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`Cannot call a namespace` error with rpt2 but not `tsc`

See original GitHub issue

What happens and why it is wrong

When I run tsc -p . on my project, everything compiles as expected, but when I use rollup and rollup-plugin-typescript2 with minimal config, it gives me a TypeScript error. I am using the same TypeScript version in both cases as revealed by using tsc -v at the terminal and also checking with verbosity: 3.

You can see a repro here.

Please note that I am using a fork of Rollup in there which fixed a sourcemap issue that actually allows me to see the underlying TypeScript problem.

The TypeScript error is just a random error with the qrcode-generator NPM package, it says Cannot call a namespace, but the usage should be fine.

Environment

Windows 10
Rollup fork, see above

Versions

typescript: tsc -v = Version 2.7.2 but I also have a dev dependency on TypeScript 2.7.2
rollup: adrianheine/rollup#sourcemap see above
rollup-plugin-typescript2: 0.11.1

rollup.config.js

import resolve from 'rollup-plugin-node-resolve';
import typescript from 'rollup-plugin-typescript2';

export default {
  input: 'index.ts',
  output: {
    file: 'bundle.js',
    format: 'iife'
  },
  plugins: [
    resolve(),
    typescript()
  ]
};

tsconfig.json

{
  "compilerOptions": {
    
  }
}

package.json

{
  "name": "rollup",
  "version": "1.0.0",
  "main": "bundle.js",
  "repository": "https://gitlab.com/TomasHubelbauer/bloggo-rollup.git",
  "author": "Tomáš Hübelbauer <tomas@hubelbauer.net>",
  "license": "MIT",
  "scripts": {
    "start": "node node_modules/rollup/bin/rollup -c"
  },
  "devDependencies": {
    "rollup": "adrianheine/rollup#sourcemap",
    "rollup-plugin-node-resolve": "^3.0.3",
    "rollup-plugin-typescript2": "^0.11.1",
    "tslint": "^5.9.1",
    "typescript": "^2.7.2"
  },
  "dependencies": {
    "jsqr": "^1.0.2",
    "qrcode-generator": "^1.3.1"
  }
}

plugin output with verbosity 3

rpt2: typescript version: 2.7.2
rpt2: rollup-plugin-typescript2 version: 0.11.1
rpt2: plugin options:
{
    "verbosity": 3,
    "check": true,
    "clean": false,
    "cacheRoot": "C:\\Users\\Tom\\Desktop\\bloggo-rollup/.rpt2_cache",
    "include": [
        "*.ts+(|x)",
        "**/*.ts+(|x)"
    ],
    "exclude": [
        "*.d.ts",
        "**/*.d.ts"
    ],
    "abortOnError": true,
    "rollupCommonJSResolveHack": false,
    "typescript": "version 2.7.2",
    "useTsconfigDeclarationDir": false,
    "tsconfigOverride": {},
    "tsconfigDefaults": {}
}
rpt2: rollup config:
{
    "input": "index.ts",
    "plugins": [
        {
            "name": "node-resolve"
        },
        {
            "name": "rpt2"
        }
    ],
    "entry": "index.ts",
    "external": [
        "",
        ""
    ]
}
rpt2: built-in options overrides: {
    "module": 5,
    "noEmitHelpers": false,
    "importHelpers": true,
    "noResolve": false,
    "noEmit": false,
    "outDir": "C:\\Users\\Tom\\Desktop\\bloggo-rollup",
    "moduleResolution": 2,
    "declarationDir": null
}
rpt2: parsed tsconfig: {
    "options": {
        "module": 5,
        "noEmitHelpers": false,
        "importHelpers": true,
        "noResolve": false,
        "noEmit": false,
        "outDir": "C:\\Users\\Tom\\Desktop\\bloggo-rollup",
        "moduleResolution": 2,
        "declarationDir": null,
        "configFilePath": "C:\\Users\\Tom\\Desktop\\bloggo-rollup/tsconfig.json"
    },
    "fileNames": [
        "C:/Users/Tom/Desktop/bloggo-rollup/index.ts"
    ],
    "typeAcquisition": {
        "enable": false,
        "include": [],
        "exclude": []
    },
    "raw": {
        "compilerOptions": {}
    },
    "errors": [],
    "wildcardDirectories": {
        "c:/users/tom/desktop/bloggo-rollup": 1
    },
    "compileOnSave": false,
    "configFileSpecs": {
        "includeSpecs": [
            "**/*"
        ],
        "validatedIncludeSpecs": [
            "**/*"
        ],
        "wildcardDirectories": {
            "c:/users/tom/desktop/bloggo-rollup": 1
        }
    }
}
rpt2: included:
'[
    "*.ts+(|x)",
    "**/*.ts+(|x)"
]'
rpt2: excluded:
'[
    "*.d.ts",
    "**/*.d.ts"
]'
rpt2: Ambient types:
rpt2: transpiling 'C:\Users\Tom\Desktop\bloggo-rollup\index.ts'
rpt2:     cache: 'C:\Users\Tom\Desktop\bloggo-rollup/.rpt2_cache/22ff6e2bd8b463bdcea5bf8a6a76797d32066ea4/code/cache/f4e451f1a8985ff1269065353acafb08210b840d'
rpt2:     cache miss
rpt2:     cache: 'C:\Users\Tom\Desktop\bloggo-rollup/.rpt2_cache/22ff6e2bd8b463bdcea5bf8a6a76797d32066ea4/syntacticDiagnostics/cache/f4e451f1a8985ff1269065353acafb08210b840d'
rpt2:     cache miss
rpt2:     cache: 'C:\Users\Tom\Desktop\bloggo-rollup/.rpt2_cache/22ff6e2bd8b463bdcea5bf8a6a76797d32066ea4/semanticDiagnostics/cache/f4e451f1a8985ff1269065353acafb08210b840d'
rpt2:     cache miss
[!] Error: Cannot call a namespace ('qrcode')
index.ts (2:9)
1: import * as jsqr from 'jsqr';
2: import * as qrcode from 'qrcode-generator';
            ^
3:
4: const qr = qrcode(0, 'H');

error Command failed with exit code 1.