jbrowse-desktop-git

maintainer balwierz · 0 votes · scanned 2026-08-03 00:08:14.047287

LOW

Why flagged Package builds from the official GMOD/jbrowse-components GitHub repo using pnpm with a frozen lockfile; the flagged 'undeclared external package' is just pnpm installing the project's own monorepo dependencies scoped to the desktop subgraph, not an unrelated third-party package. The SKIP checksum is expected for a git source. No obfuscation, no exfiltration, no untrusted binary downloads.

Triggered rules

LOW AI review downgraded a static finding llm_review

The static rules flagged this MEDIUM, but an AI model (anthropic/claude-4.6-sonnet-20260217) reviewed the full PKGBUILD and judged it LOW (confidence 75%): Package builds from the official GMOD/jbrowse-components GitHub repo using pnpm with a frozen lockfile; the flagged 'undeclared external package' is just pnpm installing the project's own monorepo dependencies scoped to the desktop subgraph, not an unrelated third-party package. The SKIP checksum is expected for a git source. No obfuscation, no exfiltration, no untrusted binary downloads.

1 higher static finding superseded - not the current verdict (shown for transparency)

MEDIUM npm/yarn/pnpm install of an undeclared external package npm_install_external

Runs `npm/yarn/pnpm install <package>` for a package not in source=(), pulling unpinned, unreviewed code at build time. Severity downgraded: the package declares/looks like a Node.js consumer, where build-time installs are expected.

PKGBUILD:42 pnpm install --frozen-lockfile --filter "@jbrowse/desktop..."

PKGBUILD

1 offending line(s) highlighted

      1# Maintainer: Piotr Balwierz <nikt@tuta.com>
    
      2pkgname=jbrowse-desktop-git
    
      3_appname=jbrowse-desktop
    
      4pkgver=4.3.0.r11311.g76002d07d6
    
      5pkgrel=1
    
      6pkgdesc="JBrowse 2 — pluggable open-source genome browser (desktop Electron app, git version)"
    
      7arch=('any')
    
      8url="https://jbrowse.org/jb2/"
    
      9license=('Apache-2.0')
    
      10# Runtime: system Electron (upstream targets electron ^42). Renderer + main are
    
      11# bundled at build time (esbuild main with external:electron, webpack renderer),
    
      12# so no node_modules are needed at runtime.
    
      13depends=('electron42' 'hicolor-icon-theme')
    
      14makedepends=('git' 'pnpm' 'nodejs')
    
      15provides=('jbrowse-desktop')
    
      16conflicts=('jbrowse-desktop')
    
      17options=('!strip' '!debug')
    
      18source=("$_appname::git+https://github.com/GMOD/jbrowse-components.git")
    
      19sha256sums=('SKIP')
    
      20
    
      21pkgver() {
    
      22  cd "$srcdir/$_appname"
    
      23  local _v
    
      24  _v=$(node -p "require('./products/jbrowse-desktop/package.json').version")
    
      25  printf "%s.r%s.g%s" "$_v" "$(git rev-list --count HEAD)" "$(git rev-parse --short HEAD)"
    
      26}
    
      27
    
      28build() {
    
      29  cd "$srcdir/$_appname"
    
      30  # Keep npm/pnpm caches inside srcdir; skip the unused bundled Electron binary
    
      31  # (we run on system electron42) and give Node headroom for the webpack build.
    
      32  export ELECTRON_SKIP_BINARY_DOWNLOAD=1
    
      33  # e2e-only tooling pulled in as devDeps; their browser/binary downloads are
    
      34  # not needed to build and can fail on flaky networks.
    
      35  export PUPPETEER_SKIP_DOWNLOAD=1
    
      36  export npm_config_cache="$srcdir/.npm-cache"
    
      37  export NODE_OPTIONS="--max-old-space-size=8192"
    
      38
    
      39  # Scope install to the desktop subgraph only — the default whole-monorepo
    
      40  # install builds website/jbrowse-img deps (sharp/libvips, node-canvas) that
    
      41  # have no prebuilt binaries for the host Node and fail to compile.
    
      42  pnpm install --frozen-lockfile --filter "@jbrowse/desktop..."
    
      43  cd products/jbrowse-desktop
    
      44  pnpm build
    
      45}
    
      46
    
      47package() {
    
      48  cd "$srcdir/$_appname/products/jbrowse-desktop"
    
      49
    
      50  # The app's *internal* version must be valid semver (electron-updater parses
    
      51  # app.getVersion() and throws otherwise) — use upstream's, not the Arch pkgver.
    
      52  local _ver
    
      53  _ver=$(node -p "require('./package.json').version")
    
      54
    
      55  # App payload: the built renderer + bundled electron main.
    
      56  # The packaged main loads the renderer from `app.getAppPath()/index.html`
    
      57  # (= the dir holding package.json), so flatten build/'s contents into the app
    
      58  # root — index.html, static/ and electron.js all sit next to package.json.
    
      59  install -dm755 "$pkgdir/usr/lib/$_appname"
    
      60  cp -r build/. "$pkgdir/usr/lib/$_appname/"
    
      61
    
      62  # Minimal runtime package.json so `electron <dir>` finds the entry point
    
      63  cat > "$pkgdir/usr/lib/$_appname/package.json" <<EOF
    
      64{
    
      65  "name": "jbrowse-desktop",
    
      66  "productName": "JBrowse 2",
    
      67  "version": "$_ver",
    
      68  "type": "module",
    
      69  "main": "electron.js"
    
      70}
    
      71EOF
    
      72
    
      73  # Launcher using the system Electron 42 runtime
    
      74  install -dm755 "$pkgdir/usr/bin"
    
      75  cat > "$pkgdir/usr/bin/$_appname" <<EOF
    
      76#!/bin/sh
    
      77exec electron42 /usr/lib/$_appname --ozone-platform-hint=auto "\$@"
    
      78EOF
    
      79  chmod 755 "$pkgdir/usr/bin/$_appname"
    
      80
    
      81  # Icon (size-agnostic location so it is always found) + hicolor
    
      82  install -Dm644 assets/icon.png "$pkgdir/usr/share/pixmaps/$_appname.png"
    
      83  install -Dm644 assets/icon.png "$pkgdir/usr/share/icons/hicolor/512x512/apps/$_appname.png"
    
      84
    
      85  # Desktop entry
    
      86  install -dm755 "$pkgdir/usr/share/applications"
    
      87  cat > "$pkgdir/usr/share/applications/$_appname.desktop" <<EOF
    
      88[Desktop Entry]
    
      89Type=Application
    
      90Name=JBrowse 2
    
      91GenericName=Genome Browser
    
      92Comment=A pluggable open-source genome browser
    
      93Exec=$_appname %U
    
      94Icon=$_appname
    
      95Terminal=false
    
      96Categories=Science;Biology;Education;
    
      97StartupWMClass=JBrowse 2
    
      98EOF
    
      99
    
      100  install -Dm644 "$srcdir/$_appname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
    
      101}
    
      102

Scan history

Scanned at (UTC)	Severity	Rules
2026-08-03 00:08:14	LOW	2
2026-08-02 00:16:08	LOW	2
2026-08-01 00:11:18	LOW	2
2026-07-31 00:14:10	LOW	2
2026-07-30 00:17:23	LOW	2
2026-07-29 00:25:53	LOW	2
2026-07-28 00:07:28	LOW	2
2026-07-27 00:24:32	LOW	2
2026-07-26 00:07:32	LOW	2
2026-07-25 00:13:44	LOW	2
2026-07-24 00:02:28	LOW	2
2026-07-23 00:14:47	LOW	2
2026-07-22 00:29:32	LOW	2
2026-07-21 00:24:15	LOW	2
2026-07-20 00:19:49	LOW	2
2026-07-19 00:17:08	LOW	2
2026-07-18 00:14:48	LOW	2
2026-07-17 00:06:16	LOW	2
2026-07-16 00:05:41	LOW	2
2026-07-15 00:09:25	LOW	2