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Posted to issues@arrow.apache.org by "thisisnic (via GitHub)" <gi...@apache.org> on 2023/07/21 09:21:47 UTC
[GitHub] [arrow] thisisnic opened a new issue, #36802: [R] CRAN packaging checklist for version 13.0.0
thisisnic opened a new issue, #36802:
URL: https://github.com/apache/arrow/issues/36802
# 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).
## Before the release candidate is cut
- [ ] [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.
- [ ] 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).
- [ ] 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
## Optional: PRs for autobrew and rtools (release candidate)
Make pull requests into the [autobrew](https://github.com/autobrew) and
[rtools-packages](https://github.com/r-windows/rtools-packages) repositories
used by the configure script on MacOS and Windows. These pull requests will
use the release candidate as the source.
- [ ] Pull request to modify
[the apache-arrow autobrew formula]( https://github.com/autobrew/homebrew-core/blob/high-sierra/Formula/apache-arrow.rb)
to update the release version, SHA256 checksum of the release source file (which can be found in the same directory as the release source file), and any changes to dependencies and build steps that have changed in the
[copy of the formula we have of that formula in the Arrow repo](https://github.com/apache/arrow/blob/main/dev/tasks/homebrew-formulae/autobrew/apache-arrow.rb)
- [ ] Pull request to modify
[the apache-arrow-static autobrew formula](https://github.com/autobrew/homebrew-cran/blob/master/Formula/apache-arrow-static.rb)
to update the version, SHA, and any changes to dependencies and build steps that have changed in the
[copy of the formula we have of that formula in the Arrow repo](https://github.com/apache/arrow/blob/main/dev/tasks/homebrew-formulae/autobrew/apache-arrow-static.rb)
- [ ] Pull request to modify the
[autobrew script](https://github.com/autobrew/scripts/blob/master/apache-arrow)
to include any additions made to
[r/tools/autobrew](https://github.com/apache/arrow/blob/main/r/tools/autobrew).
- [ ] Pull request to modify the
[RTools PKGBUILD script](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-arrow/PKGBUILD)
to reflect changes in
[ci/PKGBUILD](https://github.com/apache/arrow/blob/main/ci/scripts/PKGBUILD),
uncommenting the line that says "uncomment to test the rc".
## 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
- [ ] Release vote passed!
## PRs for autobrew and rtools (official release)
Create new autobrew and r-windows PRs such that they use the *release*
instead of the *release candidate*:
- [ ] PR into autobrew/homebrew-core (apache-arrow autobrew formula)
- [ ] PR into autobrew/homebrew-core (apache-arrow-static autobrew formula)
- [ ] PR into autobrew/scripts
- [ ] PR into r-windows/rtools-packages
## 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.
- [ ] 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 the docs with `pkgdown::build_site(examples = FALSE, lazy = TRUE, install = FALSE)` and submit a PR to [the `asf-site` branch of the docs site](https://github.com/apache/arrow-site) with the contents of `r/docs/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!
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1698795204
I've also cherry-picked this into this branch as we were failing on R-devel: #37457
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1645299653
TODO: follow-up on discussions in https://github.com/apache/arrow/pull/36551 to see if we need to do anything difference for this release
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[GitHub] [arrow] thisisnic closed issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic closed issue #36802: [R] CRAN packaging checklist for version 13.0.0
URL: https://github.com/apache/arrow/issues/36802
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[GitHub] [arrow] paleolimbot commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "paleolimbot (via GitHub)" <gi...@apache.org>.
paleolimbot commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1648059717
I ran the revdepchecks using `archery` and got one failure for nanoarrow (will be fixed by and I will cherry pick + submit ASAP). I also ran them more manually and got failures for `dataversionr` and `pins` related to the class of the output of `read_parquet()`.
<details>
## dataversionr
### With CRAN arrow
```
-- R CMD check results --------------------------------- dataversionr 0.9.0 ----
Duration: 2m 20.5s
0 errors v | 0 warnings v | 0 notes v
```
### With local arrow
```
-- R CMD check results --------------------------------- dataversionr 0.9.0 ----
Duration: 2m 28.9s
> checking tests ...
See below...
-- Test failures ------------------------------------------------- testthat ----
> library(testthat)
> library(dataversionr)
>
> test_check("dataversionr")
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'tidyr'
The following object is masked from 'package:testthat':
matches
Some features are not enabled in this build of Arrow. Run `arrow_info()` for more information.
Attaching package: 'arrow'
The following object is masked from 'package:testthat':
matches
The following object is masked from 'package:utils':
timestamp
Attaching package: 'lubridate'
The following object is masked from 'package:arrow':
duration
The following objects are masked from 'package:base':
date, intersect, setdiff, union
Committing diff to dataset...
Verifying diff can be retrieved from dataset...
A parquet file can be read from the target path...
Remote diff is identical to local diff.
Committing diff to dataset...
Verifying diff can be retrieved from dataset...
A parquet file can be read from the target path...
Remote diff is identical to local diff.
Checking that new_df can be diffed...
Diff test passed.
Checking that new_df can be diffed...
Diff test passed.
Checking that new_df can be diffed...
Checking that new_df can be diffed...
Diff test passed.
Checking that new_df can be diffed...
Diff test passed.
destination parameter is a string. Coercing to local FileSystem.
destination parameter is a string. Coercing to local FileSystem.
[ FAIL 6 | WARN 19 | SKIP 0 | PASS 43 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-backup_ops.R:27:13'): local get backup ───────────────────────
{
...
} (`actual`) not equal to `old_df` (`expected`).
`class(actual)`: "tbl_df" "tbl" "data.frame"
`class(expected)`: "data.frame"
── Failure ('test-backup_ops.R:161:13'): local read_dv_backup ──────────────────
{
...
} (`actual`) not equal to `old_df` (`expected`).
`class(actual)`: "tbl_df" "tbl" "data.frame"
`class(expected)`: "data.frame"
── Failure ('test-diff_ops.R:67:3'): local retrieve diff works ─────────────────
... %>% select(-diff_timestamp) (`actual`) not equal to `diff_df` (`expected`).
`class(actual)`: "tbl_df" "tbl" "data.frame"
`class(expected)`: "data.frame"
── Failure ('test-dv_ops.R:107:13'): local read_dv ─────────────────────────────
{
...
} (`actual`) not equal to `newer_df` (`expected`).
`class(actual)`: "tbl_df" "tbl" "data.frame"
`class(expected)`: "data.frame"
── Failure ('test-dv_ops.R:124:13'): local read_dv via backup ──────────────────
{
...
} (`actual`) not equal to new_df %>% select(sort(colnames(.))) (`expected`).
`class(actual)`: "tbl_df" "tbl" "data.frame"
`class(expected)`: "data.frame"
── Failure ('test-latest_ops.R:29:13'): local get latest ───────────────────────
{
...
} (`actual`) not equal to `new_df` (`expected`).
`class(actual)`: "tbl_df" "tbl" "data.frame"
`class(expected)`: "data.frame"
[ FAIL 6 | WARN 19 | SKIP 0 | PASS 43 ]
Error: Test failures
Execution halted
1 error x | 0 warnings v | 0 notes v
```
## gbifdb
### With CRAN arrow
```
-- R CMD check results --------------------------------------- gbifdb 0.1.2 ----
Duration: 15.3s
> checking tests ...
See below...
-- Test failures ------------------------------------------------- testthat ----
> library(testthat)
> library(gbifdb)
>
> test_check("gbifdb")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_gbifdb.R:53:3', 'test_gbifdb.R:66:3'
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ]
>
> proc.time()
user system elapsed
0.711 0.067 0.808
Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
Error: bad value
Execution halted
1 error x | 0 warnings v | 0 notes v
```
### With local arrow
```
-- R CMD check results --------------------------------------- gbifdb 0.1.2 ----
Duration: 15.9s
0 errors v | 0 warnings v | 0 notes v
```
## nanoarrow
### With CRAN arrow
```
-- R CMD check results ---------------------------------- nanoarrow 0.2.0.1 ----
Duration: 18.7s
0 errors v | 0 warnings v | 0 notes v
```
### With local arrow
```
-- R CMD check results ---------------------------------- nanoarrow 0.2.0.1 ----
Duration: 19.4s
> checking Rd cross-references ... WARNING
Missing link or links in documentation object 'as_nanoarrow_array.Rd':
‘[arrow:array]{arrow::Array}’ ‘[arrow:array]{arrow::StructArray}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
0 errors v | 1 warning x | 0 notes v
```
## pins
### With CRAN arrow
```
-- R CMD check results ----------------------------------------- pins 1.2.0 ----
Duration: 42.4s
0 errors v | 0 warnings v | 0 notes v
```
### With local arrow
```
-- R CMD check results ----------------------------------------- pins 1.2.0 ----
Duration: 43.1s
> checking tests ...
See below...
-- Test failures ------------------------------------------------- testthat ----
> library(testthat)
> library(pins)
>
> test_check("pins")
Guessing `type = 'rds'`
> <http://127.0.0.1:49432/data.txt> is not cacheable
> <http://127.0.0.1:49432/x.rds> is not cacheable
> <http://127.0.0.1:49436/x/20230724T142915Z-c3943/data.txt> is not cacheable
> <http://127.0.0.1:49436/x/20230724T142915Z-c3943/x.json> is not cacheable
> <http://127.0.0.1:49440/y/20230724T142915Z-cba09/data.txt> is not cacheable
> <http://127.0.0.1:49440/y/20230724T142915Z-5026d/data.txt> is not cacheable
[ FAIL 3 | WARN 0 | SKIP 66 | PASS 183 ]
══ Skipped tests (66) ══════════════════════════════════════════════════════════
• On CRAN (52): 'test-board_connect_bundle.R:36:3',
'test-board_connect_bundle.R:41:3', 'test-board_connect_server.R:22:3',
'test-board_connect_server.R:31:3', 'test-board_connect_server.R:51:3',
'test-board_connect_server.R:60:3', ???, ???, 'test-board_folder.R:9:3',
'test-board_folder.R:34:3', 'test-board_folder.R:42:3',
'test-board_folder.R:88:3', 'test-board_url.R:54:3',
'test-board_url.R:154:3', 'test-board_url.R:168:3', 'test-board_url.R:180:3',
'test-board_url.R:199:3', 'test-board_url.R:218:3', 'test-board_url.R:237:3',
'test-legacy_board.R:2:3', 'test-legacy_datatxt.R:4:3',
'test-legacy_datatxt.R:16:3', 'test-legacy_datatxt.R:25:3',
'test-legacy_datatxt.R:35:3', 'test-legacy_local.R:43:3',
'test-legacy_packages.R:23:3', 'test-legacy_registry.R:30:3',
'test-meta.R:13:3', 'test-meta.R:20:3', 'test-meta.R:24:3',
'test-pin-delete.R:11:3', 'test-pin-meta.R:2:3',
'test-pin-read-write.R:35:3', 'test-pin-read-write.R:41:3',
'test-pin-read-write.R:58:3', 'test-pin-read-write.R:80:3',
'test-pin-read-write.R:88:3', 'test-pin-upload-download.R:17:3',
'test-pin-upload-download.R:46:3', 'test-pin-upload-download.R:61:3',
'test-pin.R:76:3', 'test-pin.R:108:3', 'test-pin_info.R:5:3',
'test-pin_info.R:23:3', 'test-pin_info.R:33:3', 'test-pin_search.R:27:3',
'test-pin_versions.R:8:3', 'test-pin_versions.R:18:3',
'test-pin_versions.R:26:3', 'test-pin_versions.R:41:3',
'test-pin_versions.R:67:3', 'test-pin_versions.R:91:3'
• board_azure() tests require PINS_AZURE_KEY (3):
'test-board_azure_adls2.R:1:1', 'test-board_azure_blob.R:1:1',
'test-board_azure_file.R:1:1'
• board_connect() tests requires `creds.rds` (4): 'test-board_connect.R:2:1',
'test-board_connect_url.R:4:3', 'test-board_connect_url.R:22:3',
'test-board_connect_url.R:33:3'
• board_gcs() tests require PINS_GCS_PASSWORD (1): 'test-board_gcs.R:1:1'
• board_ms365() tests require PINS_MS365_TEST_DRIVE (1):
'test-board_ms365.R:1:1'
• board_s3() tests require PINS_AWS_ACCESS_KEY, PINS_AWS_SECRET_ACCESS_KEY (1):
'test-board_s3.R:1:1'
• legacy_azure() tests require TEST_AZURE_CONTAINER, TEST_AZURE_ACCOUNT,
TEST_AZURE_KEY (1): 'test-legacy_azure.R:16:1'
• legacy_gcloud() tests require TEST_GOOGLE_BUCKET (1):
'test-legacy_gcloud.R:12:1'
• legacy_github() tests require TEST_GITHUB_REPO, TEST_GITHUB_BRANCH (1):
'test-legacy_github.R:1:1'
• legacy_s3() tests require TEST_AWS_BUCKET, TEST_AWS_KEY, TEST_AWS_SECRET,
TEST_AWS_REGION (1): 'test-legacy_s3.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-pin-read-write.R:12:3'): can round trip all types ────────────
pin_read(board, "df-2") (`actual`) not equal to `df` (`expected`).
`class(actual)`: "tbl_df" "tbl" "data.frame"
`class(expected)`: "data.frame"
── Failure ('test-pin-read-write.R:15:3'): can round trip all types ────────────
pin_read(board, "df-2") (`actual`) not equal to `df` (`expected`).
`class(actual)`: "tbl_df" "tbl" "data.frame"
`class(expected)`: "data.frame"
── Failure ('test-pin-read-write.R:18:3'): can round trip all types ────────────
pin_read(board, "df-3") (`actual`) not equal to `df` (`expected`).
`class(actual)`: "tbl_df" "tbl" "data.frame"
`class(expected)`: "data.frame"
[ FAIL 3 | WARN 0 | SKIP 66 | PASS 183 ]
Error: Test failures
Execution halted
1 error x | 0 warnings v | 0 notes v
```
</details>
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1693149953
And this one so we don't fail on CRAN: #37387
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1651189315
We also want to cherry pick #36884
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1664020652
I've opened https://github.com/rstudio/pins-r/issues/761 on the pins repo
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1663867047
We should flag #34775 as a breaking change
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1689524661
We need to also grab the missing NEWS items documentation: #37326
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1708443689
Done!
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1664036921
We might also need a fix for the gbifdb failure, which is the same as the error reported in #36907
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[GitHub] [arrow] thisisnic commented on issue #36802: [R] CRAN packaging checklist for version 13.0.0
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on issue #36802:
URL: https://github.com/apache/arrow/issues/36802#issuecomment-1645328416
We'll need to cherry-pick the NEWS update into here: #36806
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