r-base 4.5.0 by IsabelParedes · Pull Request #369 · conda-forge/r-base-feedstock

IsabelParedes · 2025-04-22T17:20:11Z

Checklist

Used a personal fork of the feedstock to propose changes
Bumped the build number (if the version is unchanged)
Reset the build number to 0 (if the version changed)
Re-rendered with the latest conda-smithy (Use the phrase @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
Ensured the license file is being packaged.

Fixes #368

conda-forge-admin · 2025-04-22T17:21:46Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe/meta.yaml) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipe/meta.yaml:

ℹ️ The recipe is not parsable by parser conda-souschef (grayskull). This parser is not currently used by conda-forge, but may be in the future. We are collecting information to see which recipes are compatible with grayskull.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/15440730222. Examine the logs at this URL for more detail.}

IsabelParedes · 2025-04-22T17:26:28Z

@conda-forge-admin, please rerender

IsabelParedes · 2025-04-22T17:27:02Z

Requires conda-forge/autoconf-feedstock#40

xhochy · 2025-04-25T19:13:50Z

autoconf >=2.72 * does not exist

See conda-forge/autoconf-feedstock#40

IsabelParedes · 2025-05-13T17:55:19Z

@conda-forge-admin, please rerender

IsabelParedes · 2025-05-13T17:57:20Z

autoconf $v2.72$ now available 🎉

IsabelParedes · 2025-05-13T18:19:35Z

m2-autoconf >=2.72 * does not exist for win

Attempting to add it here conda-forge/m2-binary-packages-feedstock#17

IsabelParedes · 2025-05-14T09:46:54Z

Running aclocal in a directory with an empty configure.ac triggers the same error

- autom4te: error: need GNU m4 1.4 or later: /home/conda/feedstock_root/build_artifacts/autoconf_1746873733042/_build_env/bin/m4

IsabelParedes · 2025-05-14T10:22:28Z

It seems that autoconf is the problem
conda-forge/autoconf-feedstock#41 $\leftarrow$ fixed 🎉

IsabelParedes · 2025-05-20T10:23:01Z

@conda-forge-admin, please rerender

…nda-forge-pinning 2025.05.20.06.20.57

ZheFrench · 2025-05-22T14:52:18Z

Hi @conda-forge/r-base-feedstock-maintainers,

I hope you’re all doing well! I noticed that PR #369 to bump r-base to 4.5.0 was opened on April 22 and has cleared most review tasks. Could you please let me know if there’s anything outstanding preventing its merge, and roughly when we might expect the new r-base 4.5.0 package to become available on conda-forge?

Thank you for your work on maintaining this feedstock—I’m looking forward to testing some of the new features in R 4.5.0!

…nda-forge-pinning 2025.05.26.22.22.49

xhochy · 2025-05-27T10:23:15Z

We're now down to LAPACK related linkage errors:

D:/bld/r-base-split_1748339898149/_build_env/Library/bin/../lib/gcc/x86_64-w64-mingw32/13.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot export dgemmtr_: symbol not defined
D:/bld/r-base-split_1748339898149/_build_env/Library/bin/../lib/gcc/x86_64-w64-mingw32/13.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot export zgemmtr_: symbol not defined

IsabelParedes · 2025-05-27T10:30:37Z

We're now down to LAPACK related linkage errors:

D:/bld/r-base-split_1748339898149/_build_env/Library/bin/../lib/gcc/x86_64-w64-mingw32/13.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot export dgemmtr_: symbol not defined
D:/bld/r-base-split_1748339898149/_build_env/Library/bin/../lib/gcc/x86_64-w64-mingw32/13.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot export zgemmtr_: symbol not defined

For the win build, would it be ok to use the internal BLAS/LAPACK implementation instead of the external libblas and liblapack packages?

xhochy · 2025-05-27T14:46:37Z

The new mentioned routines are new: https://developer.r-project.org/blosxom.cgi/R-4-5-branch/NEWS/2025/04/02

xhochy · 2025-05-27T14:55:09Z

The changelog as a bit more information: https://cran.r-project.org/doc/manuals/r-release/NEWS.html

isuruf · 2025-05-27T14:59:05Z

    export LIBRARY_PATH=${PREFIX}/Library/lib

+    # Support older BLAS implementations (pre-2025)
+    sed -i '/^LIBSOURCES =/ s/$/ dgemmtr.f zgemmtr.f/' src/modules/lapack/Makefile.win


That's going to be a lot slower than intended.

Then we need to update the blas version used here. I guess this means we need to get in conda-forge/blas-feedstock#114 first, right?

We need to update to 3.12.1 or backport the dgemmtr routines to 3.9

The other option is to remove these symbols altogether. They are only used in lapack.

Is removing the symbols preferable to the included patch which adds the symbols and it's working?

Yes, removing them is preferable. can you send a PR to remove them?

Hi @isuruf !

New PR here #379

conda-forge-admin · 2025-06-04T12:03:59Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipe/meta.yaml) and found some lint.

Here's what I've got...

For recipe/meta.yaml:

❌ Selectors are suggested to take a <two spaces>#<one space>[<expression>] form. See lines [27]

For recipe/meta.yaml:

ℹ️ The recipe is not parsable by parser conda-souschef (grayskull). This parser is not currently used by conda-forge, but may be in the future. We are collecting information to see which recipes are compatible with grayskull.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/15441741720. Examine the logs at this URL for more detail.}

conda-forge-admin · 2025-06-04T12:27:25Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe/meta.yaml) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipe/meta.yaml:

ℹ️ The recipe is not parsable by parser conda-souschef (grayskull). This parser is not currently used by conda-forge, but may be in the future. We are collecting information to see which recipes are compatible with grayskull.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/15445224626. Examine the logs at this URL for more detail.}

IsabelParedes · 2025-06-04T13:10:21Z

Hi @xhochy and @isuruf !

I added a patch following the instructions in src/extra/blas/Makefile.win to integrate the new symbols into Rblas.dll and it finally passes.

Rblas.dll imports xerbla_ from R.dll
OpenBLAS 0.3.29 includes [dz]gemmtr but ATLAS does not.
So to use latter, copy [dz]gemmtr.f from ../../modules/lapack
and add dgemmtr.o zgemmtr.o to the dependencies.

IsabelParedes · 2025-06-04T14:22:13Z

@conda-forge-admin, please rerender

…nda-forge-pinning 2025.06.04.10.18.16

IsabelParedes · 2025-06-04T14:33:45Z

@conda-forge-admin, please rerender

…nda-forge-pinning 2025.06.04.10.18.16

ZheFrench · 2025-06-10T08:46:08Z

Hi @conda-forge/r-base-feedstock-maintainers,

I hope you’re all doing well! I noticed that PR #369 to bump r-base to 4.5.0 was opened on April 22 and has cleared most review tasks. Could you please let me know if there’s anything outstanding preventing its merge, and roughly when we might expect the new r-base 4.5.0 package to become available on conda-forge?

Thank you for your work on maintaining this feedstock—I’m looking forward to testing some of the new features in R 4.5.0!

May I ask the same question ?

IsabelParedes · 2025-06-20T10:27:33Z

Newer version #378

IsabelParedes · 2025-06-20T12:00:39Z

Newer version has been merged 🎉

IsabelParedes marked this pull request as ready for review April 22, 2025 17:35

IsabelParedes requested review from a team, isuruf, mbargull, mingwandroid, ocefpaf, sodre and xhochy as code owners April 22, 2025 17:35

regro-cf-autotick-bot and others added 5 commits May 20, 2025 12:19

updated v4.5.0

51ba893

Fix error: Autoconf version 2.72 or higher is required

d6bd251

Debug m4

0407abe

Add verbosity

8c7ac16

Set M4 env var

6951c18

IsabelParedes force-pushed the 4.5.0_h6106e3 branch from 43384bc to 6951c18 Compare May 20, 2025 10:22

conda-forge-webservices[bot] and others added 2 commits May 20, 2025 10:25

MNT: Re-rendered with conda-build 25.4.2, conda-smithy 3.48.1, and co…

c029f8c

…nda-forge-pinning 2025.05.20.06.20.57

Restore build recipe

987fa86

justinaskav mentioned this pull request May 26, 2025

Bioconductor 3.21 packages bioconda/bioconda-recipes#55833

Open

IsabelParedes added 2 commits May 26, 2025 23:49

Trigger ci

701681a

Try m2-autoconf2.72

b37a4fb

xhochy added 6 commits May 27, 2025 09:01

MNT: Re-rendered with conda-build 25.4.2, conda-smithy 3.48.1, and co…

5463f8d

…nda-forge-pinning 2025.05.26.22.22.49

Limit CI matrix (for debugging)

85e8a08

Set autom4te path

cb48662

MNT: Re-rendered with conda-build 25.4.2, conda-smithy 3.48.1, and co…

ea9d3ad

…nda-forge-pinning 2025.05.26.22.22.49

Fix condition for AUTOM4TE

b7368d0

Call explicit versioned autoconf

bacf6ce

Support older BLAS implementations on win

4229726

isuruf reviewed May 27, 2025

View reviewed changes

IsabelParedes added 3 commits June 4, 2025 13:09

Try internal blas/lapack for win

5afc1de

Revert last commit

cf79fe8

Try following instructions

5b28f07

Add new syms to atlas also

819b212

Restore ci files

2d75f5e

conda-forge-webservices[bot] and others added 2 commits June 4, 2025 14:24

MNT: Re-rendered with conda-build 25.5.0, conda-smithy 3.50.0, and co…

c51d294

…nda-forge-pinning 2025.06.04.10.18.16

Restore matrix

3ffc755

MNT: Re-rendered with conda-build 25.5.0, conda-smithy 3.50.0, and co…

2a107b5

…nda-forge-pinning 2025.06.04.10.18.16

IsabelParedes closed this Jun 20, 2025

isuruf mentioned this pull request Jun 20, 2025

Update pin for r_base conda-forge/conda-forge-pinning-feedstock#7496

Merged

2 tasks

Uh oh!

Uh oh!

Conversation

IsabelParedes commented Apr 22, 2025 • edited by xhochy Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

conda-forge-admin commented Apr 22, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

IsabelParedes commented Apr 22, 2025

Uh oh!

IsabelParedes commented Apr 22, 2025

Uh oh!

xhochy commented Apr 25, 2025

Uh oh!

IsabelParedes commented May 13, 2025

Uh oh!

IsabelParedes commented May 13, 2025

Uh oh!

IsabelParedes commented May 13, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

IsabelParedes commented May 14, 2025

Uh oh!

IsabelParedes commented May 14, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

IsabelParedes commented May 20, 2025

Uh oh!

ZheFrench commented May 22, 2025

Uh oh!

xhochy commented May 27, 2025

Uh oh!

IsabelParedes commented May 27, 2025

Uh oh!

xhochy commented May 27, 2025

Uh oh!

xhochy commented May 27, 2025

Uh oh!

isuruf May 27, 2025

Choose a reason for hiding this comment

Uh oh!

xhochy May 27, 2025

Choose a reason for hiding this comment

Uh oh!

isuruf May 27, 2025

Choose a reason for hiding this comment

Uh oh!

isuruf Jun 10, 2025

Choose a reason for hiding this comment

Uh oh!

IsabelParedes Jun 11, 2025

Choose a reason for hiding this comment

Uh oh!

isuruf Jun 20, 2025

Choose a reason for hiding this comment

Uh oh!

IsabelParedes Jun 23, 2025

Choose a reason for hiding this comment

Uh oh!

conda-forge-admin commented Jun 4, 2025

Uh oh!

conda-forge-admin commented Jun 4, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

IsabelParedes commented Jun 4, 2025

Uh oh!

IsabelParedes commented Jun 4, 2025

Uh oh!

IsabelParedes commented Jun 4, 2025

Uh oh!

ZheFrench commented Jun 10, 2025

Uh oh!

IsabelParedes commented Jun 20, 2025

Uh oh!

IsabelParedes commented Jun 20, 2025

Uh oh!

Reviewers

Assignees

Labels

IsabelParedes commented Apr 22, 2025 •

edited by xhochy

Loading

conda-forge-admin commented Apr 22, 2025 •

edited

Loading

IsabelParedes commented May 13, 2025 •

edited

Loading

IsabelParedes commented May 14, 2025 •

edited

Loading

conda-forge-admin commented Jun 4, 2025 •

edited

Loading