3.5.16) segfaults in a test when embedding. | | Details are at https://bugs.debian.org/1071362 | | If you kee 1071

Bug#1071362: rpy2 segfaults in tests under Debian bulk rebuild

2024-05-18 Thread Dirk Eddelbuettel
On 18 May 2024 at 07:59, Dirk Eddelbuettel wrote: | | Hi Laurent, | | We a build issue in Debian found via bulk rebuilds. Which everything current | in 'unstable', rpy2 (version 3.5.16) segfaults in a test when embedding. | | Details are at https://bugs.debian.org/1071362 | | If you kee 1071

Bug#1071380: RM: r-cran-randomfields -- ROM; Package removed from CRAN

2024-05-18 Thread Dirk Eddelbuettel
Appears to be a duplicate of 1071379, maybe check if your script meant to remove another one. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault

2024-05-18 Thread Dirk Eddelbuettel
On 17 May 2024 at 23:05, Santiago Vila wrote: | Dirk Eddelbuettel wrote: | > Is there a chance this could be spurious? | | Unlikely because it also happens here: | | https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rpy2.html Ok, I will get in touch with Laurent. D

Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault

2024-05-18 Thread Dirk Eddelbuettel
On 17 May 2024 at 23:05, Santiago Vila wrote: | Dirk Eddelbuettel wrote: | > Is there a chance this could be spurious? | | Unlikely because it also happens here: | | https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rpy2.html Ok, I will get in touch with Laurent. D

Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault

2024-05-17 Thread Dirk Eddelbuettel
Is there a chance this could be spurious? The R API is reasonably stable, including the part for embedding R (and I am upstream for a small project doing that from C++). rpy2 is also mature and stable. So could this be a one-off? Dirk -- dirk.eddelbuettel.com | @eddelbuettel |

Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault

2024-05-17 Thread Dirk Eddelbuettel
Is there a chance this could be spurious? The R API is reasonably stable, including the part for embedding R (and I am upstream for a small project doing that from C++). rpy2 is also mature and stable. So could this be a one-off? Dirk -- dirk.eddelbuettel.com | @eddelbuettel |

Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

2024-05-16 Thread Dirk Eddelbuettel
On 16 May 2024 at 05:34, Duncan Murdoch wrote: | I forget now, but presumably the thinking at the time was that Suggested | packages would always be available for building and checking vignettes. Yes. I argued for years (cf https://dirk.eddelbuettel.com/blog/2017/03/22/ from seven (!!) years

Bug#1070840: r-cran-ff: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 06:28, Dirk Eddelbuettel wrote: | | On 10 May 2024 at 10:54, Graham Inggs wrote: | | Source: r-cran-ff | | Version: 4.0.12+ds-1 | | Severity: serious | | X-Debbugs-Cc: Dirk Eddelbuettel | | User: debian...@lists.debian.org | | Usertags: regression | | | | Hi Maintainer

Bug#1070840: r-cran-ff: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 06:28, Dirk Eddelbuettel wrote: | | On 10 May 2024 at 10:54, Graham Inggs wrote: | | Source: r-cran-ff | | Version: 4.0.12+ds-1 | | Severity: serious | | X-Debbugs-Cc: Dirk Eddelbuettel | | User: debian...@lists.debian.org | | Usertags: regression | | | | Hi Maintainer

Bug#1070842: r-bioc-mutationalpatterns: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 11:01, Graham Inggs wrote: | Source: r-bioc-mutationalpatterns | Version: 3.12.0+dfsg-1 | Severity: serious | X-Debbugs-Cc: Dirk Eddelbuettel | User: debian...@lists.debian.org | Usertags: regression | | Hi Maintainer | | r-bioc-mutationalpatterns' autopkgtest regresses when

Bug#1070843: r-bioc-s4vectors: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 11:04, Graham Inggs wrote: | Source: r-bioc-s4vectors | Version: 0.40.2+dfsg-1 | Severity: serious | X-Debbugs-Cc: Dirk Eddelbuettel | User: debian...@lists.debian.org | Usertags: regression | | Hi Maintainer | | r-bioc-s4vectors' autopkgtest regresses when tested with r

Bug#1070842: r-bioc-mutationalpatterns: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 11:01, Graham Inggs wrote: | Source: r-bioc-mutationalpatterns | Version: 3.12.0+dfsg-1 | Severity: serious | X-Debbugs-Cc: Dirk Eddelbuettel | User: debian...@lists.debian.org | Usertags: regression | | Hi Maintainer | | r-bioc-mutationalpatterns' autopkgtest regresses when

Bug#1070843: r-bioc-s4vectors: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 11:04, Graham Inggs wrote: | Source: r-bioc-s4vectors | Version: 0.40.2+dfsg-1 | Severity: serious | X-Debbugs-Cc: Dirk Eddelbuettel | User: debian...@lists.debian.org | Usertags: regression | | Hi Maintainer | | r-bioc-s4vectors' autopkgtest regresses when tested with r

Bug#1070841: r-bioc-iranges: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 10:58, Graham Inggs wrote: | Source: r-bioc-iranges | Version: 2.36.0-1 | Severity: serious | X-Debbugs-Cc: Dirk Eddelbuettel | User: debian...@lists.debian.org | Usertags: regression | | Hi Maintainer | | r-bioc-iranges' autopkgtest regresses when tested with r-base 4.4.0

Bug#1070841: r-bioc-iranges: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 10:58, Graham Inggs wrote: | Source: r-bioc-iranges | Version: 2.36.0-1 | Severity: serious | X-Debbugs-Cc: Dirk Eddelbuettel | User: debian...@lists.debian.org | Usertags: regression | | Hi Maintainer | | r-bioc-iranges' autopkgtest regresses when tested with r-base 4.4.0

Bug#1070840: r-cran-ff: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 10:54, Graham Inggs wrote: | Source: r-cran-ff | Version: 4.0.12+ds-1 | Severity: serious | X-Debbugs-Cc: Dirk Eddelbuettel | User: debian...@lists.debian.org | Usertags: regression | | Hi Maintainer | | r-cran-ff's autopkgtest regresses when tested with r-base 4.4.0 [1

Bug#1070840: r-cran-ff: autopkgtest regression with r-base 4.4.0

2024-05-10 Thread Dirk Eddelbuettel
On 10 May 2024 at 10:54, Graham Inggs wrote: | Source: r-cran-ff | Version: 4.0.12+ds-1 | Severity: serious | X-Debbugs-Cc: Dirk Eddelbuettel | User: debian...@lists.debian.org | Usertags: regression | | Hi Maintainer | | r-cran-ff's autopkgtest regresses when tested with r-base 4.4.0 [1

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

2024-05-09 Thread Dirk Eddelbuettel
Software Heritage (see [1] for their website and [2] for a brief intro I gave at useR! 2019 in Toulouse) covers GitHub and CRAN [3]. It is by now 'in collaboration with UNESCO', supported by a long and posh list of sponsors [4] and about as good as it gets to 'ensure longevity of artifacts'. It

Re: [R-pkg-devel] Fast Matrix Serialization in R?

2024-05-08 Thread Dirk Eddelbuettel
On 9 May 2024 at 03:20, Sameh Abdulah wrote: | I need to serialize and save a 20K x 20K matrix as a binary file. Hm that is an incomplete specification: _what_ do you want to do with it? Read it back in R? Share it with other languages (like Python) ? I.e. what really is your use case? Also,

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

2024-05-08 Thread Dirk Eddelbuettel
On 8 May 2024 at 11:02, Josiah Parry wrote: | CRAN has rejected this package with: | | * Size of tarball: 18099770 bytes* | | *Please reudce to less than 5 MB for a CRAN package.* Are you by chance confusing a NOTE (issued, but can be overruled) with a WARNING (more severe, likely a

Bug#1070240: r-cran-tmb: Please rebuild under updated Matrix package

2024-05-02 Thread Dirk Eddelbuettel
Package: r-cran-tmb Version: 1.9.11-1 Severity: important CRAN package Matrix had a new release 1.7.0 bringing in a new SuiteSparse API which requires a rebuild if (and only if) the Matrix headers are used. Your package is one of those that do, and therefore needs a rebuild. This was

Bug#1070239: r-cran-openmx: Please rebuild under updated Matrix package

2024-05-02 Thread Dirk Eddelbuettel
Package: r-cran-openmx Version: 2.21.11+dfsg-3 Severity: important CRAN package Matrix had a new release 1.7.0 bringing in a new SuiteSparse API which requires a rebuild if (and only if) the Matrix headers are used. Your package is one of those that do, and therefore needs a rebuild. This was

Bug#1070238: r-cran-irlba: Please rebuild under updated Matrix package

2024-05-02 Thread Dirk Eddelbuettel
Package: r-cran-irlba Version: 2.3.5.1-3 Severity: important CRAN package Matrix had a new release 1.7.0 bringing in a new SuiteSparse API which requires a rebuild if (and only if) the Matrix headers are used. Your package is one of those that do, and therefore needs a rebuild. This was

Re: [Rd] Patches for CVE-2024-27322

2024-04-30 Thread Dirk Eddelbuettel
On 30 April 2024 at 11:59, peter dalgaard wrote: | svn diff -c 86235 ~/r-devel/R Which is also available as https://github.com/r-devel/r-svn/commit/f7c46500f455eb4edfc3656c3fa20af61b16abb7 Dirk | (or 86238 for the port to the release branch) should be easily backported. | | (CC Luke in

Bug#1070009: r-cran-data.table: Update to current upstream

2024-04-30 Thread Dirk Eddelbuettel
The file 'issue_563_fread.txt' appears to be an input to data.table::fread() for a test on encodings, glancing at the context. I can run 'R CMD check --as-cran data.table_1.15.4.tar.gz' just fine [1] here without any failing tests (and I have no locale or anything set). It's not my package but

Bug#1070009: r-cran-data.table: Update to current upstream

2024-04-30 Thread Dirk Eddelbuettel
The package is pristine at CRAN https://cran.r-project.org/web/checks/check_results_data.table.html (apart from some new warnings several packages now get about interal R API headers, nothing to do with tests) Maybe you can sort this with upstream -- data.table is effectively holding up

Re: [R-pkg-devel] Problem with loading package "devtools" from CRAN.

2024-04-29 Thread Dirk Eddelbuettel
On 30 April 2024 at 01:21, Rolf Turner wrote: | On Mon, 29 Apr 2024 06:30:20 -0500 | Dirk Eddelbuettel wrote: | | | | > These days, I strongly recommend r2u [1]. As you already use R via | > CRAN through apt, r2u adds one more repository after which _all_ R | > packages are ha

Re: [R-pkg-devel] Problem with loading package "devtools" from CRAN.

2024-04-29 Thread Dirk Eddelbuettel
Rolf, This question might have been more appropriate for r-sig-debian than here. But as Simon noted, the lack of detail makes is difficult to say anything to aid. It likely was an issue local to your setup and use. These days, I strongly recommend r2u [1]. As you already use R via CRAN

Bug#1070009: r-cran-data.table: Update to current upstream

2024-04-28 Thread Dirk Eddelbuettel
Package: r-cran-data.table Version: 1.14.10+dfsg-1 Severity: normal data.table had a release 1.15.0 in January -- the first new one in three years! -- and two follow-ups since bringing it 1.15.4 at CRAN. Please update the Debian package to the current upstream version. This should likely

Re: [ESS] Error installing on ubuntu

2024-04-27 Thread Dirk Eddelbuettel via ESS-help
On 27 April 2024 at 10:53, 신선영(수학과) via ESS-help wrote: | Dear all, | | I get the following error message: | | make -C lisp all | make[1]: Entering directory '/home/mathi/ess-24.01.1/lisp' | test -f ../etc/.IS.RELEASE || wget -qO -

Bug#1069842: rjava: FTBFS: /usr/bin/ld: cannot find -ldeflate: No such file or directory

2024-04-25 Thread Dirk Eddelbuettel
reassign 1069842 r-base thanks On 25 April 2024 at 18:27, Santiago Vila wrote: | Package: src:rjava | Version: 1.0-11-1 | Severity: serious | Tags: ftbfs | | Dear maintainer: | | During a rebuild of all packages in unstable, your package failed to build: Thanks for this. It is caused by the

Bug#1069842: rjava: FTBFS: /usr/bin/ld: cannot find -ldeflate: No such file or directory

2024-04-25 Thread Dirk Eddelbuettel
reassign 1069842 r-base thanks On 25 April 2024 at 18:27, Santiago Vila wrote: | Package: src:rjava | Version: 1.0-11-1 | Severity: serious | Tags: ftbfs | | Dear maintainer: | | During a rebuild of all packages in unstable, your package failed to build: Thanks for this. It is caused by the

Re: [Rd] Question regarding .make_numeric_version with non-character input

2024-04-25 Thread Dirk Eddelbuettel
Hi Kurt, On 25 April 2024 at 08:07, Kurt Hornik wrote: | > Hervé Pagès writes: | | > Hi Kurt, | > Is it intended that numeric_version() returns an error by default on | > non-character input in R 4.4.0? | | Dear Herve, yes, that's the intention. | | > It seems that I can turn this into

Re: R 4.4.0 coming April 24

2024-04-21 Thread Dirk Eddelbuettel
On 21 April 2024 at 15:25, Sebastiaan Couwenberg wrote: | On 4/21/24 3:04 PM, Dirk Eddelbuettel wrote: | > R upstream no longer releases or tests for 32 bits (and has not since the R | > 4.3.0 release a year ago) so 'expect trouble there'. I think you all in the | > release team

Re: R 4.4.0 coming April 24

2024-04-21 Thread Dirk Eddelbuettel
Hi Graham, Hi Release Team, On 21 April 2024 at 13:37, Graham Inggs wrote: | On Thu, 18 Apr 2024 at 13:38, Dirk Eddelbuettel wrote: | > Right now it now only shows 'all reports (re-)running'. | | That was because of the new upload, but I see the results there now. | | The packa

Re: R 4.4.0 coming April 24

2024-04-18 Thread Dirk Eddelbuettel
Hi Paul, On 18 April 2024 at 11:50, Paul Gevers wrote: | Hi Dirk, | | On 18-04-2024 4:41 a.m., Dirk Eddelbuettel wrote: | > I uploaded a first | > beta release r-base_4.3.3.20240409-1 to 'experimental' a week ago, I just | > followed up with a rc release r-base_4.3.3.20240416-1. |

R 4.4.0 coming April 24

2024-04-17 Thread Dirk Eddelbuettel
R 4.4.0 will be released on April 24 (following the long established pattern of annual 'a.b.0' releases). As is common, nightlies (as alpha, betas, rc) have been made available for four weeks leading up to it. I uploaded a first beta release r-base_4.3.3.20240409-1 to 'experimental' a week ago,

R 4.4.0 coming April 24

2024-04-17 Thread Dirk Eddelbuettel
R 4.4.0 will be released on April 24 (following the long established pattern of annual 'a.b.0' releases). As is common, nightlies (as alpha, betas, rc) have been made available for four weeks leading up to it. I uploaded a first beta release r-base_4.3.3.20240409-1 to 'experimental' a week ago,

Re: [Rd] read.csv

2024-04-16 Thread Dirk Eddelbuettel
As an aside, the odd format does not seem to bother data.table::fread() which also happens to be my personally preferred workhorse for these tasks: > fname <- "/tmp/r/filename.csv" > read.csv(fname) Gene SNP prot log10p 1 YWHAE 13:62129097_C_T 1433 7.35 2 YWHAE 4:72617557_T_TA

Re: [Rd] read.csv

2024-04-16 Thread Dirk Eddelbuettel
On 16 April 2024 at 10:46, jing hua zhao wrote: | Dear R-developers, | | I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, | | Gene,SNP,prot,log10p |

Bug#970021: Seeking a small group to package Apache Arrow (was: Bug#970021: RFP: apache-arrow -- cross-language development platform for in-memory analytics)

2024-04-09 Thread Dirk Eddelbuettel
On 9 April 2024 at 18:45, Jose Manuel Abuin Mosquera wrote: | If possible, I would like to contribute. At work we use the Go and | Python implementations, also, in the short term, we will start using the | Rust one. Similar for us, and we have seen plenty of build headaches across pypi or

Bug#970021: Seeking a small group to package Apache Arrow (was: Bug#970021: RFP: apache-arrow -- cross-language development platform for in-memory analytics)

2024-04-09 Thread Dirk Eddelbuettel
On 9 April 2024 at 18:45, Jose Manuel Abuin Mosquera wrote: | If possible, I would like to contribute. At work we use the Go and | Python implementations, also, in the short term, we will start using the | Rust one. Similar for us, and we have seen plenty of build headaches across pypi or

Re: Seeking a small group to package Apache Arrow (was: Bug#970021: RFP: apache-arrow -- cross-language development platform for in-memory analytics)

2024-04-09 Thread Dirk Eddelbuettel
On 9 April 2024 at 18:45, Jose Manuel Abuin Mosquera wrote: | If possible, I would like to contribute. At work we use the Go and | Python implementations, also, in the short term, we will start using the | Rust one. Similar for us, and we have seen plenty of build headaches across pypi or

Bug#1068117: dieharder: dab_monobit2 crashes with ntuple > 17

2024-04-08 Thread Dirk Eddelbuettel
On 8 April 2024 at 18:21, Lucas Thode wrote: | Apologies for the confusion, I didn't realize the patch in question was a new | addition.  Just confirmed that it errors out instead of segfaulting or hanging. Thanks for confirming! Dirk | On Sat, Apr 6, 2024 at 5:32 PM Dirk Eddelbuettel

Bug#1068117: dieharder: dab_monobit2 crashes with ntuple > 17

2024-04-06 Thread Dirk Eddelbuettel
Hi Lucas, As Milan suggested, please sure you are current. If in doubt, park you current checkout and start from git checkout https://github.com/eddelbuettel/dieharder.git where you should see today's commit from merging PR 24. edd@rob:~/git/dieharder(master)$ git ls | head *

Bug#1068117: dieharder: dab_monobit2 crashes with ntuple > 17

2024-04-05 Thread Dirk Eddelbuettel
Hi Lucas, On 30 March 2024 at 22:47, Lucas Thode wrote: | Package: dieharder | Version: 3.31.1.4-1.1 | Severity: normal | X-Debbugs-Cc: thode...@gmail.com | | Dear Maintainer, | | `dieharder -d 209 -n $nvalue` crashes for $nvalue>17: | | $ dieharder -d 209 |

Re: [Rd] RSS Feed of NEWS needs a hand

2024-04-02 Thread Dirk Eddelbuettel
On 2 April 2024 at 09:41, Duncan Murdoch wrote: | On 02/04/2024 8:50 a.m., Dirk Eddelbuettel wrote: | > On 2 April 2024 at 07:37, Dirk Eddelbuettel wrote: | > blosxom, simple as it is, takes (IIRC) filesystem ctime as the posting | > timestamp so would be best if you had a backup wit

Re: [Rd] RSS Feed of NEWS needs a hand

2024-04-02 Thread Dirk Eddelbuettel
On 2 April 2024 at 07:37, Dirk Eddelbuettel wrote: | | On 2 April 2024 at 08:21, Duncan Murdoch wrote: | | I have just added R-4-4-branch to the feeds. I think I've also fixed | | the \I issue, so today's news includes a long list of old changes. | | These feeds can fussy: looks like you

Re: [Rd] RSS Feed of NEWS needs a hand

2024-04-02 Thread Dirk Eddelbuettel
On 2 April 2024 at 08:21, Duncan Murdoch wrote: | I have just added R-4-4-branch to the feeds. I think I've also fixed | the \I issue, so today's news includes a long list of old changes. These feeds can fussy: looks like you triggered many updates. Feedly currently greets me with 569 new

Re: [R-pkg-devel] Order of repo access from options("repos")

2024-04-02 Thread Dirk Eddelbuettel
On 1 April 2024 at 17:44, Uwe Ligges wrote: | Untested: | | install.packages() calls available.packages() to find out which packages | are available - and passes a "filters" argument if supplied. | That can be a user defined filter. It should be possible to write a user | defined filter which

Re: [R-pkg-devel] Order of repo access from options("repos")

2024-03-31 Thread Dirk Eddelbuettel
On 31 March 2024 at 11:43, Martin Morgan wrote: | So all repositories are consulted and then the result filtered to contain just | the most recent version of each. Does it matter then what order the | repositories are visited? Right. I fall for that too often, as I did here. The order matters

Bug#970021: Seeking a small group to package Apache Arrow (was: Bug#970021: RFP: apache-arrow -- cross-language development platform for in-memory analytics)

2024-03-31 Thread Dirk Eddelbuettel
Julian, Arrow is a complicated and large package. We use it at work (where there is a fair amount of Python, also to Conda etc) and do have issues with more complex builds especially because it is 'data infrastructure' and can come in from different parts. I would recommend against packaging at

Bug#970021: Seeking a small group to package Apache Arrow (was: Bug#970021: RFP: apache-arrow -- cross-language development platform for in-memory analytics)

2024-03-31 Thread Dirk Eddelbuettel
Julian, Arrow is a complicated and large package. We use it at work (where there is a fair amount of Python, also to Conda etc) and do have issues with more complex builds especially because it is 'data infrastructure' and can come in from different parts. I would recommend against packaging at

Re: Seeking a small group to package Apache Arrow (was: Bug#970021: RFP: apache-arrow -- cross-language development platform for in-memory analytics)

2024-03-31 Thread Dirk Eddelbuettel
Julian, Arrow is a complicated and large package. We use it at work (where there is a fair amount of Python, also to Conda etc) and do have issues with more complex builds especially because it is 'data infrastructure' and can come in from different parts. I would recommend against packaging at

Re: Seeking a small group to package Apache Arrow (was: Bug#970021: RFP: apache-arrow -- cross-language development platform for in-memory analytics)

2024-03-31 Thread Dirk Eddelbuettel
Julian, Arrow is a complicated and large package. We use it at work (where there is a fair amount of Python, also to Conda etc) and do have issues with more complex builds especially because it is 'data infrastructure' and can come in from different parts. I would recommend against packaging at

Re: Seeking a small group to package Apache Arrow (was: Bug#970021: RFP: apache-arrow -- cross-language development platform for in-memory analytics)

2024-03-31 Thread Dirk Eddelbuettel
Julian, Arrow is a complicated and large package. We use it at work (where there is a fair amount of Python, also to Conda etc) and do have issues with more complex builds especially because it is 'data infrastructure' and can come in from different parts. I would recommend against packaging at

Re: [R-pkg-devel] Order of repo access from options("repos")

2024-03-31 Thread Dirk Eddelbuettel
Greg, There are AFAICT two issues here: how R unrolls the named vector that is the 'repos' element in the list 'options', and how your computer resolves DNS for localhost vs 172.17.0.1. I would try something like options(repos = c(CRAN = "http://localhost:3001/proxy;,

Re: [Rd] Question regarding .make_numeric_version with non-character input

2024-03-29 Thread Dirk Eddelbuettel
On 29 March 2024 at 17:56, Andrea Gilardi via R-devel wrote: | Dear all, | | I have a question regarding the R-devel version of .make_numeric_version() function. As far as I can understand, the current code

Re: [R-sig-Debian] Problem Installing R 4.3.3 on Vanilla based Jammy Ubuntu

2024-03-27 Thread Dirk Eddelbuettel
Marco, It usually helps to be aware of one's hardware platform ;-) There is an option for Docker command to tell it to switch to x86_64, my colleagues who are on M1 and alike use that to access the generally richer eco-system of binaries for the Intel world. If on the other hand you prefer to

Re: [R-pkg-devel] using portable simd instructions

2024-03-27 Thread Dirk Eddelbuettel
: https://github.com/google/highway docs: https://google.github.io/highway/en/master/ | | Op di 26 mrt 2024 om 15:41 schreef Dirk Eddelbuettel : | > | > | > On 26 March 2024 at 10:53, jesse koops wrote: | > | How can I make this portable and CRAN-acceptable? | > | > But wri

Re: [Rd] paths capability FALSE on devel?

2024-03-27 Thread Dirk Eddelbuettel
On 27 March 2024 at 11:03, Prof Brian Ripley via R-devel wrote: | On 27/03/2024 10:28, Alexandre Courtiol wrote: | > Hi all, | > | > I don't know if it is a local issue on my hands or not, but after | > installing R-devel the output of grDevices::dev.capabilities()$paths is | > FALSE, while it

Re: [R-pkg-devel] Check results on r-devel-windows claiming error but tests seem to pass?

2024-03-26 Thread Dirk Eddelbuettel
On 26 March 2024 at 09:37, Dirk Eddelbuettel wrote: | | Avi, | | That was a hickup and is now taken care of. When discussing this (off-line) | with Jeroen we (rightly) suggested that keeping an eye on Typo, as usual, "he (rightly) suggested". My bad. D. | |https://con

Re: [R-pkg-devel] using portable simd instructions

2024-03-26 Thread Dirk Eddelbuettel
On 26 March 2024 at 10:53, jesse koops wrote: | How can I make this portable and CRAN-acceptable? But writing (or borrowing ?) some hardware detection via either configure / autoconf or cmake. This is no different than other tasks decided at install-time. Start with 'Writing R Extensions', as

Re: [R-pkg-devel] Check results on r-devel-windows claiming error but tests seem to pass?

2024-03-26 Thread Dirk Eddelbuettel
Avi, That was a hickup and is now taken care of. When discussing this (off-line) with Jeroen we (rightly) suggested that keeping an eye on https://contributor.r-project.org/svn-dashboard/ is one possibility to keep track while we have no status alert system from CRAN. I too was quite

Re: [R-pkg-devel] How to store large data to be used in an R package?

2024-03-26 Thread Dirk Eddelbuettel
On 25 March 2024 at 11:12, Jairo Hidalgo Migueles wrote: | I'm reaching out to seek some guidance regarding the storage of relatively | large data, ranging from 10-40 MB, intended for use within an R package. | Specifically, this data consists of regression and random forest models | crucial for

Re: CRAN Package Matrix update and a possible transition or not

2024-03-23 Thread Dirk Eddelbuettel
On 23 March 2024 at 07:25, Dirk Eddelbuettel wrote: | | On 22 March 2024 at 11:12, Dirk Eddelbuettel wrote: | | | | On 27 February 2024 at 19:01, Dirk Eddelbuettel wrote: | | | A couple of days ago, the (effective) Maintainer and rather active developer | | | of the Matrix package Mikael

Re: CRAN Package Matrix update and a possible transition or not

2024-03-23 Thread Dirk Eddelbuettel
On 23 March 2024 at 07:25, Dirk Eddelbuettel wrote: | | On 22 March 2024 at 11:12, Dirk Eddelbuettel wrote: | | | | On 27 February 2024 at 19:01, Dirk Eddelbuettel wrote: | | | A couple of days ago, the (effective) Maintainer and rather active developer | | | of the Matrix package Mikael

Re: CRAN Package Matrix update and a possible transition or not

2024-03-23 Thread Dirk Eddelbuettel
On 22 March 2024 at 11:12, Dirk Eddelbuettel wrote: | | On 27 February 2024 at 19:01, Dirk Eddelbuettel wrote: | | 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

Re: CRAN Package Matrix update and a possible transition or not

2024-03-23 Thread Dirk Eddelbuettel
On 22 March 2024 at 11:12, Dirk Eddelbuettel wrote: | | On 27 February 2024 at 19:01, Dirk Eddelbuettel wrote: | | 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

Re: CRAN Package Matrix update and a possible transition or not

2024-03-22 Thread Dirk Eddelbuettel
On 27 February 2024 at 19:01, Dirk Eddelbuettel wrote: | 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

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