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Posted to github@arrow.apache.org by "fernandomayer (via GitHub)" <gi...@apache.org> on 2023/09/30 00:19:22 UTC
[GitHub] [arrow] fernandomayer opened a new pull request, #37961: MINOR: [R] Failing installation script
fernandomayer opened a new pull request, #37961:
URL: https://github.com/apache/arrow/pull/37961
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### Rationale for this change
The latest version of `r/R/install-arrow.R` was not working properly, since it was relying on the `on_rosetta()` function, which is not defined elsewhere. I just fixed the identification of rosetta in the script.
With the current code, the following gives an error
````r
> source("https://raw.githubusercontent.com/apache/arrow/master/r/R/install-arrow.R")
> install_arrow()
Error in on_rosetta() : could not find function "on_rosetta"
````
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Why are you proposing this change? If this is already explained clearly in the issue then this section is not needed.
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### What changes are included in this PR?
It only removed the `on_rosetta()` function, which was not defined elsewhere, and reverted back to the `rosetta` object to identify if rosetta is present or not on a user's system.
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### Are these changes tested?
Yes. It was tested with the current code and the proposed PR. The proposed PR works as expected.
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### Are there any user-facing changes?
No.
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1760315088
I hope you don't mind that I pushed those changes requested to this branch so that we can get this in before the upcoming release.
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on code in PR #37961:
URL: https://github.com/apache/arrow/pull/37961#discussion_r1353475618
##########
r/R/install-arrow.R:
##########
@@ -267,3 +268,8 @@ wslify_path <- function(path) {
end_path <- strsplit(path, drive_expr)[[1]][-1]
file.path(wslified_drive, end_path)
}
+
+on_rosetta <- function() {
+ identical(tolower(Sys.info()[["sysname"]]), "darwin") &&
+ identical(system("sysctl -n sysctl.proc_translated", intern = TRUE), "1")
Review Comment:
We do actually need / want to `suppressWarnings()` and `ignore.stderr = TRUE` here as well. On x86 machines this call will throw a warning + print to the console complaining that it can't find the `proc_translated` argument there.
```suggestion
identical(suppressWarnings(system("sysctl -n sysctl.proc_translated", intern = TRUE, ignore.stderr = TRUE), "1")
```
##########
r/R/install-arrow.R:
##########
@@ -267,3 +268,8 @@ wslify_path <- function(path) {
end_path <- strsplit(path, drive_expr)[[1]][-1]
file.path(wslified_drive, end_path)
}
+
+on_rosetta <- function() {
+ identical(tolower(Sys.info()[["sysname"]]), "darwin") &&
Review Comment:
It would be nice to also keep this comment (though edited a bit for clarity):
```suggestion
# make sure to suppress warnings and ignore the stderr so that this is silent on x86
identical(tolower(Sys.info()[["sysname"]]), "darwin") &&
```
##########
r/R/install-arrow.R:
##########
@@ -79,7 +80,8 @@ install_arrow <- function(nightly = FALSE,
# On the M1, we can't use the usual autobrew, which pulls Intel dependencies
apple_m1 <- grepl("arm-apple|aarch64.*darwin", R.Version()$platform)
# On Rosetta, we have to build without JEMALLOC, so we also can't autobrew
- if (on_rosetta()) {
+ rosetta <- identical(sysname, "darwin") && identical(system("sysctl -n sysctl.proc_translated", intern = TRUE), "1")
+ if (rosetta) {
Review Comment:
> So my proposal would be to just change the on_rosetta() function from r/R/arrow-package.R to r/R/install-arrow.R, as this would not affect the former, but it would make the latter self-contained again.
This is a good catch, I'm working on a review, but overall I'm pro moving this function to `install-arrow.R` so that it remains self-contained. Thank you for catching it!
> In this way, the on_rosetta() function is not found, as the script is not self-contained anymore.
We don't have to do this here, but we should at least make an issue that we should write a test that tests that the script remains self-contained. It would have caught this bug, for example!
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1742944463
Thanks for making this PR! One small change, otherwise looks good to go :)
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1760315177
@github-actions crossbow submit test-r-install-local
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1761580859
Thanks again @fernandomayer for the issue + PR
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1760316601
Once the crossbow build is done I'm going to merge this, unless there are objections
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "conbench-apache-arrow[bot] (via GitHub)" <gi...@apache.org>.
conbench-apache-arrow[bot] commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1765523095
After merging your PR, Conbench analyzed the 6 benchmarking runs that have been run so far on merge-commit 7b7bbdc49250a1a91df079995a38208d55d45d42.
There were no benchmark performance regressions. 🎉
The [full Conbench report](https://github.com/apache/arrow/runs/17762999835) has more details. It also includes information about 6 possible false positives for unstable benchmarks that are known to sometimes produce them.
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "fernandomayer (via GitHub)" <gi...@apache.org>.
fernandomayer commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1761576746
Thanks @jonkeane and @thisisnic
I can confirm that now the command
```r
source("https://raw.githubusercontent.com/apache/arrow/main/r/R/install-arrow.R")
install_arrow()
```
works as expected again, as stated in the documentation https://arrow.apache.org/docs/r/articles/install.html?q=install_arrow#using-install_arrow
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1760318335
Revision: dfec06a3dbc7c42ad96dece52ff35fe72b82617c
Submitted crossbow builds: [ursacomputing/crossbow @ actions-efacb091fb](https://github.com/ursacomputing/crossbow/branches/all?query=actions-efacb091fb)
|Task|Status|
|----|------|
|test-r-install-local|[](https://github.com/ursacomputing/crossbow/actions/runs/6500562289/job/17656169537)|
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on code in PR #37961:
URL: https://github.com/apache/arrow/pull/37961#discussion_r1342634870
##########
r/R/install-arrow.R:
##########
@@ -61,6 +61,7 @@ install_arrow <- function(nightly = FALSE,
verbose = Sys.getenv("ARROW_R_DEV", FALSE),
repos = getOption("repos"),
...) {
+ sysname <- tolower(Sys.info()[["sysname"]])
Review Comment:
```suggestion
```
##########
r/R/install-arrow.R:
##########
@@ -79,7 +80,8 @@ install_arrow <- function(nightly = FALSE,
# On the M1, we can't use the usual autobrew, which pulls Intel dependencies
apple_m1 <- grepl("arm-apple|aarch64.*darwin", R.Version()$platform)
# On Rosetta, we have to build without JEMALLOC, so we also can't autobrew
- if (on_rosetta()) {
+ rosetta <- identical(sysname, "darwin") && identical(system("sysctl -n sysctl.proc_translated", intern = TRUE), "1")
+ if (rosetta) {
Review Comment:
```suggestion
rosetta <- on_rosetta()
if (rosetta) {
```
Another PR implemented a function `on_rosetta()` that already does these checks, so we can simplify this bit here, and remove the creation of the `sysname` variable above.
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on code in PR #37961:
URL: https://github.com/apache/arrow/pull/37961#discussion_r1347650593
##########
r/R/install-arrow.R:
##########
@@ -79,7 +80,8 @@ install_arrow <- function(nightly = FALSE,
# On the M1, we can't use the usual autobrew, which pulls Intel dependencies
apple_m1 <- grepl("arm-apple|aarch64.*darwin", R.Version()$platform)
# On Rosetta, we have to build without JEMALLOC, so we also can't autobrew
- if (on_rosetta()) {
+ rosetta <- identical(sysname, "darwin") && identical(system("sysctl -n sysctl.proc_translated", intern = TRUE), "1")
+ if (rosetta) {
Review Comment:
I don't see the standalone use being suggested, maybe we need to clarify the docs? As I understand it `install_arrow` is for use when you have the arrow package installed but want to do one of the following:
```
You have arrow installed and want to upgrade to a different version
You want to try to reinstall and fix issues with Linux C++ binaries
You want to install a development build
```
@thisisnic please correct me if my assessment on that is wrong?
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1756286287
@jonkeane You most recently worked on the code that this PR touches and I'm not sure where is best for this function - I don't suppose you'd mind giving this a quick look over?
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1760322701
I've also created https://github.com/apache/arrow/issues/38251 to track adding a test for this self-containedness
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "fernandomayer (via GitHub)" <gi...@apache.org>.
fernandomayer commented on code in PR #37961:
URL: https://github.com/apache/arrow/pull/37961#discussion_r1344457832
##########
r/R/install-arrow.R:
##########
@@ -79,7 +80,8 @@ install_arrow <- function(nightly = FALSE,
# On the M1, we can't use the usual autobrew, which pulls Intel dependencies
apple_m1 <- grepl("arm-apple|aarch64.*darwin", R.Version()$platform)
# On Rosetta, we have to build without JEMALLOC, so we also can't autobrew
- if (on_rosetta()) {
+ rosetta <- identical(sysname, "darwin") && identical(system("sysctl -n sysctl.proc_translated", intern = TRUE), "1")
+ if (rosetta) {
Review Comment:
Hi @thisisnic
I believe that for the package this is fine. I saw that the `on_rosetta()` function was defined in `r/R/arrow-package.R` and that should work.
However, I'm thinking of the case where the user just uses the `r/R/install-arrow.R` as a standalone script, as suggested [here](https://arrow.apache.org/docs/r/articles/install.html#using-install_arrow) (as it's the way I use, for example). In this way, the `on_rosetta()` function is not found, as the script is not self-contained anymore.
So my proposal would be to just change the `in_rosetta()` function from `r/R/arrow-package.R` to `r/R/install-arrow.R`, as this would not affect the former, but it would make the latter self-contained again.
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1756145353
@thisisnic should we merge this before the release?
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1756288146
> @thisisnic should we merge this before the release?
Yes, but it'll need a final change before merging
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic commented on code in PR #37961:
URL: https://github.com/apache/arrow/pull/37961#discussion_r1350198070
##########
r/R/install-arrow.R:
##########
@@ -79,7 +80,8 @@ install_arrow <- function(nightly = FALSE,
# On the M1, we can't use the usual autobrew, which pulls Intel dependencies
apple_m1 <- grepl("arm-apple|aarch64.*darwin", R.Version()$platform)
# On Rosetta, we have to build without JEMALLOC, so we also can't autobrew
- if (on_rosetta()) {
+ rosetta <- identical(sysname, "darwin") && identical(system("sysctl -n sysctl.proc_translated", intern = TRUE), "1")
+ if (rosetta) {
Review Comment:
@assignUser It's here: https://arrow.apache.org/docs/r/articles/install.html?q=install_arrow#using-install_arrow
> Although this function is part of the arrow package, it is also available as a standalone script, so you can access it without first installing the package:
In the case of "You want to install a development build", folks may not already have arrow installed.
On a different note, there have been other PRs in this area of the codebase merged recently, so this PR may need a rebase to see how the changes affect it, and what needs doing.
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "fernandomayer (via GitHub)" <gi...@apache.org>.
fernandomayer commented on code in PR #37961:
URL: https://github.com/apache/arrow/pull/37961#discussion_r1344457832
##########
r/R/install-arrow.R:
##########
@@ -79,7 +80,8 @@ install_arrow <- function(nightly = FALSE,
# On the M1, we can't use the usual autobrew, which pulls Intel dependencies
apple_m1 <- grepl("arm-apple|aarch64.*darwin", R.Version()$platform)
# On Rosetta, we have to build without JEMALLOC, so we also can't autobrew
- if (on_rosetta()) {
+ rosetta <- identical(sysname, "darwin") && identical(system("sysctl -n sysctl.proc_translated", intern = TRUE), "1")
+ if (rosetta) {
Review Comment:
Hi @thisisnic
I believe that for the package this is fine. I saw that the `on_rosetta()` function was defined in `r/R/arrow-package.R` and that should work.
However, I'm thinking of the case where the user just uses the `r/R/install-arrow.R` as a standalone script, as suggested [here](https://arrow.apache.org/docs/r/articles/install.html#using-install_arrow) (as it's the way I use, for example). In this way, the `on_rosetta()` function is not found, as the script is not self-contained anymore.
So my proposal would be to just change the `on_rosetta()` function from `r/R/arrow-package.R` to `r/R/install-arrow.R`, as this would not affect the former, but it would make the latter self-contained again.
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "assignUser (via GitHub)" <gi...@apache.org>.
assignUser commented on PR #37961:
URL: https://github.com/apache/arrow/pull/37961#issuecomment-1756646162
It looks like this would also fix a nightly fail/cran warning: https://github.com/ursacomputing/crossbow/actions/runs/6463099167/job/17545762151#step:6:3794
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "thisisnic (via GitHub)" <gi...@apache.org>.
thisisnic merged PR #37961:
URL: https://github.com/apache/arrow/pull/37961
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Re: [PR] GH-37907: [R] Setting rosetta variable is missing [arrow]
Posted by "jonkeane (via GitHub)" <gi...@apache.org>.
jonkeane commented on code in PR #37961:
URL: https://github.com/apache/arrow/pull/37961#discussion_r1357460372
##########
r/R/install-arrow.R:
##########
@@ -267,3 +268,9 @@ wslify_path <- function(path) {
end_path <- strsplit(path, drive_expr)[[1]][-1]
file.path(wslified_drive, end_path)
}
+
+on_rosetta <- function() {
+ # make sure to suppress warnings and ignore the stderr so that this is silent where proc_translated doesn't exist
+ identical(tolower(Sys.info()[["sysname"]]), "darwin") &&
+ identical(suppressWarnings(system("sysctl -n sysctl.proc_translated", intern = TRUE, ignore.stderr = TRUE)), "1")
+}
Review Comment:
```suggestion
}
```
To appease the linter
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