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Posted to issues@arrow.apache.org by "jonkeane (via GitHub)" <gi...@apache.org> on 2024/07/18 02:05:13 UTC
[I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
jonkeane opened a new issue, #43317:
URL: https://github.com/apache/arrow/issues/43317
### Describe the enhancement requested
# Packaging checklist for CRAN release
For a high-level overview of the release process see the
[Apache Arrow Release Management Guide](https://arrow.apache.org/docs/developers/release.html#post-release-tasks).
cc @jonkeane @amoeba @nealrichardson @assignUser @paleolimbot for coordination on the various tasks to release
We will want to cherry pick:
* https://github.com/apache/arrow/pull/43243
* https://github.com/apache/arrow/pull/43189
* https://github.com/apache/arrow/pull/43173
* https://github.com/apache/arrow/pull/43172
* https://github.com/apache/arrow/pull/43162
## Before the release candidate is cut
- [x] [Create a GitHub issue](https://github.com/apache/arrow/issues/new/) entitled `[R] CRAN packaging checklist for version X.X.X` and copy this checklist to the issue.
- [] Review deprecated functions to advance their deprecation status, including removing preprocessor directives that no longer apply (search for `ARROW_VERSION_MAJOR` in r/src).
- [x] Evaluate the status of any failing [nightly tests and nightly packaging builds](http://crossbow.voltrondata.com). These checks replicate most of the checks that CRAN runs, so we need them all to be passing or to understand that the failures may (though won't necessarily) result in a rejection from CRAN.
- [] Check [current CRAN check results](https://cran.rstudio.org/web/checks/check_results_arrow.html)
- [] Ensure the contents of the README are accurate and up to date.
- [] Run `urlchecker::url_check()` on the R directory at the release candidate.
commit. Ignore any errors with badges as they will be removed in the CRAN release branch.
- [] [Polish NEWS](https://style.tidyverse.org/news.html#news-release) but do **not** update version numbers (this is done automatically later). You can find commits by, for example, `git log --oneline aa057d0..HEAD | grep "\[R\]"`
- [] Run preliminary reverse dependency checks using `archery docker run r-revdepcheck`.
- [ ] For major releases, prepare tweet thread highlighting new features.
Wait for the release candidate to be cut:
## After release candidate has been cut
- [] Create a CRAN-release branch from the release candidate commit
## Prepare and check the .tar.gz that will be released to CRAN.
- [] `git fetch upstream && git checkout release-X.X.X-rcXX && git clean -f -d`
- [] Run `make build`. This copies Arrow C++ into tools/cpp, prunes some
unnecessary components, and runs `R CMD build` to generate the source tarball.
Because this will install the package, you will need to ensure that the version
of Arrow C++ available to the configure script is the same as the version
that is vendored into the R package (e.g., you may need to unset `ARROW_HOME`).
- [] `devtools::check_built("arrow_X.X.X.tar.gz")` locally
- [] Run reverse dependency checks using `archery docker run r-revdepcheck`.
## Release vote
- [x] Release vote passed!
## Generate R package to submit to CRAN
- [] If the release candidate commit updated, rebase the CRAN release branch
on that commit.
- [] Pick any commits that were made to main since the release commit that
were needed to fix CRAN-related submission issues identified in the above
steps.
- [] Remove badges from README.md
- [] Run `urlchecker::url_check()` on the R directory
- [] Create a PR entitled `WIP: [R] Verify CRAN release-10.0.1-rc0`. Add
a comment `@github-actions crossbow submit --group r` to run all R crossbow
jobs against the CRAN-specific release branch.
- [] Run `Rscript tools/update-checksums.R <libarrow version>` to download the checksums for the pre-compiled binaries from the ASF artifactory into the tools directory.
- [] Regenerate arrow_X.X.X.tar.gz (i.e., `make build`)
Ensure linux binary packages are available:
- [] Ensure linux binaries are available in the artifactory:
https://apache.jfrog.io/ui/repos/tree/General/arrow/r
## Check binary Arrow C++ distributions specific to the R package
- [ ] Upload the .tar.gz to [win-builder](https://win-builder.r-project.org/upload.aspx) (r-devel only)
and confirm (with Nic, who will automatically receive an email about the results) that the check is clean.
This step cannot be completed before Jeroen has put the binaries in the MinGW repository, i.e. [here](https://ftp.opencpu.org/rtools/ucrt64/), [here](https://ftp.opencpu.org/rtools/mingw64/), and [here](https://ftp.opencpu.org/rtools/mingw32/).
- [ ] Upload the .tar.gz to [MacBuilder](https://mac.r-project.org/macbuilder/submit.html)
and confirm that the check is clean
- [] Check `install.packages("arrow_X.X.X.tar.gz")` on Ubuntu and ensure that the
hosted binaries are used
- [] `devtools::check_built("arrow_X.X.X.tar.gz")` locally one more time (for luck)
## CRAN submission
- [] Upload arrow_X.X.X.tar.gz to the
[CRAN submit page](https://xmpalantir.wu.ac.at/cransubmit/)
- [] Confirm the submission email
Wait for CRAN...
- [] Accepted!
- [] Tag the tip of the CRAN-specific release branch
- [ ] Add a new line to the matrix in the [backwards compatability job](https://github.com/apache/arrow/blob/main/dev/tasks/r/github.linux.arrow.version.back.compat.yml)
- [ ] (patch releases only) Update the package version in `ci/scripts/PKGBUILD`, `dev/tasks/homebrew-formulae/autobrew/apache-arrow.rb`, `r/DESCRIPTION`, and `r/NEWS.md`
- [ ] (CRAN-only releases) Rebuild news page with `pkgdown::build_news()` and submit a PR to the asf-site branch of the docs site with the contents of `arrow/r/docs/news/index.html` replacing the current contents of `arrow-site/docs/r/news/index.html`
- [ ] (CRAN-only releases) Bump the version number in `r/pkgdown/assets/versions.json`, and update this on the [the `asf-site` branch of the docs site](https://github.com/apache/arrow-site) too.
- [ ] Update the packaging checklist template to reflect any new realities of the
packaging process.
- [] Wait for CRAN-hosted binaries on the
[CRAN package page](https://cran.r-project.org/package=arrow) to reflect the
new version
- [ ] Tweet!
### Component(s)
R
### Component(s)
R
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2241290928
Ah, that is a regression on us: #43349 I need to step away for a bit, in case someone wants to investigate what's up there. I don't think much has changed with our altrep code, but this could be from our non-api avoidance changes (or possibly the change we made to avoid executing functions while reading data).
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2346695334
It looks like the macOS x86_64 binary finally got built, see https://cran.r-project.org/web/packages/arrow/index.html. The binary for oldrel still isn't built but I don't think that should prevent any announcement about the release. Thoughts?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2303339699
I haven't seen a draft yet. @thisisnic do you want to take this on again?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2305217122
I can get it started later today, I'll drop a link in here for reviews when that's done.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2368684912
Thanks @jonkeane. Do we need to update the `r-universe-release` tag still and add a `r-17.0.01` tag?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2309294996
Thanks @jonkeane and @thisisnic for taking a look at the social media doc. I accepted suggestions and added code screenshots to the Drive folder where appropriate, see https://drive.google.com/drive/folders/1DzGoZNHbiZXNca2oHWjpBtJrEti3W-zQ?usp=drive_link, so I think this is ready for me and @jonkeane to post when x86_64 binaries go live.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2307598674
Language here looks great, thanks @amoeba!
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261389626
Here's a workaround for the tidyquery failure: https://github.com/apache/arrow/pull/43498
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261734247
Womp womp. I received the not-passing-auto-checks email. The problem is that we are calling XXX on <4.2 and CRAN's checks for these apparently are static and not actually checking if we are truly calling them (on R versions that they run on).
I'm partially tempted to wait and see if they end up accepting it anyway after seeing what's going on. I could also reply and explain (though I have extremely low hopes of that landing, even though it is simply a fact that before 4.2 the approved thing does not exist!). @nealrichardson do I remember you having an idea on possibly obfuscating this call for our compatibility branch?
The only NOTE is:
```
* checking compiled code ... NOTE
File 'arrow/libs/x64/arrow.dll':
Found non-API calls to R: 'Rf_findVarInFrame3', 'SETLENGTH',
'SET_GROWABLE_BIT', 'SET_TRUELENGTH'
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
```
https://win-builder.r-project.org/incoming_pretest/arrow_17.0.0_20240801_011430/Windows/00check.log
https://win-builder.r-project.org/incoming_pretest/arrow_17.0.0_20240801_011430/Debian/00check.log
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2237112306
I added the NEWS.md entry from https://github.com/apache/arrow/pull/43189 to the [release blog post PR](https://github.com/apache/arrow-site/pull/537).
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2241285240
No problem, I've got one at https://github.com/apache/arrow/pull/43348
This isn't a here-and-now problem, but boy do I wish we could say "these notes we don't care about but all the others we do" for things like this 🤦
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2258537403
For example, I see the message from this line in the logs: https://github.com/apache/arrow/blob/main/cpp/cmake_modules/ThirdpartyToolchain.cmake#L352 But I don't see either of the messages that should follow, about whether lz4 was found or not.
When you say you don't see either of the messages that follow are you talking about https://github.com/apache/arrow/blob/48782e75708157f2296ab95699239207c5588871/cpp/cmake_modules/ThirdpartyToolchain.cmake#L354 or https://github.com/apache/arrow/blob/48782e75708157f2296ab95699239207c5588871/cpp/cmake_modules/ThirdpartyToolchain.cmake#L358 ? If so, that first one (line 354) is actually where the log line that you're seeing is emitted, I believe. The line you linked 352 is adding to the string, but the part that starts with `Using ...` is emitted at line 354 (so we do get there!)
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2258538798
@kou might have some ideas + help here too (sorry I should have tagged you on that original comment)
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261788123
You could wait to see if Uwe waves it through, or you could reply and explain that these are ifdef'd for backwards compatibility only.
The in-case-of-emergency hack would be to sed out these references from the .cpp files in the `configure` script if R is > 4.4 (the checks are only on devel now, right?). But it seems like this is a more general problem CRAN will have to solve, if they're adding new "official" API functions to replace some of these things but they're only in R-devel, how can you be on CRAN if you depend on them?
What's surprising to me is that, at least by the internal function names `check` is calling, they're looking at the compiled object files, which I would expect not to have these symbols in them because of the `#ifdef`: https://github.com/wch/r-source/blob/032b8240be6c8cf5e8e85ecde6f3f23e46739716/src/library/tools/R/sotools.R#L721-L768 And that function is wrapping `nm`.
In fact, I do see these symbols showing up locally, on new enough R, for example:
```
npr@nealrichardson-3P29 r % nm src/arrow.so | grep Rf_findVarInFrame3
U _Rf_findVarInFrame3
```
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261263566
@assignUser Do you know if we will need to re-generate the Apache-hosted binaries to include https://github.com/apache/arrow/pull/43468 and https://github.com/apache/arrow/pull/43157 and use those in this CRAN release? Or are we ok without those in the binaries since those are both build tools only?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2241279935
> Which I suspect is from https://github.com/apache/arrow/pull/41576/files and can be dealt with by adding `dplyr::` onto those calls again
Sorry! I thought I fixed those but I guess I added more. LMK if you need me to make a PR.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2307635612
Thanks, this is really great! I'll also post it on linked in (though not as a series)
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2307879366
We are missing a checkbox to move the r-univerese tag, I'll move the tag forward in a bit
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2235164136
@assignUser Did you use `Rscript tools/update-checksums.R <libarrow version>` in the past to generate the contents of https://github.com/apache/arrow/commit/12ec842516f8dc9503dc7eb7bf79286ca2468ef3 ?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2303941731
I was taking this release "off" to focus on my other commitments, though would be happy to review it if someone else wanted to write something up?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2368908855
Yeah, if we don't have one already we should. Sorry I didn't look at that
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2241289837
Hey @jonkeane, I think that's the right interpretation.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2258424654
I just got a note about errors from lz4 on [CRAN's devel debian runners](https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/arrow-00install.html).
> With current Debian testing, installation now fails, see the install log. Apparently this is from yesterday's system upgrade of
>
> `liblz4-dev:amd64 (1.9.4-2, 1.9.4-3), liblz4-1:amd64 (1.9.4-2, 1.9.4-3)`
>
> I can confirm that ARROW_WITH_LZ4=OFF ./configure works where ./configure now fails.
We will need to fix this as will in our 17 submission (and get it in within two weeks too).
We are linking against the shared, system lz4 which is fine in this case because CRAN does not distribute these binaries. But one possibility is to force non-shared lz4 and it'll grab source + build.
cc @assignUser @nealrichardson
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2260538591
FYI, I got another email from CRAN preponing the deadline to ~today since CRAN shuts down for two weeks tomorrow 😬
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261789280
Of course CRAN is closed starting tomorrow (and it's already tomorrow CEST), so this is probably not something we can solve until they're back.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2289034257
Need to cherry-pick https://github.com/apache/arrow/pull/43649 into the CRAN release
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2351581302
Agreed, let's call it. The oldrelease is one that I've asked about before on mailing lists and they sometimes are super slow, but I've seen periods where they don't build for any packages for weeks and eventually sort themselves.
I can RTFS, but does anyone know how / if we can update the docs website to show the 17.0.0.1 number?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2240906134
@jonkeane mac builder: https://mac.r-project.org/macbuilder/results/1721447405-da61deb72185bfbc/
win builder should reach you by mail, if that's clean I think only a revdep check is missing. @paleolimbot didn't you have a super quick script that doesn't take a million hours to run?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2241260115
I brought in the changes from `maint-17.0.0-r` (see my [main branch](https://github.com/amoeba/arrow/commits/main/)) and kicked off two [recheck](https://github.com/r-devel/recheck) jobs ([1](https://github.com/amoeba/arrow/actions/runs/10022377061), [2](https://github.com/amoeba/arrow/actions/runs/10022377585)).
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2259413906
Ah thanks @kou! I was just exploring the lz4 that comes with debian:testing you are right: `foreach(_cmake_expected_target IN ITEMS LZ4::lz4_shared LZ4::lz4_static)`
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261994886
Hmmmm, yeah something strange is going on here. It's possible that the `#IFDEF` isn't the right thing for detecting functions (https://stackoverflow.com/questions/6234755/does-ifdef-or-other-preprocessor-directives-work-for-function-declarations-t) and instead we should do something like `#if (R_VERSION >= R_Version(4, 2, 0))` buuuuut I actually still see `_Rf_findvarInFrame3` even if I remove any calls (conditional or otherwise) from `arrow_cpp11.h` (which is also the only place that calls it in our code) 🫠I do see it in cpp11 https://github.com/r-lib/cpp11/blob/1c9dbb65cc9279a404f035f2fca990b338c9f602/inst/include/cpp11/environment.hpp#L37-L38 so maybe that's where it's coming from?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2262027098
Ah yes, I think it is, indeed, coming from cpp11's `environment.hpp`. I just tried removing all of our imports / references to that and only _then_ is `nm -v src/arrow.so | grep Rf_findVarInFrame3` clean.
We still need #43504 but will still have an issue on that automatic checks until cpp11 fixes + releases their fix.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2354476667
I scheduled tweets/toots to go out tomorrow morning.
Re: The website showing version 17.0.0... I think we might want to find a better workflow but for now I created https://github.com/apache/arrow-site/pull/542 to do the update. My steps are described there.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261299681
Looks like tidyquery is still an issue (I'm surprised we didn't catch this the first time we ran through those!)
I'm seeing a bunch of errors like this one. Which I suspect are coming from https://github.com/apache/arrow/blob/7e50097ba4239cf9368b77f438d877d4176141c9/r/R/dplyr-eval.R#L204
```
✖ | 3 1 1 | arrow-dataset
──────────────────────────────────────────────────────────────────────────────────────────────────
Error (test-arrow-dataset.R:3:3): Simple SELECT example query #1 returns expected result on Arrow Dataset
Error in `match.call()`: ... used in a situation where it does not exist
Backtrace:
â–†
1. ├─testthat::expect_equal(...) at test-arrow-dataset.R:3:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─... %>% as.data.frame()
5. ├─base::as.data.frame(.)
6. ├─tidyquery::query("SELECT Species, COUNT(*) AS n FROM iris_ad GROUP BY Species")
7. │ └─tidyquery:::query_(data, sql, TRUE) at tidyquery-9546a7d191009cc56c2c11c5a54c33d3330a42f3/R/query.R:77:3
8. │ └─... %>% verb(ungroup) at tidyquery-9546a7d191009cc56c2c11c5a54c33d3330a42f3/R/query.R:275:7
9. ├─tidyquery:::verb(., ungroup)
10. │ └─base::paste(...) at tidyquery-9546a7d191009cc56c2c11c5a54c33d3330a42f3/R/query.R:450:3
11. ├─tidyquery:::verb(...)
12. │ └─input$data %>% fun(...) at tidyquery-9546a7d191009cc56c2c11c5a54c33d3330a42f3/R/query.R:450:3
13. ├─dplyr (local) fun(., ...)
14. └─arrow:::summarise.arrow_dplyr_query(., ...)
15. ├─arrow:::try_arrow_dplyr(...)
16. │ └─base::evalq(call <- match.call(), parent)
17. │ └─base::evalq(call <- match.call(), parent)
18. └─base::match.call()
```
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2259532400
Thank you (again) @kou !
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2260963654
Whoops, sorry about that @jonkeane. New revdep check runs are now here: [strong](https://github.com/amoeba/arrow/actions/runs/10184097767), [most](https://github.com/amoeba/arrow/actions/runs/10184099379). Those are being run from the latest maint-17.0.0-r. They seem to be stuck at the moment so hopefully they'll start soon.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261423107
So the lz4 one changes our bundled find module so that could affect the precompiled binaries. But only in theory as we are using either pkg-config to find and set flags or have them hardcoded and don't use cmake.
So both only matter when building from source.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2254199459
Ok, I've merged the fix for the altrep thing that was hitting parquetize. @amoeba would you mind triggering the revdep checks again?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2241248683
Thanks for sending those, Jacob.
Here's the winbuilder output: https://win-builder.r-project.org/SrOKYg8yT1lm/
https://win-builder.r-project.org/SrOKYg8yT1lm/00check.log
The only thing in there that looks worrying is
```
* checking R code for possible problems ... [33s] NOTE
mutate.ArrowTabular: no visible global function definition for
'left_join'
mutate.Dataset: no visible global function definition for 'left_join'
mutate.RecordBatchReader: no visible global function definition for
'left_join'
mutate.arrow_dplyr_query: no visible global function definition for
'left_join'
Undefined global functions or variables:
left_join
* checking Rd files ... OK
```
Which I suspect is from https://github.com/apache/arrow/pull/41576/files and can be dealt with by adding `dplyr::` onto those calls again
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2302967060
Aaaand we have been accepted 🎉
Do we already have a draft social media post?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2307561019
Draft social media content is [here](https://docs.google.com/document/d/1_iIWYzUWTgHtWa0BhHQioTpViSF6Jik8i1-0QGerdvg/edit). I still need to generate some code images for the examples and tweak a bit of the language but please have a look to see if I missed any tweet-worthy highlights. I see binaries are almost all up on CRAN which is great.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2260550149
```
------- Check for regressions ------
Changes:
Package: parquetize
Check: examples
Old result: OK
New result: ERROR
Package: parquetize
Check: tests
Old result: OK
New result: ERROR
Package: tidyquery
Check: tests
Error: Found potential problems
Execution halted
Old result: OK
New result: ERROR
```
Weird, I see ^^^ in the logs https://github.com/amoeba/arrow/actions/runs/10172857322/job/28137640795 but when I download the archives I don't see any issues with either of those in the actual logs.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2258462721
We can work around that, sure, but if that's failing, then it sounds like there's something off in our cmake routine in this case, and that should get addressed. For example, I see the message from this line in the logs: https://github.com/apache/arrow/blob/main/cpp/cmake_modules/ThirdpartyToolchain.cmake#L352 But I don't see either of the messages that should follow, about whether lz4 was found or not.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2260628757
I've also tried to replicate the CRAN devel image locally (I'll push a PR up with that for CI after this fire drill). After Kou's change, we get past LZ4. But then it seems to fail with the following. This isn't related directly to the LZ4 change I don't think, and as far as I could tell on github that abseil code hasn't changed in years. This could be a false positive, since I don't have an exact replica of the CRAN runner, but wonder if anyone has any ideas about what this might be.
```
[ 55%] Building CXX object absl/strings/CMakeFiles/str_format_internal.dir/internal/str_format/extension.cc.o
-- stderr output is:
...skipping to end...
230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:45:1: note: in expansion of macro ‘ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_’
45 | ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_(ABSL_INTERNAL_CHAR_SET_CASE, )
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:44:13: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
44 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::c;
| ^~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.h:167:3: note: in expansion of macro ‘ABSL_INTERNAL_CHAR_SET_CASE’
167 | X_VAL(g) X_SEP X_VAL(G) X_SEP X_VAL(a) X_SEP X_VAL(A) X_SEP \
| ^~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:45:1: note: in expansion of macro ‘ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_’
45 | ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_(ABSL_INTERNAL_CHAR_SET_CASE, )
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:44:13: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
44 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::c;
| ^~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.h:167:18: note: in expansion of macro ‘ABSL_INTERNAL_CHAR_SET_CASE’
167 | X_VAL(g) X_SEP X_VAL(G) X_SEP X_VAL(a) X_SEP X_VAL(A) X_SEP \
| ^~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:45:1: note: in expansion of macro ‘ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_’
45 | ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_(ABSL_INTERNAL_CHAR_SET_CASE, )
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:44:13: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
44 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::c;
| ^~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.h:167:33: note: in expansion of macro ‘ABSL_INTERNAL_CHAR_SET_CASE’
167 | X_VAL(g) X_SEP X_VAL(G) X_SEP X_VAL(a) X_SEP X_VAL(A) X_SEP \
| ^~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:45:1: note: in expansion of macro ‘ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_’
45 | ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_(ABSL_INTERNAL_CHAR_SET_CASE, )
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:44:13: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
44 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::c;
| ^~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.h:167:48: note: in expansion of macro ‘ABSL_INTERNAL_CHAR_SET_CASE’
167 | X_VAL(g) X_SEP X_VAL(G) X_SEP X_VAL(a) X_SEP X_VAL(A) X_SEP \
| ^~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:45:1: note: in expansion of macro ‘ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_’
45 | ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_(ABSL_INTERNAL_CHAR_SET_CASE, )
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:44:13: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
44 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::c;
| ^~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.h:169:3: note: in expansion of macro ‘ABSL_INTERNAL_CHAR_SET_CASE’
169 | X_VAL(n) X_SEP X_VAL(p)
| ^~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:45:1: note: in expansion of macro ‘ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_’
45 | ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_(ABSL_INTERNAL_CHAR_SET_CASE, )
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:44:13: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
44 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::c;
| ^~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.h:169:18: note: in expansion of macro ‘ABSL_INTERNAL_CHAR_SET_CASE’
169 | X_VAL(n) X_SEP X_VAL(p)
| ^~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:45:1: note: in expansion of macro ‘ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_’
45 | ABSL_INTERNAL_CONVERSION_CHARS_EXPAND_(ABSL_INTERNAL_CHAR_SET_CASE, )
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:49:11: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
49 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::kStar;
| ^~~~~~~~~~~~~~~~~~~~~~~
| FormatConversionCharInternal
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:51:11: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
51 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::kIntegral;
| ^~~~~~~~~~~~~~~~~~~~~~~
| FormatConversionCharInternal
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:53:11: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
53 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::kFloating;
| ^~~~~~~~~~~~~~~~~~~~~~~
| FormatConversionCharInternal
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:55:11: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
55 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::kNumeric;
| ^~~~~~~~~~~~~~~~~~~~~~~
| FormatConversionCharInternal
/tmp/RtmpabvneB/file7a47e230e44/absl_ep-prefix/src/absl_ep/absl/strings/internal/str_format/extension.cc:57:11: error: ‘FormatConversionCharSet’ does not name a type; did you mean ‘FormatConversionCharInternal’?
57 | constexpr FormatConversionCharSet FormatConversionCharSetInternal::kPointer;
| ^~~~~~~~~~~~~~~~~~~~~~~
| FormatConversionCharInternal
make[5]: *** [absl/strings/CMakeFiles/str_format_internal.dir/build.make:104: absl/strings/CMakeFiles/str_format_internal.dir/internal/str_format/extension.cc.o] Error 1
make[5]: *** Waiting for unfinished jobs....
make[4]: *** [CMakeFiles/Makefile2:2382: absl/strings/CMakeFiles/str_format_internal.dir/all] Error 2
make[3]: *** [Makefile:136: all] Error 2
```
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2366793139
I've also made [an article on linkedin](https://www.linkedin.com/pulse/arrow-17001-out-jonathan-keane-llyac) not sure if that's the right level of linked in posting, but I'll keep an eye on if it gets engagement.
Thanks for the help, everyone! I'm going to close this out.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2351120981
Let's do it! Thanks @amoeba!
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2235165622
Yes :)
Let me know if I can help with anything!
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2241286353
@amoeba am I reading these logs from recheck correctly that with new arrow `parquetize` is failing in this example:
```
> ### Name: csv_to_parquet
> ### Title: Convert a csv or a txt file to parquet format
> ### Aliases: csv_to_parquet
>
> ### ** Examples
>
>
> # Conversion from a local csv file to a single parquet file :
>
> csv_to_parquet(
+ path_to_file = parquetize_example("region_2022.csv"),
+ path_to_parquet = tempfile(fileext=".parquet")
+ )
Reading data...
Writing data...
Error in Table__from_dots(dots, schema, option_use_threads()) :
No Set_elt found for ALTSTRING class [class: vroom_chr, pkg: vroom]
Calls: csv_to_parquet ... as_arrow_table.data.frame -> <Anonymous> -> Table__from_dots
Reading data...
Execution halted
```
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2295282339
Ok, I've cherry-picked the latest fix onto this branch (#43735). I'll resubmit later this evening — in case anyone has any objections + suggestions for other things.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2295460433
I have resubmitted 17.0.0.1
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261351529
@jonkeane pretty sure they only affect the source build but I'll check
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2262862588
We may need to vendor (and possibly patch) cpp11 for this release then.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2261644450
Thanks for all of the help, everyone. I just sent the submission, I'll keep this issue posted if there are other issues.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2260975172
https://github.com/apache/arrow/issues/36969 looks similar to your above output, maybe this is the same cause?
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "nealrichardson (via GitHub)" <gi...@apache.org>.
nealrichardson commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2258571400
Ah my bad, you are right.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "kou (via GitHub)" <gi...@apache.org>.
kou commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2259409582
https://github.com/apache/arrow/pull/43468 will solve the problem. I'll complete it soon.
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "amoeba (via GitHub)" <gi...@apache.org>.
amoeba commented on issue #43317:
URL: https://github.com/apache/arrow/issues/43317#issuecomment-2259542806
Revdepchecks are running at https://github.com/amoeba/arrow/actions. It looks like one already failed but I don't have enough signal to check right now (will tomorrow).
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Re: [I] [R] CRAN packaging checklist for version 17.0.0 [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane closed issue #43317: [R] CRAN packaging checklist for version 17.0.0
URL: https://github.com/apache/arrow/issues/43317
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