[BUG] Reproducible build fails on v1.2.6

[TheRealGramdalf]

💻 Platform

• Desktop (Linux - Arch/Hyprland/Niri/Other)
  • Part of [FEAT] Nix/NixOS support: meta/tracking issue #996
• Desktop (macOS)
• Desktop (Windows)
• Mobile (Android)
• Mobile (iOS)

🧭 Affected Area

• Sync / data consistency
• UI / interaction
• Projects / areas / sections
• Search / filter
• Settings / preferences
• Notifications / reminders
• Recurrence / calendar
• Attachments
• Audio / transcription
• Other
  • Build

ℹ️ Environment

• App Version: v1.2.7
• Install Channel: mindwtr-flake
• OS Version: N/A
• Device: N/A

Install channel examples (Click to expand)

• Desktop Linux: Flathub, APT, AUR, distro package, release file (.deb, .rpm, AppImage), source/dev build
• Desktop macOS: App Store, Homebrew, release file (.dmg), source/dev build
• Desktop Windows: Microsoft Store, winget, release file (.exe / .msi), source/dev build
• Android: Play Store, F-Droid, release file / sideloaded APK, source/dev build
• iOS: App Store, TestFlight, source/dev build

🚨 Impact

• Blocks core workflow
• Data loss or data mismatch
• Crash / freeze
• Visual issue only

📝 Description

After updating from v1.2.5 to v1.2.6, building the webapp fails with connection refused

🔄 Steps to Reproduce (REQUIRED)

Note: Requires the nix build system

1. Clone https://github.com/TheRealGramdalf/mindwtr-flake/tree/update-v1.2.6
2. Run nix build .#mindwtr-web

🎯 Expected Behavior

Build succeeds as usual

🧪 Regression?

• This worked in a previous version
• Last known working version (if known): v1.2.5

📸 Screenshots / Logs

If applicable, add screenshots or paste relevant logs.

mindwtr-flake on  update-v1.2.6 via ❄️  impure (mindwtr-bun2nix-env)
❯ nix log /nix/store/pn144f22ka8kryd76jr5vk5gs8dq02n4-mindwtr-web-1.2.6.drv | cat
Running phase: unpackPhase
@nix { "action": "setPhase", "phase": "unpackPhase" }
unpacking source archive /nix/store/0sqy1yafc0kdx30nm1dbda83hlybkfhk-source
source root is source
Running phase: patchPhase
@nix { "action": "setPhase", "phase": "patchPhase" }
Running phase: bunSetInstallCacheDirPhase
@nix { "action": "setPhase", "phase": "bunSetInstallCacheDirPhase" }
Using bun root: "/build/source"
Running phase: bunPatchPhase
@nix { "action": "setPhase", "phase": "bunPatchPhase" }
patching script interpreter paths in .
./scripts/push-all.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/update-flathub-checkout.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/resolve-release-version.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/should-upload-fastlane-screenshots.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/write-asc-private-key.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/test-build-macos-widget.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/install_core_dependencies.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/apply_bun_patches.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/prepare-fastlane-metadata.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/validate-docker-cloud-secret-runtime.sh: interpreter directive changed from "#!/usr/bin/env sh" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/sh"
./scripts/ci/install_mobile_dependencies.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/asc-api-utils.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/decode-base64-to-file.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/build-macos-widget.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/bump-version.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./docker/cloud/entrypoint.sh: interpreter directive changed from "#!/usr/bin/env sh" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/sh"
./apps/mobile/scripts/android_build.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./apps/mobile/scripts/android_build_debug.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./apps/mobile/scripts/android_startup_benchmark.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./apps/mobile/scripts/fdroid_prep.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
Running phase: updateAutotoolsGnuConfigScriptsPhase
@nix { "action": "setPhase", "phase": "updateAutotoolsGnuConfigScriptsPhase" }
Running phase: configurePhase
@nix { "action": "setPhase", "phase": "configurePhase" }
no configure script, doing nothing
Running phase: bunNodeModulesInstallPhase
@nix { "action": "setPhase", "phase": "bunNodeModulesInstallPhase" }
/build/source /build/source
bun install flags: --linker=hoisted --ignore-scripts
bun install v1.3.13 (bf2e2cec)
37 |     "@eslint/eslintrc": {
                             ^
warn: Bun currently does not support nested "overrides"
   at /build/source/package.json:37:25

40 |     "eslint": {
                   ^
warn: Bun currently does not support nested "overrides"
   at /build/source/package.json:40:15

43 |     "eslint-plugin-expo": {
                               ^
warn: Bun currently does not support nested "overrides"
   at /build/source/package.json:43:27

error: ConnectionRefused downloading package manifest react-test-renderer

error: ConnectionRefused downloading package manifest typescript

error: ConnectionRefused downloading package manifest decode-uri-component

error: ConnectionRefused downloading package manifest @types/react-test-renderer

error: ConnectionRefused downloading package manifest @react-navigation/bottom-tabs

error: ConnectionRefused downloading package manifest @react-navigation/drawer

error: ConnectionRefused downloading package manifest @types/react

error: FailedToOpenSocket downloading package manifest eslint-config-expo

error: ConnectionRefused downloading package manifest @react-navigation/native

error: ConnectionRefused downloading package manifest @react-native-community/datetimepicker

error: ConnectionRefused downloading package manifest babel-preset-expo

error: FailedToOpenSocket downloading package manifest date-fns

error: ConnectionRefused downloading package manifest expo-intent-launcher

error: ConnectionRefused downloading package manifest expo-linking

error: ConnectionRefused downloading package manifest @react-navigation/elements

error: FailedToOpenSocket downloading package manifest @op-engineering/op-sqlite

error: ConnectionRefused downloading package manifest expo-file-system

error: ConnectionRefused downloading package manifest expo-font

error: ConnectionRefused downloading package manifest @expo/vector-icons

error: ConnectionRefused downloading package manifest eslint

error: FailedToOpenSocket downloading package manifest @expo/metro-runtime

error: ConnectionRefused downloading package manifest expo-calendar

error: ConnectionRefused downloading package manifest expo-clipboard

error: ConnectionRefused downloading package manifest vitest

error: ConnectionRefused downloading package manifest @fugood/react-native-audio-pcm-stream

error: FailedToOpenSocket downloading package manifest expo-image-picker

error: ConnectionRefused downloading package manifest expo-asset

error: ConnectionRefused downloading package manifest expo-audio

error: ConnectionRefused downloading package manifest expo-haptics

error: ConnectionRefused downloading package manifest @react-native-async-storage/async-storage

error: FailedToOpenSocket downloading package manifest expo-document-picker

error: ConnectionRefused downloading package manifest react-native-android-widget

error: ConnectionRefused downloading package manifest react-native-draggable-flatlist

error: ConnectionRefused downloading package manifest expo-constants

error: ConnectionRefused downloading package manifest @babel/runtime

error: FailedToOpenSocket downloading package manifest expo-build-properties

error: ConnectionRefused downloading package manifest query-string

error: ConnectionRefused downloading package manifest react

error: ConnectionRefused downloading package manifest expo-auth-session

error: ConnectionRefused downloading package manifest expo-image

error: FailedToOpenSocket downloading package manifest expo-application

error: ConnectionRefused downloading package manifest expo-web-browser

error: ConnectionRefused downloading package manifest invariant

error: ConnectionRefused downloading package manifest react-native-fs

error: ConnectionRefused downloading package manifest expo-dev-client

error: FailedToOpenSocket downloading package manifest react-native-alarm-notification

error: ConnectionRefused downloading package manifest expo-status-bar

error: ConnectionRefused downloading package manifest expo-store-review

error: ConnectionRefused downloading package manifest react-dom

error: ConnectionRefused downloading package manifest expo-background-task

error: FailedToOpenSocket downloading package manifest nullthrows

error: ConnectionRefused downloading package manifest expo-router

error: ConnectionRefused downloading package manifest expo-secure-store

error: ConnectionRefused downloading package manifest lucide-react-native

error: ConnectionRefused downloading package manifest expo

error: FailedToOpenSocket downloading package manifest expo-task-manager

error: ConnectionRefused downloading package manifest react-native-quick-crypto

error: ConnectionRefused downloading package manifest react-native-reanimated

error: ConnectionRefused downloading package manifest expo-symbols

error: ConnectionRefused downloading package manifest react-native

error: FailedToOpenSocket downloading package manifest expo-splash-screen

error: ConnectionRefused downloading package manifest react-native-url-polyfill

error: ConnectionRefused downloading package manifest react-native-web

error: ConnectionRefused downloading package manifest expo-share-intent

error: ConnectionRefused downloading package manifest nativewind

error: FailedToOpenSocket downloading package manifest expo-network

error: ConnectionRefused downloading package manifest tailwindcss

error: ConnectionRefused downloading package manifest whatwg-fetch

error: ConnectionRefused downloading package manifest react-native-gesture-handler

error: ConnectionRefused downloading package manifest expo-system-ui

error: FailedToOpenSocket downloading package manifest react-native-quick-base64

error: ConnectionRefused downloading package manifest chrono-node

error: ConnectionRefused downloading package manifest date-fns-jalali

error: ConnectionRefused downloading package manifest react-native-safe-area-context

error: ConnectionRefused downloading package manifest expo-sharing

error: FailedToOpenSocket downloading package manifest react-native-svg

error: ConnectionRefused downloading package manifest react-native-nitro-modules

error: ConnectionRefused downloading package manifest semver

error: ConnectionRefused downloading package manifest react-native-widgetkit

error: ConnectionRefused downloading package manifest expo-local-authentication

error: FailedToOpenSocket downloading package manifest whatwg-url-without-unicode

error: ConnectionRefused downloading package manifest react-native-worklets

error: ConnectionRefused downloading package manifest fflate

error: ConnectionRefused downloading package manifest react-native-screens

error: ConnectionRefused downloading package manifest @noble/hashes

error: FailedToOpenSocket downloading package manifest whisper.rn

error: ConnectionRefused downloading package manifest zustand
error: @types/react@~19.1.0 failed to resolve
error: @types/react-test-renderer@^19.1.0 failed to resolve
error: babel-preset-expo@~54.0.10 failed to resolve
error: eslint@^9.39.1 failed to resolve
error: eslint-config-expo@~10.0.0 failed to resolve
error: react-test-renderer@19.1.0 failed to resolve
error: typescript@~5.9.2 failed to resolve
error: vitest@^3.2.4 failed to resolve
error: @babel/runtime@^7.28.4 failed to resolve
error: @expo/metro-runtime@^6.1.2 failed to resolve
error: @expo/vector-icons@^15.0.3 failed to resolve
error: @fugood/react-native-audio-pcm-stream@^1.1.4 failed to resolve
error: @op-engineering/op-sqlite@^17.1.2 failed to resolve
error: @react-native-async-storage/async-storage@2.2.0 failed to resolve
error: @react-native-community/datetimepicker@8.4.4 failed to resolve
error: @react-navigation/bottom-tabs@^7.4.0 failed to resolve
error: @react-navigation/drawer@^7.5.0 failed to resolve
error: @react-navigation/elements@^2.6.3 failed to resolve
error: @react-navigation/native@^7.1.8 failed to resolve
error: date-fns@^4.1.0 failed to resolve
error: decode-uri-component@0.5.0 failed to resolve
error: expo@~54.0.30 failed to resolve
error: expo-application@~7.0.8 failed to resolve
error: expo-asset@~12.0.12 failed to resolve
error: expo-audio@~1.1.1 failed to resolve
error: expo-auth-session@~7.0.11 failed to resolve
error: expo-background-task@~1.0.10 failed to resolve
error: expo-build-properties@~1.0.10 failed to resolve
error: expo-calendar@~15.0.8 failed to resolve
error: expo-clipboard@~8.0.8 failed to resolve
error: expo-constants@~18.0.13 failed to resolve
error: expo-dev-client@~6.0.21 failed to resolve
error: expo-document-picker@^14.0.8 failed to resolve
error: expo-file-system@~19.0.21 failed to resolve
error: expo-font@~14.0.10 failed to resolve
error: expo-haptics@~15.0.8 failed to resolve
error: expo-image@~3.0.11 failed to resolve
error: expo-image-picker@~17.0.11 failed to resolve
error: expo-intent-launcher@~13.0.8 failed to resolve
error: expo-linking@~8.0.12 failed to resolve
error: expo-local-authentication@~17.0.9 failed to resolve
error: expo-network@~8.0.8 failed to resolve
error: expo-router@~6.0.21 failed to resolve
error: expo-secure-store@~15.0.8 failed to resolve
error: expo-share-intent@^5.1.1 failed to resolve
error: expo-sharing@^14.0.8 failed to resolve
error: expo-splash-screen@~31.0.13 failed to resolve
error: expo-status-bar@~3.0.9 failed to resolve
error: expo-store-review@~9.0.9 failed to resolve
error: expo-symbols@~1.0.8 failed to resolve
error: expo-system-ui@~6.0.9 failed to resolve
error: expo-task-manager@~14.0.9 failed to resolve
error: expo-web-browser@~15.0.11 failed to resolve
error: invariant@^2.2.4 failed to resolve
error: lucide-react-native@^0.556.0 failed to resolve
error: nativewind@^4.2.1 failed to resolve
error: nullthrows@^1.1.1 failed to resolve
error: query-string@7.1.3 failed to resolve
error: react@19.1.0 failed to resolve
error: react-dom@19.1.0 failed to resolve
error: react-native@0.81.5 failed to resolve
error: react-native-alarm-notification@^1.8.0 failed to resolve
error: react-native-android-widget@^0.17.2 failed to resolve
error: react-native-draggable-flatlist@^4.0.2 failed to resolve
error: react-native-fs@^2.20.0 failed to resolve
error: react-native-gesture-handler@~2.28.0 failed to resolve
error: react-native-nitro-modules@0.33.2 failed to resolve
error: react-native-quick-base64@^3.0.1 failed to resolve
error: react-native-quick-crypto@^1.1.7 failed to resolve
error: react-native-reanimated@~4.1.1 failed to resolve
error: react-native-safe-area-context@~5.6.0 failed to resolve
error: react-native-screens@~4.16.0 failed to resolve
error: react-native-svg@15.12.1 failed to resolve
error: react-native-url-polyfill@^3.0.0 failed to resolve
error: react-native-web@~0.21.0 failed to resolve
error: react-native-widgetkit@^1.0.9 failed to resolve
error: react-native-worklets@0.5.1 failed to resolve
error: semver@^7.7.2 failed to resolve
error: tailwindcss@3.3.2 failed to resolve
error: whatwg-fetch@^3.6.20 failed to resolve
error: whatwg-url-without-unicode@^8.0.0-3 failed to resolve
error: whisper.rn@^0.5.3 failed to resolve
error: @types/react@~19.1.0 failed to resolve
error: typescript@~5.9.2 failed to resolve
error: vitest@^3.2.4 failed to resolve
error: @babel/runtime@^7.28.4 failed to resolve
error: @noble/hashes@^2.3.0 failed to resolve
error: chrono-node@^2.9.0 failed to resolve
error: date-fns@^4.1.0 failed to resolve
error: date-fns-jalali@4.4.0-0 failed to resolve
error: fflate@^0.8.2 failed to resolve
error: zustand@^4.5.0 failed to resolve

📋 How to collect logs (Click to expand)

For detailed instructions, please see the Diagnostics and Logs docs.

Desktop:

1. Go to Settings → Sync.
2. Toggle Debug logging to ON.
3. Reproduce the issue.
4. Go to Settings → Sync → Diagnostics to find the Log file path.
5. Attach the log file here.
   • Note: You can also clear old logs from this screen.

Mobile:

1. Go to Settings → Diagnostics.
2. Toggle Debug logging to ON.
3. Reproduce the issue.
4. Tap Share log to export the file and attach it here.

Note: Logs are local-only and redact common credentials.

📋 Additional Context

• This seems similar to the lockfile desync in [BUG] Building desktop app via Nix from v1.1.5 fails #981
• I chose mindwtr-web for this bug report since it builds quickly compared to the desktop app; they both fail to build in the same way
• This is also present on v1.2.7
• I have made no changes to the build system between testing - same package revisions, same bun version, same build hooks. That should narrow it down to changes in this repository only.

[dongdongbh]

I cannot reproduce this from the tag, so I need one datapoint from your sandbox.

What I ran: the v1.2.6 tree, a bun cache holding every package in bun.lock and nothing else, no network at all (an empty network namespace), bun 1.3.13, bun install --linker=hoisted --ignore-scripts, with and without the bun2nix hook's del(.patchedDependencies) rewrite of package.json and bun.lock. It installs every time, and v1.2.5 behaves the same. bun install --frozen-lockfile with network also passes on v1.2.6 and rewrites nothing, so the lock and the package.json files agree, unlike #981.

The error shape says bun re-resolved the core and mobile workspaces instead of installing them from the lock. When I remove a package from my cache, bun fails with one downloading tarball <name> line instead. The one v1.2.6 change that touches exactly those two workspaces: the mobile app now pins query-string@7.1.3 with a patch, and because the root resolves 9.3.1 the lock stores it nested as mobile/query-string. It is the first patched dependency that is not hoisted. Your bun.nix does contain query-string@7.1.3 and decode-uri-component@0.5.0, I checked.

Two things would settle it. Add --frozen-lockfile to bunInstallFlags for mindwtr-web: bun then refuses to resolve and prints what it thinks changed, which is the line I need. And from nix develop, in a copy of the tag with the hook's two yq rewrites applied, run bun install --frozen-lockfile with network. If that passes while the sandbox fails, the difference is in the generated cache and the fix belongs in bun2nix-baseline.

[TheRealGramdalf]

I cannot reproduce this from the tag, so I need one datapoint from your sandbox.

All good! Thank you for the thorough response.

What I ran: the v1.2.6 tree, a bun cache holding every package in bun.lock and nothing else, no network at all (an empty network namespace), bun 1.3.13, bun install --linker=hoisted --ignore-scripts, with and without the bun2nix hook's del(.patchedDependencies) rewrite of package.json and bun.lock. It installs every time, and v1.2.5 behaves the same. bun install --frozen-lockfile with network also passes on v1.2.6 and rewrites nothing, so the lock and the package.json files agree, unlike #981.

That is incredibly odd. I have some suspicions, see the very bottom of the comment.

Side note; I'm not super familiar with bun (it probably shows). mindwtr-web is currently built with the hoisted linker in my flake, whereas mindwtr (desktop) is built with the isolated linker - is this consistent with your CI/development process?
I'm not sure how bunfig.toml works in a monorepo like this, since the one at the project root specifies the hoisted linker, and the one under app/desktop does not specify anything.
Does apps/desktop inherit the bunfig from the repo root?
AFAIK the webapp is built from the desktop app source, so does it use the same linker type?

The error shape says bun re-resolved the core and mobile workspaces instead of installing them from the lock. When I remove a package from my cache, bun fails with one downloading tarball <name> line instead. The one v1.2.6 change that touches exactly those two workspaces: the mobile app now pins query-string@7.1.3 with a patch, and because the root resolves 9.3.1 the lock stores it nested as mobile/query-string. It is the first patched dependency that is not hoisted. Your bun.nix does contain query-string@7.1.3 and decode-uri-component@0.5.0, I checked.
Two things would settle it. Add --frozen-lockfile to bunInstallFlags for mindwtr-web: bun then refuses to resolve and prints what it thinks changed, which is the line I need.

This doesn't seem to be doing the same for me. It spits out what appears to be the exact same error, though the ordering and types are different (I believe the step is asynchronous)

mindwtr-flake on  update-v1.2.6 [!] took 13s
❯ nix log /nix/store/vcngivs59g68nplr28icjhlyiwi4wwg5-mindwtr-web-1.2.6.drv | cat
Running phase: unpackPhase
@nix { "action": "setPhase", "phase": "unpackPhase" }
unpacking source archive /nix/store/0sqy1yafc0kdx30nm1dbda83hlybkfhk-source
source root is source
Running phase: patchPhase
@nix { "action": "setPhase", "phase": "patchPhase" }
Running phase: bunSetInstallCacheDirPhase
@nix { "action": "setPhase", "phase": "bunSetInstallCacheDirPhase" }
Using bun root: "/build/source"
Running phase: bunPatchPhase
@nix { "action": "setPhase", "phase": "bunPatchPhase" }
patching script interpreter paths in .
./scripts/ci/update-flathub-checkout.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/validate-docker-cloud-secret-runtime.sh: interpreter directive changed from "#!/usr/bin/env sh" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/sh"
./scripts/ci/install_core_dependencies.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/should-upload-fastlane-screenshots.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/install_mobile_dependencies.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/apply_bun_patches.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/resolve-release-version.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/decode-base64-to-file.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/prepare-fastlane-metadata.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/asc-api-utils.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/test-build-macos-widget.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/ci/write-asc-private-key.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/push-all.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/bump-version.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./scripts/build-macos-widget.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./docker/cloud/entrypoint.sh: interpreter directive changed from "#!/usr/bin/env sh" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/sh"
./apps/mobile/scripts/android_build.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./apps/mobile/scripts/fdroid_prep.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./apps/mobile/scripts/android_build_debug.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
./apps/mobile/scripts/android_startup_benchmark.sh: interpreter directive changed from "#!/usr/bin/env bash" to "/nix/store/byi2zpy2bgcf3dr6y0l8m50rmjj8z7q1-bash-5.3p15/bin/bash"
Running phase: updateAutotoolsGnuConfigScriptsPhase
@nix { "action": "setPhase", "phase": "updateAutotoolsGnuConfigScriptsPhase" }
Running phase: configurePhase
@nix { "action": "setPhase", "phase": "configurePhase" }
no configure script, doing nothing
Running phase: bunNodeModulesInstallPhase
@nix { "action": "setPhase", "phase": "bunNodeModulesInstallPhase" }
/build/source /build/source
bun install flags: --linker=hoisted --frozen-lockfile --ignore-scripts
bun install v1.3.13 (bf2e2cec)
37 |     "@eslint/eslintrc": {
                             ^
warn: Bun currently does not support nested "overrides"
   at /build/source/package.json:37:25

40 |     "eslint": {
                   ^
warn: Bun currently does not support nested "overrides"
   at /build/source/package.json:40:15

43 |     "eslint-plugin-expo": {
                               ^
warn: Bun currently does not support nested "overrides"
   at /build/source/package.json:43:27

error: ConnectionRefused downloading package manifest @expo/metro-runtime

error: ConnectionRefused downloading package manifest @expo/vector-icons

error: ConnectionRefused downloading package manifest eslint-config-expo

error: ConnectionRefused downloading package manifest react-test-renderer

error: ConnectionRefused downloading package manifest expo-font

error: ConnectionRefused downloading package manifest expo-haptics

error: ConnectionRefused downloading package manifest @types/react

error: FailedToOpenSocket downloading package manifest @babel/runtime

error: ConnectionRefused downloading package manifest expo-clipboard

error: ConnectionRefused downloading package manifest expo-constants

error: ConnectionRefused downloading package manifest typescript

error: FailedToOpenSocket downloading package manifest eslint

error: ConnectionRefused downloading package manifest expo-audio

error: ConnectionRefused downloading package manifest expo-auth-session

error: ConnectionRefused downloading package manifest @types/react-test-renderer

error: FailedToOpenSocket downloading package manifest expo-file-system

error: ConnectionRefused downloading package manifest date-fns

error: ConnectionRefused downloading package manifest decode-uri-component

error: ConnectionRefused downloading package manifest expo-dev-client

error: ConnectionRefused downloading package manifest vitest

error: FailedToOpenSocket downloading package manifest expo-calendar

error: ConnectionRefused downloading package manifest @react-native-community/datetimepicker

error: ConnectionRefused downloading package manifest @react-navigation/bottom-tabs

error: ConnectionRefused downloading package manifest expo-background-task

error: ConnectionRefused downloading package manifest babel-preset-expo

error: FailedToOpenSocket downloading package manifest expo-asset

error: ConnectionRefused downloading package manifest react-native-draggable-flatlist

error: ConnectionRefused downloading package manifest react-native-fs

error: ConnectionRefused downloading package manifest expo

error: ConnectionRefused downloading package manifest expo-document-picker

error: FailedToOpenSocket downloading package manifest @react-navigation/native

error: ConnectionRefused downloading package manifest react

error: ConnectionRefused downloading package manifest react-dom

error: ConnectionRefused downloading package manifest @react-navigation/drawer

error: ConnectionRefused downloading package manifest expo-build-properties

error: FailedToOpenSocket downloading package manifest @react-native-async-storage/async-storage

error: ConnectionRefused downloading package manifest invariant

error: ConnectionRefused downloading package manifest lucide-react-native

error: ConnectionRefused downloading package manifest @fugood/react-native-audio-pcm-stream

error: ConnectionRefused downloading package manifest expo-application

error: FailedToOpenSocket downloading package manifest react-native-android-widget

error: ConnectionRefused downloading package manifest expo-store-review

error: ConnectionRefused downloading package manifest expo-symbols

error: ConnectionRefused downloading package manifest react-native

error: ConnectionRefused downloading package manifest @react-navigation/elements

error: FailedToOpenSocket downloading package manifest query-string

error: ConnectionRefused downloading package manifest expo-secure-store

error: ConnectionRefused downloading package manifest expo-share-intent

error: ConnectionRefused downloading package manifest nativewind

error: ConnectionRefused downloading package manifest @op-engineering/op-sqlite

error: FailedToOpenSocket downloading package manifest expo-web-browser

error: ConnectionRefused downloading package manifest expo-intent-launcher

error: ConnectionRefused downloading package manifest expo-linking

error: ConnectionRefused downloading package manifest expo-system-ui

error: ConnectionRefused downloading package manifest react-native-alarm-notification

error: FailedToOpenSocket downloading package manifest expo-status-bar

error: ConnectionRefused downloading package manifest react-native-quick-crypto

error: ConnectionRefused downloading package manifest react-native-reanimated

error: ConnectionRefused downloading package manifest expo-sharing

error: ConnectionRefused downloading package manifest nullthrows

error: FailedToOpenSocket downloading package manifest expo-router

error: ConnectionRefused downloading package manifest react-native-url-polyfill

error: ConnectionRefused downloading package manifest react-native-web

error: ConnectionRefused downloading package manifest expo-local-authentication

error: ConnectionRefused downloading package manifest expo-task-manager

error: FailedToOpenSocket downloading package manifest expo-image-picker

error: ConnectionRefused downloading package manifest tailwindcss

error: ConnectionRefused downloading package manifest whatwg-fetch

error: ConnectionRefused downloading package manifest react-native-gesture-handler

error: ConnectionRefused downloading package manifest expo-splash-screen

error: FailedToOpenSocket downloading package manifest react-native-quick-base64

error: ConnectionRefused downloading package manifest chrono-node

error: ConnectionRefused downloading package manifest date-fns-jalali

error: ConnectionRefused downloading package manifest react-native-safe-area-context

error: ConnectionRefused downloading package manifest expo-network

error: FailedToOpenSocket downloading package manifest react-native-svg

error: ConnectionRefused downloading package manifest react-native-nitro-modules

error: ConnectionRefused downloading package manifest semver

error: ConnectionRefused downloading package manifest react-native-widgetkit

error: ConnectionRefused downloading package manifest expo-image

error: FailedToOpenSocket downloading package manifest whatwg-url-without-unicode

error: ConnectionRefused downloading package manifest react-native-worklets

error: ConnectionRefused downloading package manifest fflate

error: ConnectionRefused downloading package manifest react-native-screens

error: ConnectionRefused downloading package manifest @noble/hashes

error: FailedToOpenSocket downloading package manifest whisper.rn

error: ConnectionRefused downloading package manifest zustand
error: @types/react@~19.1.0 failed to resolve
error: @types/react-test-renderer@^19.1.0 failed to resolve
error: babel-preset-expo@~54.0.10 failed to resolve
error: eslint@^9.39.1 failed to resolve
error: eslint-config-expo@~10.0.0 failed to resolve
error: react-test-renderer@19.1.0 failed to resolve
error: typescript@~5.9.2 failed to resolve
error: vitest@^3.2.4 failed to resolve
error: @babel/runtime@^7.28.4 failed to resolve
error: @expo/metro-runtime@^6.1.2 failed to resolve
error: @expo/vector-icons@^15.0.3 failed to resolve
error: @fugood/react-native-audio-pcm-stream@^1.1.4 failed to resolve
error: @op-engineering/op-sqlite@^17.1.2 failed to resolve
error: @react-native-async-storage/async-storage@2.2.0 failed to resolve
error: @react-native-community/datetimepicker@8.4.4 failed to resolve
error: @react-navigation/bottom-tabs@^7.4.0 failed to resolve
error: @react-navigation/drawer@^7.5.0 failed to resolve
error: @react-navigation/elements@^2.6.3 failed to resolve
error: @react-navigation/native@^7.1.8 failed to resolve
error: date-fns@^4.1.0 failed to resolve
error: decode-uri-component@0.5.0 failed to resolve
error: expo@~54.0.30 failed to resolve
error: expo-application@~7.0.8 failed to resolve
error: expo-asset@~12.0.12 failed to resolve
error: expo-audio@~1.1.1 failed to resolve
error: expo-auth-session@~7.0.11 failed to resolve
error: expo-background-task@~1.0.10 failed to resolve
error: expo-build-properties@~1.0.10 failed to resolve
error: expo-calendar@~15.0.8 failed to resolve
error: expo-clipboard@~8.0.8 failed to resolve
error: expo-constants@~18.0.13 failed to resolve
error: expo-dev-client@~6.0.21 failed to resolve
error: expo-document-picker@^14.0.8 failed to resolve
error: expo-file-system@~19.0.21 failed to resolve
error: expo-font@~14.0.10 failed to resolve
error: expo-haptics@~15.0.8 failed to resolve
error: expo-image@~3.0.11 failed to resolve
error: expo-image-picker@~17.0.11 failed to resolve
error: expo-intent-launcher@~13.0.8 failed to resolve
error: expo-linking@~8.0.12 failed to resolve
error: expo-local-authentication@~17.0.9 failed to resolve
error: expo-network@~8.0.8 failed to resolve
error: expo-router@~6.0.21 failed to resolve
error: expo-secure-store@~15.0.8 failed to resolve
error: expo-share-intent@^5.1.1 failed to resolve
error: expo-sharing@^14.0.8 failed to resolve
error: expo-splash-screen@~31.0.13 failed to resolve
error: expo-status-bar@~3.0.9 failed to resolve
error: expo-store-review@~9.0.9 failed to resolve
error: expo-symbols@~1.0.8 failed to resolve
error: expo-system-ui@~6.0.9 failed to resolve
error: expo-task-manager@~14.0.9 failed to resolve
error: expo-web-browser@~15.0.11 failed to resolve
error: invariant@^2.2.4 failed to resolve
error: lucide-react-native@^0.556.0 failed to resolve
error: nativewind@^4.2.1 failed to resolve
error: nullthrows@^1.1.1 failed to resolve
error: query-string@7.1.3 failed to resolve
error: react@19.1.0 failed to resolve
error: react-dom@19.1.0 failed to resolve
error: react-native@0.81.5 failed to resolve
error: react-native-alarm-notification@^1.8.0 failed to resolve
error: react-native-android-widget@^0.17.2 failed to resolve
error: react-native-draggable-flatlist@^4.0.2 failed to resolve
error: react-native-fs@^2.20.0 failed to resolve
error: react-native-gesture-handler@~2.28.0 failed to resolve
error: react-native-nitro-modules@0.33.2 failed to resolve
error: react-native-quick-base64@^3.0.1 failed to resolve
error: react-native-quick-crypto@^1.1.7 failed to resolve
error: react-native-reanimated@~4.1.1 failed to resolve
error: react-native-safe-area-context@~5.6.0 failed to resolve
error: react-native-screens@~4.16.0 failed to resolve
error: react-native-svg@15.12.1 failed to resolve
error: react-native-url-polyfill@^3.0.0 failed to resolve
error: react-native-web@~0.21.0 failed to resolve
error: react-native-widgetkit@^1.0.9 failed to resolve
error: react-native-worklets@0.5.1 failed to resolve
error: semver@^7.7.2 failed to resolve
error: tailwindcss@3.3.2 failed to resolve
error: whatwg-fetch@^3.6.20 failed to resolve
error: whatwg-url-without-unicode@^8.0.0-3 failed to resolve
error: whisper.rn@^0.5.3 failed to resolve
error: @types/react@~19.1.0 failed to resolve
error: typescript@~5.9.2 failed to resolve
error: vitest@^3.2.4 failed to resolve
error: @babel/runtime@^7.28.4 failed to resolve
error: @noble/hashes@^2.3.0 failed to resolve
error: chrono-node@^2.9.0 failed to resolve
error: date-fns@^4.1.0 failed to resolve
error: date-fns-jalali@4.4.0-0 failed to resolve
error: fflate@^0.8.2 failed to resolve
error: zustand@^4.5.0 failed to resolve

And from nix develop, in a copy of the tag with the hook's two yq rewrites applied, run bun install --frozen-lockfile with network. If that passes while the sandbox fails, the difference is in the generated cache and the fix belongs in bun2nix-baseline.

I was not aware that bun2nix modified the lock file, I think this caused the issue. Patched dependencies are removed unconditionally, and there are helper functions available for applying patches, but this isn't mentioned anywhere in the documentation. I'll see if that can fix it for me

[dongdongbh]

That frozen run is the datapoint. With --frozen-lockfile bun fetches no manifest when it has a lockfile it can read; it errors with "lockfile had changes" instead. Fetching manifests for whole workspaces under that flag means bun did not take bun.lock at all and started a fresh resolve, so the rewritten lock your hook leaves behind is the right suspect. Two checks would confirm it: run bun install --frozen-lockfile with network against a tree where only the hook's yq rewrite was applied, and look at what the rewrite produced. bun.lock is JSON with trailing commas, and if the yq in your sandbox is the Python wrapper rather than yq-go, -o=json is a flag it does not know. If skipping the rewrite makes the build pass, the patch helpers are the cleaner route; the query-string patch only matters for the mobile app anyway.

On linkers: the root bunfig.toml sets linker = "hoisted" and bun applies it to the whole workspace. apps/desktop has no bunfig of its own and inherits it. The web app is Vite building the desktop sources, so it uses the same node_modules. CI and every release build run hoisted. Isolated is stricter, which is how #981 surfaced, so either works; hoisted matches what ships.

[TheRealGramdalf]

The following has been done with the patch helper applied, which still fails to build

That frozen run is the datapoint. With --frozen-lockfile bun fetches no manifest when it has a lockfile it can read; it errors with "lockfile had changes" instead. Fetching manifests for whole workspaces under that flag means bun did not take bun.lock at all and started a fresh resolve, so the rewritten lock your hook leaves behind is the right suspect. Two checks would confirm it: run bun install --frozen-lockfile with network against a tree where only the hook's yq rewrite was applied, and look at what the rewrite produced.

If I'm understanding you correctly:

• I've run the build steps manually (with nix develop .#mindwtr-web - https://nix.dev/manual/nix/2.35/command-ref/new-cli/nix3-develop.html)
• I run all phases as normal until the failing one, bunNodeModulesInstallPhase
• Once I hit bunNodeModulesInstallPhase, I run the yq rewrite: https://github.com/TheRealGramdalf/bun2nix-baseline/blob/master/nix/mk-derivation/hook.sh#L111-L116
  • Save a copy of package.json and bun.lock for later
• nix develop has network access, so I run bun install with the same flags displayed in the failing log file (--linker=hoisted --frozen-lockfile --ignore-scripts)
• Now comparing bun.lock and package.json after running bun install to the version saved earlier shows no difference, but the step succeeds (network access presumably fixed it)

bun.lock is JSON with trailing commas, and if the yq in your sandbox is the Python wrapper rather than yq-go, -o=json is a flag it does not know. If skipping the rewrite makes the build pass, the patch helpers are the cleaner route; the query-string patch only matters for the mobile app anyway.

yq in the sandbox is yq-go, the only difference I notice is that the default bun.lock has trailing commas and single lines have been expanded:

"overrides": {
    ...
    "vite": "7.3.6",
    "ws": "8.21.0",
    "yaml": "2.8.3",
  },

"overrides": {
    ...
    "vite": "7.3.6",
    "ws": "8.21.0",
    "yaml": "2.8.3"
  },

"@0no-co/graphql.web": ["@0no-co/graphql.web@1.2.0", "", { "peerDependencies": { "graphql": "^14.0.0 || ^15.0.0 || ^16.0.0" }, "optionalPeers": ["graphql"] }, "sha512-/1iHy9TTr63gE1YcR5idjx8UREz1s0kFhydf3bBLCXyqjhkIc6igAzTOx3zPifCwFR87tsh/4Pa9cNts6d2otw=="],

"@0no-co/graphql.web": [
      "@0no-co/graphql.web@1.2.0",
      "",
      {
        "peerDependencies": {
          "graphql": "^14.0.0 || ^15.0.0 || ^16.0.0"
        },
        "optionalPeers": [
          "graphql"
        ]
      },
      "sha512-/1iHy9TTr63gE1YcR5idjx8UREz1s0kFhydf3bBLCXyqjhkIc6igAzTOx3zPifCwFR87tsh/4Pa9cNts6d2otw=="
    ],

On linkers: the root bunfig.toml sets linker = "hoisted" and bun applies it to the whole workspace. apps/desktop has no bunfig of its own and inherits it. The web app is Vite building the desktop sources, so it uses the same node_modules. CI and every release build run hoisted. Isolated is stricter, which is how #981 surfaced, so either works; hoisted matches what ships.

Got it. Once this is resolved I'll probably move to isolated then, unless you advise otherwise

[TheRealGramdalf]

I also came across this PR which may be relevant - I'll see if building from that works.

[TheRealGramdalf]

Building from the above PR works, the patch helper was just a red herring (it works with or without it). Sorry to bother you, but thanks for all the help!

[dongdongbh]

Glad it builds. For anyone landing here later: the failure was in bun2nix, not in the tag. bun reads npm manifests to resolve peer dependencies even under --frozen-lockfile, and the bun2nix cache held the extracted packages but none of the .npm manifest files, so every workspace with peers in its graph started a fresh resolve and hit ConnectionRefused. nix-community/bun2nix#103 rebuilds those manifests from bun.lock. Nothing to change on this side, and no bother at all; your frozen-lockfile run is what pinned it down.