Ark: R fails to start up due to dyld symbol not found

[DavisVaughan]

[R] /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/ark/ark --connection_file /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-tDIb2d/connection.json --log /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-tDIb2d/kernel.log --startup-file /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/scripts/startup.R --session-mode console -- --interactive --no-restore-data
[R] dyld: Symbol not found: __ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
[R]   Referenced from: /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/ark/ark (which was built for Mac OS X 14.0)
[R]   Expected in: /usr/lib/libc++.1.dylib

---

I have something similar happening here as well, though it is exit code 134. Not sure if this is related to current issue or completely different. I'm also working on an older Mac, not sure if that affects the install.

Here's some relevant output:

Console

Popups

Output -> Console: R 4.2.2

2024-07-02 13:08:34.460 [info] [Positron] Connecting to R 4.2.2 kernel (pid 23480)
2024-07-02 13:08:34.460 [info] [Positron] Streaming log file: /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-ZGjq8R/kernel.log
2024-07-02 13:08:34.460 [info] [Positron] Connecting to kernel sockets defined in /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-ZGjq8R/connection.json...
2024-07-02 13:08:34.460 [info] [Positron] Control socket created (count = 1)
2024-07-02 13:08:34.460 [info] [Positron] Shell socket created (count = 2)
2024-07-02 13:08:34.460 [info] [Positron] Stdin socket created (count = 3)
2024-07-02 13:08:34.460 [info] [Positron] I/O socket created (count = 4)
2024-07-02 13:08:34.460 [info] [Positron] Heartbeat socket created (count = 5)
2024-07-02 13:08:34.460 [info] [Positron] Control socket connecting to tcp://127.0.0.1:53155...
2024-07-02 13:08:34.460 [info] [Positron] Shell socket connecting to tcp://127.0.0.1:52511...
2024-07-02 13:08:34.460 [info] [Positron] Stdin socket connecting to tcp://127.0.0.1:54650...
2024-07-02 13:08:34.460 [info] [Positron] I/O socket connecting to tcp://127.0.0.1:53654...
2024-07-02 13:08:34.460 [info] [Positron] Heartbeat socket connecting to tcp://127.0.0.1:49175...
2024-07-02 13:08:34.460 [info] [Positron] Error setting console width: Cannot invoke 'setConsoleWidth'; no UI comm is open. (undefined)
2024-07-02 13:08:34.460 [info] [Positron] R 4.2.2 failed to start; exit code: 134
2024-07-02 13:08:34.460 [info] [Positron] R kernel status changed: starting => exited
2024-07-02 13:08:34.460 [info] [R] *** Log started at Tue Jul  2 13:08:31 CDT 2024
2024-07-02 13:08:34.460 [info] [R] *** Command line:
2024-07-02 13:08:34.460 [info] [R] /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/ark/ark --connection_file /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-ZGjq8R/connection.json --log /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-ZGjq8R/kernel.log --startup-file /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/scripts/startup.R --session-mode console -- --interactive --no-restore-data
2024-07-02 13:08:34.460 [info] [R] dyld: Symbol not found: __ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
2024-07-02 13:08:34.460 [info] [R]   Referenced from: /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/ark/ark (which was built for Mac OS X 14.0)
2024-07-02 13:08:34.460 [info] [R]   Expected in: /usr/lib/libc++.1.dylib
2024-07-02 13:08:34.460 [info] [R] 
2024-07-02 13:08:34.460 [info] [R] *** Log ended at Tue Jul  2 13:08:31 CDT 2024
2024-07-02 13:08:34.460 [info] [R] Process exit code 134
[Positron] Connecting to R 4.2.2 kernel (pid 23540)
[Positron] Streaming log file: /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-tDIb2d/kernel.log
[Positron] Connecting to kernel sockets defined in /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-tDIb2d/connection.json...
[Positron] Control socket created (count = 6)
[Positron] Shell socket created (count = 7)
[Positron] Stdin socket created (count = 8)
[Positron] I/O socket created (count = 9)
[Positron] Heartbeat socket created (count = 10)
[Positron] Control socket connecting to tcp://127.0.0.1:63446...
[Positron] Shell socket connecting to tcp://127.0.0.1:56368...
[Positron] Stdin socket connecting to tcp://127.0.0.1:54458...
[Positron] I/O socket connecting to tcp://127.0.0.1:60159...
[Positron] Heartbeat socket connecting to tcp://127.0.0.1:65359...
[Positron] R 4.2.2 failed to start; exit code: 134
[R] /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/ark/ark --connection_file /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-tDIb2d/connection.json --log /var/folders/q8/1pkzzk4n1jj1zcy_57k660100000gn/T/kernel-tDIb2d/kernel.log --startup-file /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/scripts/startup.R --session-mode console -- --interactive --no-restore-data
[R] dyld: Symbol not found: __ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
[R]   Referenced from: /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/ark/ark (which was built for Mac OS X 14.0)
[R]   Expected in: /usr/lib/libc++.1.dylib
[R] 
[R] *** Log ended at Tue Jul  2 13:12:46 CDT 2024
[R] Process exit code 134
[R] 
[Positron] R kernel status changed: starting => exited

Output -> Positron R Extension

2024-07-02 13:08:29.650 [info] Log level: Debug
2024-07-02 13:08:29.650 [info] Refreshing testthat status
2024-07-02 13:08:29.650 [info] Not working in an R package
2024-07-02 13:08:29.650 [info] Context key 'testthatIsConfigured' is 'false'
2024-07-02 13:08:29.650 [info] Context key 'testthatHasTests' is 'false'
2024-07-02 13:08:29.838 [info] Resolved R binary at /Library/Frameworks/R.framework/Versions/4.2/Resources/bin/R
2024-07-02 13:08:30.084 [info] Candidate R binary at /Library/Frameworks/R.framework/Versions/4.2/Resources/bin/R
2024-07-02 13:08:30.084 [info] R installation discovered: {
  "valid": true,
  "supported": true,
  "binpath": "/Library/Frameworks/R.framework/Versions/4.2/Resources/bin/R",
  "homepath": "/Library/Frameworks/R.framework/Resources",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.2.2",
    "major": 4,
    "minor": 2,
    "patch": 2,
    "prerelease": [],
    "build": [],
    "version": "4.2.2"
  },
  "version": "4.2.2",
  "arch": "x86_64",
  "current": true,
  "orthogonal": false
}
2024-07-02 13:08:30.085 [info] Resolved R binary at /Library/Frameworks/R.framework/Versions/4.2/Resources/bin/R
2024-07-02 13:08:30.449 [info] Candidate R binary at /Library/Frameworks/R.framework/Versions/4.2/Resources/bin/R
2024-07-02 13:08:30.449 [info] R installation discovered: {
  "valid": true,
  "supported": true,
  "binpath": "/Library/Frameworks/R.framework/Versions/4.2/Resources/bin/R",
  "homepath": "/Library/Frameworks/R.framework/Resources",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.2.2",
    "major": 4,
    "minor": 2,
    "patch": 2,
    "prerelease": [],
    "build": [],
    "version": "4.2.2"
  },
  "version": "4.2.2",
  "arch": "x86_64",
  "current": true,
  "orthogonal": false
}
2024-07-02 13:08:30.449 [info] Candidate R binary at /Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R
2024-07-02 13:08:30.449 [info] R installation discovered: {
  "valid": true,
  "supported": true,
  "binpath": "/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R",
  "homepath": "/Library/Frameworks/R.framework/Resources",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.2.2",
    "major": 4,
    "minor": 2,
    "patch": 2,
    "prerelease": [],
    "build": [],
    "version": "4.2.2"
  },
  "version": "4.2.2",
  "arch": "x86_64",
  "current": false,
  "orthogonal": false
}
2024-07-02 13:08:30.449 [info] Candidate R binary at /Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R
2024-07-02 13:08:30.449 [info] R installation discovered: {
  "valid": true,
  "supported": true,
  "binpath": "/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R",
  "homepath": "/Library/Frameworks/R.framework/Resources",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.2.2",
    "major": 4,
    "minor": 2,
    "patch": 2,
    "prerelease": [],
    "build": [],
    "version": "4.2.2"
  },
  "version": "4.2.2",
  "arch": "x86_64",
  "current": false,
  "orthogonal": false
}
2024-07-02 13:08:30.449 [info] Candidate R binary at /Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R
2024-07-02 13:08:30.449 [info] R installation discovered: {
  "valid": true,
  "supported": true,
  "binpath": "/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R",
  "homepath": "/Library/Frameworks/R.framework/Resources",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.2.2",
    "major": 4,
    "minor": 2,
    "patch": 2,
    "prerelease": [],
    "build": [],
    "version": "4.2.2"
  },
  "version": "4.2.2",
  "arch": "x86_64",
  "current": false,
  "orthogonal": false
}
2024-07-02 13:08:30.449 [info] Filtering out /Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R: not current and also not orthogonal.
2024-07-02 13:08:30.449 [info] Filtering out /Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R: not current and also not orthogonal.
2024-07-02 13:08:30.449 [info] Filtering out /Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R: not current and also not orthogonal.

Originally posted by @zajichek in #3788 (comment)

[DavisVaughan]

@zajichek a 2012 mac??? Wow!

[DavisVaughan]

Notes: This is an Intel mac, so "arch": "x86_64" applies. We should retest that ark starts up fine on an Intel mac (I have one)

Possibly related to #3732 where we think we need to set that DYLD_FALLBACK_LIBRARY_PATH env var after all?

[zajichek]

@zajichek a 2012 mac??? Wow!

I've been secretly wishing it would just explode or something for the past few years so I'd be forced to get a new one, but it keeps hanging in there

[lionel-]

Inspecting the ark's binary with otool -l, it looks like we currently require Sonoma (macOS 14).

Load command 11
      cmd LC_BUILD_VERSION
    minos 14.0
      sdk 14.4

Could this be fixed by setting a minimum version target for macOS before building with cargo? E.g. targetting Catalina (macOS 10.15):

# Target Catalina
export MACOSX_DEPLOYMENT_TARGET=10.15

However we do depend on homebrew deps for zeromq: https://github.com/posit-dev/ark/blob/fed7fa4cab33160582833c6f0ea713c145aff7c1/.github/workflows/release.yml#L90. I believe those are statically linked (along with libzmq) to our executable. But homebrew only supports up to 3 years of macOS versions (Monterey currently, i.e. version 12): https://docs.brew.sh/Installation#macos-requirements. This corresponds to official Apple support for old macOS releases: https://endoflife.date/macos

So I think either we build libsodium ourselves (should not be hard, see https://github.com/jedisct1/libsodium-sys-stable and https://github.com/jean-airoldie/zeromq-src-rs/blob/master/testcrate/Cargo.toml for an example usage), or we align our support period to homebrew's.

We probably should do the former (build libsodium ourselves to control the target platform) because Positron supports up to Catalina for x86_64:

Load command 11
      cmd LC_BUILD_VERSION
    minos 10.15
      sdk 14.0

Aligning our minimum version to that of Positron should hopefully dodge any issues of mismatched minimum version of macOS between Positron and Ark.

[DavisVaughan]

@lionel- is there a good chance that we hit other dependencies that aren't supported that far back?

[lionel-]

As long as we're building all our deps ourselves we should be good I think?

[juliasilge]

Is this related to #3921? Or different?

[lionel-]

@juliasilge This is different.