expo build errors for android (wrong kotlin version)

Hello!
I love this package, been working great for me in a managed expo / eas build project. But with my latest update, it only builds fine on iOS. On Android, it I get the following error: "Module was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.5.1, expected version is 1.1.15."
Unsure of how to tackle this, any pointers would be much appreciated. Is there a way to override the kotlin version manually?
My package versions:
...
    "expo": "^46.0.13",
    "react-native-mlkit-ocr": "0.2.5",
...

The build error logs:
[stderr] e: /home/expo/.gradle/caches/transforms-3/0485c57e77da2d74e4400ab5f4119067/transformed/jetified-kotlin-stdlib-jdk8-1.6.10.jar!/META-INF/kotlin-stdlib-jdk8.kotlin_module: Module was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] e: /home/expo/.gradle/caches/transforms-3/39ce31cacf59c39e98c8af78aab9d48a/transformed/jetified-react-native-0.69.6-release-api.jar!/META-INF/ReactAndroid_release.kotlin_module: Module was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] e: /home/expo/.gradle/caches/transforms-3/71974a8810180bf42d7354e2ae463e17/transformed/jetified-kotlin-stdlib-common-1.6.10.jar!/META-INF/kotlin-stdlib-common.kotlin_module: Module was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] e: /home/expo/.gradle/caches/transforms-3/76ffa0bc7ee35e73adab5c035a9c7f86/transformed/jetified-kotlin-stdlib-jdk7-1.6.10.jar!/META-INF/kotlin-stdlib-jdk7.kotlin_module: Module was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] e: /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/META-INF/kotlin-stdlib.kotlin_module: Module was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (21, 17): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (26, 17): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (35, 17): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (37, 17): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (38, 11): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (41, 15): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (42, 9): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (48, 5): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (49, 19): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (50, 19): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (51, 19): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (52, 19): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (54, 19): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (55, 19): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (56, 19): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (57, 19): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (68, 16): Unresolved reference: forEach
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (68, 26): Cannot infer a type for this parameter. Please specify it explicitly.
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (70, 9): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (71, 9): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (72, 9): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (88, 13): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (89, 13): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (90, 13): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (91, 24): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (95, 11): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (96, 11): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (97, 11): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (98, 11): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (100, 23): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (106, 12): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (107, 12): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (108, 12): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (109, 12): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.
[stderr] The class is loaded from /home/expo/.gradle/caches/transforms-3/f9a6c4180d9d810f143b823eeeb39ba3/transformed/jetified-kotlin-stdlib-1.6.10.jar!/kotlin/Unit.class
[stderr] e: /home/expo/workingdir/build/app/node_modules/react-native-mlkit-ocr/android/src/main/java/com/reactnativemlkitocr/MlkitOcrModule.kt: (110, 12): Class 'kotlin.Unit' was compiled with an incompatible version of Kotlin. The binary version of its metadata is 1.6.0, expected version is 1.1.15.

Update on this one: I managed to solve it from the expo / eas build side by writing a config plugin:
./kotlin-version-plugin.js:

const { withGradleProperties } = require('@expo/config-plugins');

function withKotlinGradle(config, version) {
  return withGradleProperties(config, config => {
    console.log(
      `[config-plugins/kotlin-version] Setting android.kotlinVersion to: ${version}. This could lead to Android build issues.`
    );
    config.modResults = setKotlinVersion(config.modResults, version);
    return config;
  });
}

function setKotlinVersion(gradleProperties, version) {
  const updatedProps = [...gradleProperties];
  updatedProps.push({
    type: 'property',
    key: 'kotlinVersion',
    value: version,
  });
  return updatedProps;
}

module.exports = withKotlinGradle;

app.json:

...
"plugins": [
      [
        "./kotlin-version-plugin",
        "1.6.0"
      ]
    ]
...

and now the build works :)

@jonasbetareader Thanks so much for posting this man!

Update on this one: I managed to solve it from the expo / eas build side by writing a config plugin:
./kotlin-version-plugin.js:

const { withGradleProperties } = require('@expo/config-plugins');

function withKotlinGradle(config, version) {
  return withGradleProperties(config, config => {
    console.log(
      `[config-plugins/kotlin-version] Setting android.kotlinVersion to: ${version}. This could lead to Android build issues.`
    );
    config.modResults = setKotlinVersion(config.modResults, version);
    return config;
  });
}

function setKotlinVersion(gradleProperties, version) {
  const updatedProps = [...gradleProperties];
  updatedProps.push({
    type: 'property',
    key: 'kotlinVersion',
    value: version,
  });
  return updatedProps;
}

module.exports = withKotlinGradle;

app.json:

...
"plugins": [
      [
        "./kotlin-version-plugin",
        "1.6.0"
      ]
    ]
...

and now the build works :)

Had the same issue on expo 47, tried this and it seams to be working.

You don't need to write a custom plugin. expo-build-properties lets you modify the kotlin version used. Adding this should work:
app.json:

...
"plugins": [
      [
        "expo-build-properties",
        {
           "android": {
              "kotlinVersion": "1.6.21"
           }
        }
      ]
    ]
...


convert_to_bids.py doesn't  create ses-01 in derivatives

After I run the convert_to_bids.py script the derivatives doesn't contain ses-01.
After I ran the sct_run_batch command, I got the following error

rsync -avzh /home/obito/Datasets/DataSets/D/LongitudinalMultipleSclerosisLesionSegmentationChallengeMiccai21/training_curated/derivatives/labels/sub-013/ses-01 derivatives/labels/.
sending incremental file list
rsync: link_stat "/home/obito/Datasets/DataSets/D/LongitudinalMultipleSclerosisLesionSegmentationChallengeMiccai21/training_curated/derivatives/labels/sub-013/ses-01" failed: No such file or directory (2)

Hey @obitoSad, I think this is expected: as the challenge dealt with new lesion segmentation, the GT is only associated with ses-02 (i.e. the second session) in the code. Consequently, scripts/convert_to_bids.py does not create a ses-01 folder, and the preprocessing script does not require it as well. As shown below, it only asks for ses-02 derivatives:
https://github.com/ivadomed/ms-challenge-2021/blob/3e8e5b292cbc64edcda7add17a11654969d1d080/preprocessing/preprocess_data.sh#L148-L157
In case it helps, I am attaching ls outputs to various stages of the dataset we have on our cluster below.
Original dataset from the organizers:
uzmac@romane:~$ ls ~/duke/projects/ivadomed/LongitudinalMultipleSclerosisLesionSegmentationChallengeMiccai21
README.md  training

After running scripts/convert_to_bids.py, the training subfolder should contain _curated:
uzmac@romane:~$ ls ~/duke/projects/ivadomed/LongitudinalMultipleSclerosisLesionSegmentationChallengeMiccai21/training/
013  016  019  021  026  029  032  037  043  048  051  057  068  070  077  084  089  091  095  099  _curated
015  018  020  024  027  030  035  039  047  049  052  061  069  074  083  088  090  094  096  100

An example subject in _curated only contains ses-01 subdirectory:
uzmac@romane:~$ ls ~/duke/projects/ivadomed/LongitudinalMultipleSclerosisLesionSegmentationChallengeMiccai21/training/_curated/derivatives/labels/sub-013/
ses-02

with the following content:
uzmac@romane:~$ ls ~/duke/projects/ivadomed/LongitudinalMultipleSclerosisLesionSegmentationChallengeMiccai21/training/_curated/derivatives/labels/sub-013/ses-02/anat/
sub-013_ses-02_FLAIR_lesion-manual-rater1.json    sub-013_ses-02_FLAIR_lesion-manual-rater3.nii.gz
sub-013_ses-02_FLAIR_lesion-manual-rater1.nii.gz  sub-013_ses-02_FLAIR_lesion-manual-rater4.json
sub-013_ses-02_FLAIR_lesion-manual-rater2.json    sub-013_ses-02_FLAIR_lesion-manual-rater4.nii.gz
sub-013_ses-02_FLAIR_lesion-manual-rater2.nii.gz  sub-013_ses-02_FLAIR_seg-lesion.json
sub-013_ses-02_FLAIR_lesion-manual-rater3.json    sub-013_ses-02_FLAIR_seg-lesion.nii.gz

which are read by the preprocessing script as shown with the first code block attached.
Just to confirm, do you also run preprocessing/preprocess_data.sh with the sct_run_batch command?


Terraform templates failed to execute azd up on China Cloud

Describe the issue:
Test todo-nodejs-mongo-terraform/todo-python-mongo-terraform templates on China Cloud. Run azd up, get error as follow：

Repro Steps:

Set enviroment variable ARM_ENVIRONMENT to "china".
Run azd config set cloud.name AzureChinaCloud.
Login in with command: azd auth login.
Execute command: azd init -t todo-nodejs-mongo-terraform --branch pr/2897.
Run azd up.

Environment:

Cloud: China.
Template: todo-nodejs-mongo-terraform, todo-python-mongo-terraform.
Azd version : 1.6.0-beta.1-pr.3436205 (commit 79ee6dfcae682672d0808d2590b93d298fcba844)

Expected behavior:
Run azd up can pass.
@danieljurek for notification.

@dotnet-7 -- Does this reproduce if the following are done:

Install az CLI, log into china cloud on az cli (az cloud set --name AzureChinaCloud and az login)
Set environment variable $env:ARM_ENVIRONMENT='china'

I was able to get a successful deployment using
azd.exe init -t todo-nodejs-mongo-terraform --branch pr/3452
Note that the PR number and branch name (--branch pr/3452) have changed from when this bug was opened

@danieljurek Which version of azd should I use?
Install pr/2897 version, get error : BlobNotFoundThe specified blob does not exist.
Using pr/3453 version, when run azd auth login after run azd config set cloud.name AzureChinaCloud, unable to switch to ChinaCloud.

We don't have a reliable build for https://github.com/Azure/azure-dev/pull/3452/files yet, but when we do that will be where azd should be installed from to test this scenario.
Hold on until we get that done.

https://github.com/Azure/azure-dev/pull/3481


error on return from sleep (The currently selected todo file was not found)

on Mac OS, when I open the lid and log in, often Sleek gives the following error:

The sidebar has only one icon

though the todos are still visible (but not editable)

To restore it, I have to click the "open folder" button, remove the todo.txt and add it again
Sleek version 1.19
MacOS 12.4
using Syncthing

@mshuflin did you get sleek on the Apple app store, brew or from Github? Also, could you please check https://github.com/ransome1/sleek/releases/tag/v1.2.9-rc.1 if this still happens? I'm wondering how this can happen, as I have the exact same setup with Syncthing. Have you setup any specific settings in Syncthing?

I download the file from github. I am updating to v1.2.9-rc.1 and I will test it to see if it still happens and if I can figure out some reproduction steps. Nothing special is set up in syncthing (syncthing is on my laptop, phone, and server, all with basically default settings).

It took several days, but opening my macbook this morning, I got this error again. Anything else I can do to help isolate the error?

1.3.0-rc.1 this issue has not happened. I will close for now, but reopen if it recurs

@mshuflin thanks for reporting  back!


No clone

Just to confirm, this supersedes #47 right?

this branch branches from #47  and contains all additions it has plus more. Merging this means we can close #47.


[Cosmos .NET SDK] - Introduce New User Agent to Identify Usage

Description:
The purpose of this task is to populate the ApplicationName parameter in the CosmosClientOptions so that the user agent can be generated with the necessary suffix. This will help the cosmos db team to identify the request is originated from Aspire. A sample usage can be found below:
            CosmosClientOptions cosmosClientOptions = new CosmosClientOptions();
            cosmosClientOptions.ApplicationName = "AspireMicrosoftAzureCosmosDBClient";
            cosmosClientOptions.AllowBulkExecution = false;
            cosmosClientOptions.HttpClientFactory = () => new HttpClient();

A sample of the user agent will look like the below:
cosmos-netstandard-sdk/3.39.1|0|X64|Microsoft Windows 10.0.22635|.NET 6.0.29|N|F 00000111|AspireMicrosoftAzureCosmosDBClient|
Acceptance Criteria:

The cosmos .NET SDK team needs to introduce a new user agent to identify and usage of aspire.

Just adding the ApplicationName in Aspire code base will generate the required user-agent right?
Is it the length of the user-agent the issue?

This is addressed with the following PRs:

https://github.com/dotnet/aspire/pull/3876
https://github.com/dotnet/aspire/pull/3906


STEP7 Merge objects

When I try the merge script as shown bellow:
STEP7 Merge objects
Now we are merging the Seurat objects to create one unified Seurat object for downstream analysis.
pbmc <- merge(ifnb.list[["ctrl.d1"]], y = c(ifnb.list[["ctrl.d2"]], ifnb.list[["ctrl.d3"]], ifnb.list[["ctrl.d4"]],
ifnb.list[["stim.d1"]], ifnb.list[["stim.d2"]], ifnb.list[["stim.d3"]], ifnb.list[["stim.d4"]]),
add.cell.ids = c("ctrl.d1", "ctrl.d2", "ctrl.d3", "ctrl.d4",
"stim.d1", "stim.d2", "stim.d3", "stim.d4"), project = "pbmc")
I got this:
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  :
arguments imply differing number of rows: 328912, 265024, 333086, 377833, 373465, 368554, 378246
Please help to solve this issue.
Thanks!

Hi @Ksong11 !
Can you tell me what ifnb.list gives?

Hi @Ksong11 !
Can you tell me what running ifnb.list gives?

I got this:
ifnb.list <- list("ctrl.d1" = ctrl.d1, "ctrl.d2" = ctrl.d2, "ctrl.d3" = ctrl.d3, "ctrl.d4" = ctrl.d4,

              "stim.d1" = stim.d1, "stim.d2" = stim.d2, "stim.d3" = stim.d3, "stim.d4" = stim.d4)

I mean when you just run ifnb.list I want to see what is in this object. There is a issue with this object it doesnt contain the data that is needed to complete the analysis. Thats why you are getting this error most likely!

Okay so I see that the issue is. If you look carefully at the global environment (the top right box of Rstudio, where ctrl, ctrl.d1 etc is) you will see in case of ifnb.list, this object is made up of 8 dataframes, not seurat objects. ifnb.list should be a list containing 8 seurat objects. This happens when you have not loaded Seurat in your computer and are attemptng to create a list of objects. Can you give me an output when you run sessionInfo()? I am sure you will not see Seurat come up with attached base packages: or other attached packages:
When you run ifnb.list, this is what you should see:
> ifnb.list
$ctrl.d1
An object of class Seurat
14053 features across 1658 samples within 1 assay
Active assay: RNA (14053 features, 0 variable features)

$ctrl.d2
An object of class Seurat
14053 features across 1632 samples within 1 assay
Active assay: RNA (14053 features, 0 variable features)

$ctrl.d3
An object of class Seurat
14053 features across 1598 samples within 1 assay
Active assay: RNA (14053 features, 0 variable features)

$ctrl.d4
An object of class Seurat
14053 features across 1660 samples within 1 assay
Active assay: RNA (14053 features, 0 variable features)

$stim.d1
An object of class Seurat
14053 features across 1896 samples within 1 assay
Active assay: RNA (14053 features, 0 variable features)

$stim.d2
An object of class Seurat
14053 features across 1856 samples within 1 assay
Active assay: RNA (14053 features, 0 variable features)

$stim.d3
An object of class Seurat
14053 features across 1809 samples within 1 assay
Active assay: RNA (14053 features, 0 variable features)

$stim.d4
An object of class Seurat
14053 features across 1890 samples within 1 assay
Active assay: RNA (14053 features, 0 variable features)

Sorry I closed the issue by mistake, I re-opened, so that we can continue to troubleshoot till it is resolved. Let me know if its solved if not let me know the error. Thanls!

Sorry I closed the issue by mistake, I re-opened, so that we can continue to troubleshoot till it is resolved. Let me know if its solved if not let me know the error. Thanks!

Here is what I got by doing > sessionInfo(). I will follow your instruction and restart the R.

sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods
[7] base
other attached packages:
[1] ggplot2_3.4.3         qs_0.25.5
[3] ifnb.SeuratData_3.1.0 SeuratData_0.2.1
[5] patchwork_1.1.3       Seurat_4.3.0
[7] harmony_0.1.1         Rcpp_1.0.11
[9] dplyr_1.1.2           SeuratObject_4.1.3
[11] sp_2.0-0
loaded via a namespace (and not attached):
[1] deldir_1.0-9           pbapply_1.7-2
[3] gridExtra_2.3          rlang_1.1.1
[5] magrittr_2.0.3         RcppAnnoy_0.0.21
[7] matrixStats_1.0.0      ggridges_0.5.4
[9] compiler_4.3.1         spatstat.geom_3.2-4
[11] png_0.1-8              vctrs_0.6.3
[13] reshape2_1.4.4         stringr_1.5.0
[15] crayon_1.5.2           pkgconfig_2.0.3
[17] fastmap_1.1.1          ellipsis_0.3.2
[19] utf8_1.2.3             promises_<IP_ADDRESS>
[21] purrr_1.0.1            jsonlite_1.8.7
[23] goftest_1.2-3          later_1.3.1
[25] spatstat.utils_3.0-3   irlba_<IP_ADDRESS>
[27] parallel_4.3.1         cluster_2.1.4
[29] R6_2.5.1               ica_1.0-3
[31] stringi_1.7.12         RColorBrewer_1.1-3
[33] spatstat.data_3.0-1    reticulate_1.31
[35] parallelly_1.36.0      lmtest_0.9-40
[37] scattermore_1.2        tensor_1.5
[39] future.apply_1.11.0    zoo_1.8-12
[41] sctransform_0.3.5      httpuv_1.6.11
[43] Matrix_1.6-0           splines_4.3.1
[45] igraph_1.5.1           tidyselect_1.2.0
[47] rstudioapi_0.15.0      abind_1.4-5
[49] stringfish_0.15.8      spatstat.random_3.1-5
[51] codetools_0.2-19       miniUI_<IP_ADDRESS>
[53] spatstat.explore_3.2-1 listenv_0.9.0
[55] lattice_0.21-8         tibble_3.2.1
[57] plyr_1.8.8             withr_2.5.0
[59] shiny_1.7.5            ROCR_1.0-11
[61] Rtsne_0.16             future_1.33.0
[63] survival_3.5-5         RcppParallel_5.1.7
[65] polyclip_1.10-4        fitdistrplus_1.1-11
[67] pillar_1.9.0           KernSmooth_2.23-22
[69] plotly_4.10.2          generics_0.1.3
[71] munsell_0.5.0          scales_1.2.1
[73] RApiSerialize_0.1.2    globals_0.16.2
[75] xtable_1.8-4           glue_1.6.2
[77] lazyeval_0.2.2         tools_4.3.1
[79] data.table_1.14.8      RANN_2.6.1
[81] leiden_0.4.3           cowplot_1.1.1
[83] grid_4.3.1             tidyr_1.3.0
[85] colorspace_2.1-0       nlme_3.1-163
[87] cli_3.6.1              rappdirs_0.3.3
[89] spatstat.sparse_3.0-2  fansi_1.0.4
[91] viridisLite_0.4.2      uwot_0.1.16
[93] gtable_0.3.3           digest_0.6.33
[95] progressr_0.14.0       ggrepel_0.9.3
[97] htmlwidgets_1.6.2      htmltools_0.5.5
[99] lifecycle_1.0.3        httr_1.4.7
[101] mime_0.12              MASS_7.3-60

Thanks! So as you can see we cant see Seurat anywhere. Either in the "attached base packages:", "other attached packages:" or in the "loaded via a namespace (and not attached):" headers. This means that Seurat is not loaded into your current Rstudio environment. In order for Seurat to be loaded, you need to run library(Seurat) every time you open a new Rstudio session. You only need to install it once, but loading needs to be performed every time you open a new R/Rstudio session.  Once Seurat is loaded and when you run the commands everything should work. Let me know either way.

Thanks! So as you can see we cant see Seurat anywhere. Either in the "attached base packages:", "other attached packages:" or in the "loaded via a namespace (and not attached):" headers. This means that Seurat is not loaded into your current Rstudio environment. In order for Seurat to be loaded, you need to run library(Seurat) every time you open a new Rstudio session. You only need to install it once, but loading needs to be performed every time you open a new R/Rstudio session.  Once Seurat is loaded and when you run the commands everything should work. Let me know either way.

Sorry, I can see the Seurat_4.3.0 from the other attached packages:
other attached packages:
[1] ggplot2_3.4.3         qs_0.25.5
[3] ifnb.SeuratData_3.1.0 SeuratData_0.2.1
[5] patchwork_1.1.3       Seurat_4.3.0
[7] harmony_0.1.1         Rcpp_1.0.11
[9] dplyr_1.1.2           SeuratObject_4.1.3
[11] sp_2.0-0
loaded via a namespace (and not attached):
[1] deldir_1.0-9           pbapply_1.7-2
[3] gridExtra_2.3          rlang_1.1.1
[5] magrittr_2.0.3         RcppAnnoy_0.0.21
[7] matrixStats_1.0.0      ggridges_0.5.4
[9] compiler_4.3.1         spatstat.geom_3.2-4
[11] png_0.1-8              vctrs_0.6.3
[13] reshape2_1.4.4         stringr_1.5.0
[15] crayon_1.5.2           pkgconfig_2.0.3
[17] fastmap_1.1.1          ellipsis_0.3.2
[19] utf8_1.2.3             promises_<IP_ADDRESS>
[21] purrr_1.0.1            jsonlite_1.8.7
[23] goftest_1.2-3          later_1.3.1
[25] spatstat.utils_3.0-3   irlba_<IP_ADDRESS>
[27] parallel_4.3.1         cluster_2.1.4
[29] R6_2.5.1               ica_1.0-3
[31] stringi_1.7.12         RColorBrewer_1.1-3
[33] spatstat.data_3.0-1    reticulate_1.31
[35] parallelly_1.36.0      lmtest_0.9-40
[37] scattermore_1.2        tensor_1.5
[39] future.apply_1.11.0    zoo_1.8-12
[41] sctransform_0.3.5      httpuv_1.6.11
[43] Matrix_1.6-0           splines_4.3.1
[45] igraph_1.5.1           tidyselect_1.2.0
[47] rstudioapi_0.15.0      abind_1.4-5
[49] stringfish_0.15.8      spatstat.random_3.1-5
[51] codetools_0.2-19       miniUI_<IP_ADDRESS>
[53] spatstat.explore_3.2-1 listenv_0.9.0
[55] lattice_0.21-8         tibble_3.2.1
[57] plyr_1.8.8             withr_2.5.0
[59] shiny_1.7.5            ROCR_1.0-11
[61] Rtsne_0.16             future_1.33.0
[63] survival_3.5-5         RcppParallel_5.1.7
[65] polyclip_1.10-4        fitdistrplus_1.1-11
[67] pillar_1.9.0           KernSmooth_2.23-22
[69] plotly_4.10.2          generics_0.1.3
[71] munsell_0.5.0          scales_1.2.1
[73] RApiSerialize_0.1.2    globals_0.16.2
[75] xtable_1.8-4           glue_1.6.2
[77] lazyeval_0.2.2         tools_4.3.1
[79] data.table_1.14.8      RANN_2.6.1
[81] leiden_0.4.3           cowplot_1.1.1
[83] grid_4.3.1             tidyr_1.3.0
[85] colorspace_2.1-0       nlme_3.1-163
[87] cli_3.6.1              rappdirs_0.3.3
[89] spatstat.sparse_3.0-2  fansi_1.0.4
[91] viridisLite_0.4.2      uwot_0.1.16
[93] gtable_0.3.3           digest_0.6.33
[95] progressr_0.14.0       ggrepel_0.9.3
[97] htmlwidgets_1.6.2      htmltools_0.5.5
[99] lifecycle_1.0.3        httr_1.4.7
[101] mime_0.12              MASS_7.3-60

Yes, we can see Seurat in my environment. in your environment, Seurat is not present, this is because we cant see it in any of the three headings. You need to run library(Seurat) once you do that, you will see Seurat as well in your sessionInfo() just like I can see Seurat in my sessionInfo()

Yes, we can see Seurat loaded in my environment. In your environment, Seurat is not present so its not loaded, this is because we can't see it in any of the three headings of sessionInfo(). You need to run library(Seurat), once you do that, you will see Seurat as well, in your sessionInfo() just like I can see Seurat in my sessionInfo()

Thank you so much! Restart the R helped!
Now I encountered another issue. When I ran Harmony, I got this error massage;
#Run Harmony batch correction with library and tissue source covariates

pbmc <- RunHarmony(pbmc,

               assay.use = "RNA",

               reduction = "pca",

               dims.use = 1:20,

               group.by.vars = c("donor", "stim"),

               kmeans_init_nstart=20, kmeans_init_iter_max=100,

               plot_convergence = TRUE)

Error in RunHarmony(pbmc, assay.use = "RNA", reduction = "pca", dims.use = 1:20,  :
could not find function "RunHarmony"
Please help to troubleshooting.
Thanks!

Hi @Ksong11 ! So if you look at the error, it says:
Error in RunHarmony(pbmc, assay.use = "RNA", reduction = "pca", dims.use = 1:20, :
could not find function "RunHarmony"

So the could not find function "RunHarmony" suggests that either Harmony is not installed, or if it is installed it is not loaded.
So I am guessing that you installed harmony, using:
# Install Harmony https://www.nature.com/articles/s41592-019-0619-0
# https://github.com/immunogenomics/harmony
install.packages("harmony")

In that case you need to load Harmony using:
 library(harmony)
Once you do that Harmony should work!

Remember every time you restart Rstudio or R you need to load your packages. You dont need to keep installing them again and again, installing them once is enough. But you need to activate the packages or "load" them into your current environment.
Think of it like this, when you re-start your computer, Microsoft office Word will not automatically start working. you need to double-click on Word and 'load" it, however, you don't need to re-install Word each time you restart your PC, but in order to use Word you need to double-click on the Word icon and "load" it. Only then can you use Word. R packages like seurat and harmony  are the same. Each time you restart R or Rstudio, you need to "load" packages that have been installed. So everytime you will have to run:
# Load packages into R
library(Seurat)
library(harmony)

The reason I ask for sessionInfo() is because that tells me what packages are loaded in your current Rstudio environment. Thats how I noticed that there was no seurat  loaded and that at some point due to not loading seurat  the workflow generated an error.
Hope that helps! Let me know if you have any more questions.
🐲

Once patchwork is installed you can load it via library(patchwork) like you would any other package.

Here are what I got. I think I had this package installed.
sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] harmony_0.1.1      Rcpp_1.0.11        Seurat_4.3.0
[4] SeuratObject_4.1.3 sp_2.0-0
loaded via a namespace (and not attached):
[1] deldir_1.0-9           pbapply_1.7-2          gridExtra_2.3
[4] rlang_1.1.1            magrittr_2.0.3         RcppAnnoy_0.0.21
[7] matrixStats_1.0.0      ggridges_0.5.4         compiler_4.3.1
[10] spatstat.geom_3.2-4    png_0.1-8              vctrs_0.6.3
[13] reshape2_1.4.4         stringr_1.5.0          pkgconfig_2.0.3
[16] fastmap_1.1.1          ellipsis_0.3.2         labeling_0.4.2
[19] utf8_1.2.3             promises_<IP_ADDRESS>       purrr_1.0.1
[22] jsonlite_1.8.7         goftest_1.2-3          later_1.3.1
[25] spatstat.utils_3.0-3   irlba_<IP_ADDRESS>          parallel_4.3.1
[28] cluster_2.1.4          R6_2.5.1               ica_1.0-3
[31] stringi_1.7.12         RColorBrewer_1.1-3     spatstat.data_3.0-1
[34] reticulate_1.31        parallelly_1.36.0      lmtest_0.9-40
[37] scattermore_1.2        tensor_1.5             future.apply_1.11.0
[40] zoo_1.8-12             sctransform_0.3.5      httpuv_1.6.11
[43] Matrix_1.6-0           splines_4.3.1          igraph_1.5.1
[46] tidyselect_1.2.0       rstudioapi_0.15.0      abind_1.4-5
[49] spatstat.random_3.1-5  codetools_0.2-19       miniUI_<IP_ADDRESS>
[52] spatstat.explore_3.2-1 listenv_0.9.0          lattice_0.21-8
[55] tibble_3.2.1           plyr_1.8.8             withr_2.5.0
[58] shiny_1.7.5            ROCR_1.0-11            Rtsne_0.16
[61] future_1.33.0          survival_3.5-5         polyclip_1.10-4
[64] fitdistrplus_1.1-11    pillar_1.9.0           KernSmooth_2.23-22
[67] plotly_4.10.2          generics_0.1.3         ggplot2_3.4.3
[70] munsell_0.5.0          scales_1.2.1           globals_0.16.2
[73] xtable_1.8-4           glue_1.6.2             lazyeval_0.2.2
[76] tools_4.3.1            data.table_1.14.8      RANN_2.6.1
[79] leiden_0.4.3           cowplot_1.1.1          grid_4.3.1
[82] tidyr_1.3.0            colorspace_2.1-0       nlme_3.1-163
[85] patchwork_1.1.3        cli_3.6.1              spatstat.sparse_3.0-2
[88] fansi_1.0.4            viridisLite_0.4.2      dplyr_1.1.2
[91] uwot_0.1.16            gtable_0.3.3           digest_0.6.33
[94] progressr_0.14.0       ggrepel_0.9.3          farver_2.1.1
[97] htmlwidgets_1.6.2      htmltools_0.5.5        lifecycle_1.0.3
[100] httr_1.4.7             mime_0.12              MASS_7.3-60

  packageVersion("patchwork")

[1] ‘1.1.3’

  library(patchwork)

Interesting. Perhaps ggplot2 is missing, I didn't see it in your sessioninfo. For now, you should be able to run plots and it will plot the plots.
Can you perform library(ggplot2) and then try? or try patchwork::wrap_plots(plots = plots, ncol = 1)

Yes, it works by running this! Thanks!
library(ggplot2)

  patchwork::wrap_plots(plots = plots, ncol = 1)

Great!

Now, I have another issue:
etadat <-<EMAIL_ADDRESS>

    metadat$celltype <- metadat[c('celltype')] <- str_split_i(metadat$celltype.stim.donor, "_", -3)

    metadat$stim <- metadat[c('stim')] <- str_split_i(metadat$celltype.stim.donor, '_', -2)

    metadat$donor <- metadat[c('donor')] <- str_split_i(metadat$celltype.stim.donor, '_', -1)

<EMAIL_ADDRESS>= metadat

  }

Error in str_split_i(metadat$celltype.stim.donor, "_", -3) :
could not find function "str_split_i"

Tidyverse is not loaded in your current environment :)
install.packages("tidyverse")
library(tidyverse)

It should work now. str_split are functions which is a part of stringr, which itself is a part of tidyverse

Idents(combined_pbmc) <- "celltype.stim"
b.interferon.response.aggr <- FindMarkers(combined_pbmc, ident.1 = "B_STIM", ident.2 = "B_CTRL",
slot = 'data',
test.use = "DESeq2",
min.pct = 0.1,
latent.vars = c("donor"),
logfc.threshold = 0.5849, #~1.5FC
only.pos = TRUE,
verbose = FALSE)
Warning: 'latent.vars' is only used for the following tests: negbinom, poisson, MAST, LR
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
head(b.interferon.response.aggr, n = 15)
When I ran this script above, I got this error message below and I did not get the output table. Do you think if there is anything I need to concern?
Idents(combined_pbmc) <- "celltype.stim"

  b.interferon.response.aggr <- FindMarkers(combined_pbmc, ident.1 = "B_STIM", ident.2 = "B_CTRL",

                                            slot = 'data',

                                            test.use = "DESeq2",

                                            min.pct = 0.1,

                                            latent.vars = c("donor"),

                                            logfc.threshold = 0.5849, #~1.5FC

                                            only.pos = TRUE,

                                            verbose = FALSE)

Warning: 'latent.vars' is only used for the following tests: negbinom, poisson, MAST, LR
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

  Warning: 'latent.vars' is only used for the following tests: negbinom, poisson, MAST, LR

Error: unexpected symbol in "      Warning: 'latent.vars' is"

The warning comes when one cant use a latent variable with a certain test. so for example, since you are using test.use = "DESeq2", the warning comes up because you can only select negbinom, poisson, MAST, LR if you want to adjust for latent variables. Its a warning the test should still run. DEseq2 natively corrects for library size so it should be acceptable.

Congrats, you have found the 2nd hidden test!
If you see the original package loadings, you will NOT see one for a venn diagram, so whenever you get an issue that states: Error in: could not find function "" that means you 1) either haven't installed or 2) haven't loaded your package. So, to correct this you need to first install the package: ggvenn you can acheive this by running: install.packages("ggvenn") and then loading it by performing library(ggvenn)

Should I install all of the packages as listed below?
install.packages("grid")
Warning in install.packages :
package ‘grid’ is a base package, and should not be updated

  library(ggvenn)

Loading required package: dplyr
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag

The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union

Loading required package: grid
Loading required package: ggplot2

R is smart, it does that for you on its own. All you have to do is check that its loaded into your environment. via sessionInfo() or packageVersion("ggvenn")

I'm marking this issue as complete, if you have an issue either make a new post or reopen this one, thanks.


Refactor handling of package.json alias fields

This patch separates the concept of main entries in package.json files from the one of alias fields, as per Webpack's resolver.
For example, a "browser" entry can either be a main entry, or an alias field when used to ignore or replace specific files (source).
cc @ChadKillingsworth
I will provide a follow-up patch allowing the packageJsonAliasFields to be set from the command line.

@ChadKillingsworth
could you review this code, since I believe you're the most familiar with the issues involved?
Thanks.

Sure. I am at the Polymer Summit right now so it may be next week.

Just rebased this against current master

Any news on this?

Just rebased this against current master and fixed the conflicts after #2627
cc @ChadKillingsworth

Created internal issue b/122075783


Fix the flag parsing for integration tests in go 1.13

This fixes the errors when running e2e tests.
/cc mattmoor @chaodaiG @adrcunha
/hold
we need 1.13 on prow and what now, before this can go in,
but if you patch your vendor/pkg/test/e2e... with this you'll be able to run tests again.

We will need a better plan than Prow uses go1.13 before this PR, as which would break tests in serving

Is there no way to make support for Go 1.13 backwards compatible?  I think requiring Go 1.13 is asking a lot this quickly after the release.

We can to tricks like tag:go1.13 on the copy of the file and tag:go1.12 on the existing one.
Anyway, I am not suggesting this is merged in, but if you're blocked -- this will fix ya.

Take a look at https://github.com/knative/test-infra/issues/1329#issuecomment-527704893 and further comments. I think there are less breaking ways of fixing this.

I'm playing with it too, this should be backward compatible: [WIP]
https://github.com/knative/serving/pull/5397

As I said, the easiest way is to do this change and use conditional
compilation as we did in 1.11->1.12 for reverse proxy bug. When we decide
to go full on 1.13, the old file simply is removed and the condition is
stripped.
But up to you. 5397 https://github.com/knative/serving/pull/5397 seems
much more involved and adds test main to every test.
On Wed, Sep 4, 2019 at 2:53 PM chaodaiG<EMAIL_ADDRESS>wrote:

I'm playing with it too, this should be backward compatible: [WIP]
knative/serving#5397 https://github.com/knative/serving/pull/5397
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@vagababov I assume the problem pre-1.13 is that the function doesn't exist in testing?  If so, let's wrap it in a thunk that does nothing in 1.12- and does this in 1.13+.  That seems simple and unblocks things without a ton of collateral.

Seems like simply delete the flag.Parse() also solved the problem: https://github.com/knative/serving/pull/5398
It works as testing.Init() is called in go1.13 as documented in release note: https://golang.org/doc/go1.13#testing.
However it's not clear to me why it also works in go1.12.
On the other hand, I also like the idea of thunk testing.Init() as it's more explicit and easier to understand

Sure. You want me to take care of this or @chaodaiG  will drive it through?

I already tested this change in serving and it works with go1.13: https://github.com/knative/serving/pull/5396
So it should be just a couple lines of change on your PR, I would suggest just update in this PR

SG

/assign mattmoor @chaodaiG

@chaodaiG -- do you know why the build test tried to build 1.13 file?

So my mac with 1.12 and my linux with 1.13 build this nicely.
Do we collect all the tags and then try to build with them?

yep we do collect all tags and build them

Well this ain't gonna work then :-)

:( let me play with it a little bit

Just took a look at the logic of tags collecting and building, I don't think there is a good way of making this work.
Link: https://github.com/knative/test-infra/blob/cfee08011fea83b3a3b4fc0d3dfe436789a1ac24/scripts/presubmit-tests.sh#L172

Well, unless we switch to 1.13 to build on prow :-)

Or figure out why deleting flag.Parse in serving works for go1.12 as in this PR: https://github.com/knative/serving/pull/5398
:)

It delays the flag parsing, I presume until later point. But this means
that we rely on things executing in some particular order.
On Thu, Sep 5, 2019 at 11:24 AM chaodaiG<EMAIL_ADDRESS>wrote:

Or figure out why deleting flag.Parse in serving works for go1.12 as in
this PR: knative/serving#5398
https://github.com/knative/serving/pull/5398
:)
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I think I figured it out why it works in go1.12. The execution order is:
initializeServingFlags -> testing.M.Run (where flag.Parse is invoked implicitly) -> Running each individual test
This order seems fine with me, WDYK? @vagababov @mattmoor @adrcunha
Context: deleting flag.Parse() from serving/test/e2e_flags.go seems working with both go1.12 and go1.13, in the latter it's done via testing.Init(). And the prove for it working with go1.12 is in this PR: https://github.com/knative/serving/pull/5398

Works for me :-)
On Thu, Sep 5, 2019 at 12:19 PM chaodaiG<EMAIL_ADDRESS>wrote:

I think I figured it out why it works in go1.12. The execution order is:
initializeServingFlags
https://github.com/knative/serving/blob/d2bf8fd8fb9d290f84530cbb88bb98fcef633bd0/test/e2e_flags.go#L53
-> testing.M.Run (where flag.Parse is invoked implicitly)
https://go.googlesource.com/go/+/refs/tags/go1.12.9/src/testing/testing.go#1043
-> Running each individual test
This order seems fine with me, WDYK? @vagababov
https://github.com/vagababov @mattmoor https://github.com/mattmoor
@adrcunha https://github.com/adrcunha
Context: deleting flag.Parse()
https://github.com/knative/serving/blob/d2bf8fd8fb9d290f84530cbb88bb98fcef633bd0/test/e2e_flags.go#L66
from serving/test/e2e_flags.go seems working with both go1.12 and go1.13,
in the latter it's done via testing.Init(). And the prove for it working
with go1.12 is in this PR: knative/serving#5398
https://github.com/knative/serving/pull/5398
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cool, I have cleaned up the PR and updated description, it's now ready for review

I think this PR can be closed since https://github.com/knative/serving/pull/5398 is merged

/close
On Mon, Sep 9, 2019 at 7:56 AM chaodaiG<EMAIL_ADDRESS>wrote:

I think this PR can be closed since knative/serving#5398
https://github.com/knative/serving/pull/5398 is merged
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test: clean-up

Coverage remained the same at 100.0% when pulling 06b8ce682f64b50aa0ac4df7fcdd55490134888f on clean-up into 0577e185a1c9192ae95fb33d08aba835a07ac47f on main.

:tada: This PR is included in version 1.3.2 :tada:
The release is available on:

GitHub release
npm package (@latest dist-tag)

Your semantic-release bot :package::rocket:


When a RedCall user is disabled, he still appears in the list of users, which is confusing for other users

When a RedCall user is disabled (Utilisateur autorisé unchecked),
he still appears in the list of users (with the RedCall icon next to his name), which is confusing for other users.
What's the difference between a disabled user and a deleted user ?

I don't really get the question.

a disabled volunteer is deleted from pegass
a non-triggerable volunteer don't want to be triggered
there are no deleted volunteers, only anonymized ones

talking about users, not volunteers.
What are the difference betweend the 3rd and last option
[image: image.png]
On Wed, Feb 3, 2021 at 9:20 PM Alain Tiemblo<EMAIL_ADDRESS>wrote:

I don't really get the question.

a disabled volunteer is deleted from pegass
a non-triggerable volunteer don't want to be triggered
there are no deleted volunteers, only anonymized ones

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Plugin config in yaml file not under - plugins entry

First at all I like to thank you to revive hbmqtt!
My aim is to build a well performing mqtt <-> timescaleDB gateway utilizing hbmqtt (and now amqtt).
I tried the persistence plugin. It is working, but the configuration is not nested correctly under the section -plugins:.
The plugin itself complains when the persistence information is not on top level.
(mqtt-broker-1iWrHb9Y-py3.7) pi@data:~/workspace/mqtt_broker $ hbmqtt -c broker.yaml -d
[2021-03-14 17:35:36,692] :: DEBUG - Using selector: EpollSelector
[2021-03-14 17:35:36,695] :: DEBUG - Loading plugins for namespace hbmqtt.broker.plugins
[2021-03-14 17:35:36,699] :: DEBUG -  Loading plugin persistence = hbmqtt.plugins.persistence:SQLitePlugin
[2021-03-14 17:35:36,790] :: DEBUG -  Initializing plugin persistence = hbmqtt.plugins.persistence:SQLitePlugin
[2021-03-14 17:35:36,790] :: WARNING - 'persistence' section not found in context configuration

Putting it on top level yields the correct behavior:
listeners:
  default:
    type: tcp
    bind: <IP_ADDRESS>:1883
sys_interval: 20
auth:
  allow-anonymous: true
plugins:
  - auth_file
  - auth_anonymous

persistence:
  file : 'db.sqlite'

topic-check:
  enabled: False

(mqtt-broker-1iWrHb9Y-py3.7) pi@data:~/workspace/mqtt_broker $ hbmqtt -c broker.yaml -d
[2021-03-14 17:36:16,903] :: DEBUG - Using selector: EpollSelector
[2021-03-14 17:36:16,906] :: DEBUG - Loading plugins for namespace hbmqtt.broker.plugins
[2021-03-14 17:36:16,910] :: DEBUG -  Loading plugin persistence = hbmqtt.plugins.persistence:SQLitePlugin
[2021-03-14 17:36:16,987] :: DEBUG -  Initializing plugin persistence = hbmqtt.plugins.persistence:SQLitePlugin
[2021-03-14 17:36:16,998] :: INFO - Database file 'db.sqlite' opened

I will have a look at the plugin manager and the persistance plugin code and try to come up with a fix.
Cheers
Volker

I think there are two things to consider here:

The plugin should have access to the config file in whole
The plugins should be located in a certain section to give the config more structure

As far as I can see each plugin decides by itself where it expect its config.
So the easiest solution seems to me that each plugin defines itself a property lets call it 'self.plugin_config' which points to
config['plugins']['plugin name'] and work with it to access its specific config.
ATM this behavior is partly in place. E.G:

Persistance:
            self.persistence_config = self.context.config['persistence']
Auth:

class BaseAuthPlugin:

def __init__(self, context):
    self.context = context
    try:
        self.auth_config = self.context.config['auth']

Naming the config self.<plugin_name>_config is IMHO quite redundant. I would advice to homogenize this across all plugins to a more generic property 'self.config' since it makes it easier to e.g. print all the utilized config parts. The top level config is already available via 'self.context.config' and does IMHO not need a on property on the plugin instance.

The homogenization could be made by introducing a base class for all plugins:

PluginBase():
config_path = 'plugins'   # e.g. for persistence  'plugins.persistence'
def __init__(self, context):
      ...
      self.init_config(context)
      ...

def init_config(self, context):
       temp_config = context.config
       for path_part in self.config_path.split('.'):
              temp_config = temp_config[path_part]
       self.config = temp_config

Having a base class for plugins lowers the barrier for contributors to write plugins and also prevents wild growth.

Cheers,
Volker

Hi Volker,
thank you for your insight. I do like the idea to homogenize the plugin configs.
One thing we need to consider is to not break existing plugins - at least not in the next few releases as we aim to stay compatible with hbmqtt.
PS Is your mqtt <-> timescale gateway open source?

Hi Volker,
thank you for your insight. I do like the idea to homogenize the plugin configs.
One thing we need to consider is to not break existing plugins - at least not in the next few releases as we aim to stay compatible with hbmqtt.

The changes I had in mind are not intended to break the plugin behavior. I will change the existing plugins by refactoring, keeping the API totally intact.
On the other hand ATM the documentation and the reality of the config file processing does not match.
So in any case here is some work to do. I would opt for implementing the behavior as it is already documented - which is IMHO a bugfix - so nobody can complain.
I will base my timescaledb plugin on a BasePlugin as a prove of concept. Also I recently programmed a DBBase class as an abstract DBAPI for other DB plugins.
class BaseDB():
    """
    Base API to the data base
    """

    def init_db(self):
        """
        Initialize the DB
        """

    def create_session_table(self):
        """
        Creates the session table
        """

    async def save_session(self, session):
        """
        Persist the session
        :param session: The current session
        """

    async def find_session(self, client_id):
        """
        Retrieve a session by client ID
        :param client_id:
        :returns The session
        """

    async def del_session(self, client_id):
        """
        Delete a session by ClientID
        :param client_id:
        """

    async def on_broker_post_shutdown(self):
        """
        Shutdown the database if broker has shut down
        """

This BaseDB will be utilized to support the SQLalchemy (for all DBs) interface and as an addition timescaleDB which needs some additional quirks (Hypertables an such).

PS Is your mqtt <-> timescale gateway open source?
Absolutely. I am currently at the beginning but probably I will have a first push today on GH.

My company does 90% Open Source software. If a customer likes to have closed source he pays triple the price of open source. This is quite educational :-). And it is also only fair since all projects utilize open source software.
Cheers,
Volker


Any plans for the bounding box regression with KL Loss?

Any plans for the bounding box regression with KL Loss? https://arxiv.org/abs/1809.08545

Hello， this issue has been solved yet?
@hellock

Not in our recent plan, but any PR would be appreciated


How do you get the rocket button in your discord server?

nobody else is talking about it but some discord servers have the button

About 5% of servers have the rocket button. Other servers need to use the bot to use activities.


Visual Diff Flake

Try to address the visual-diff flake with the mobile dropdown in nested dialog tests

Ran this 5 times and the mobile dropdown dialog tests didn't fail, but it wouldn't be the first time they've tricked me like that.  Hopefully this helps!


Unable to see Orphanet Disease Title

As you know, the output of Intervar.py contains two columns related with Orhphanet:

OrphaNumber: Contains the Orpha IDs which are related with the gene of interest.
Orpha: Contains detailed information about the Orphanet record such as synonyms, prevalence etc.

However, none of these columns contains exact title of the disorder. For example for the SNP with Orpha ID#319646, the Orpha column looks like that:
"319646|CDG syndrome type It
CDG-It
CDG1T|<1 / 1 000 000|Autosomal recessive|Neonatal
Infancy|614921 ~"
and the OrphaNumber column is:
319646;
The names seen in record (CDG syndrome type It) is a synonym of actual disorder which is PGM1-CDG. How can I extract the real disorder name with using Intervar instead of synonyms?

When I built the database, these are all the information. For your mentioned exact or full title, I did not have it. And you have the orphaID, you can get the complete information from Orpha website.

Thank you for the reply. As you said, I updated the intervardb/orpha.txt file and replaced synonyms with full title. I'm sharing the file: orpha_updated.txt

Thank you!
On Tue, Jun 19, 2018 at 4:33 PM, Can Holyavkin<EMAIL_ADDRESS>wrote:

Thank you for the reply. As you said, I updated the intervardb/orpha.txt
file and replaced synonyms with full title. I'm sharing the file:
orpha_updated.txt
https://github.com/WGLab/InterVar/files/2116805/orpha_updated.txt
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Thanks!  I will update it!


Feature: Un-fix top-nav on mobile

Type of feature
🎨 Style
Current behavior
The top navbar is currently fixed to the top on mobile.

Suggested solution
We should make the top navbar scroll with the rest of the page instead of keeping it fixed.
Why?

it's taking up a lot of unnecessary vertical space, which on mobile is very limited
none of our pages have a height high enough that scrolling back to the top would be tiresome (not even when showing the max amount of rows on the table, or having them all be expanded)
most navigation can be done through the sidebar anyways, and the lapel would still remain fixed and visible

⚠ Note: We want this change to only apply to mobile screens, so screens smaller than the sm breakpoint ⚠
Intended result

Additional context
No response
Code of Conduct

[X] I agree to follow this project's Code of Conduct

Contributing Docs

[X] I agree to follow this project's Contribution Docs

Just wondering if from a UX perspective if users would mind their settings/avatar disappearing on scroll.

.take


Invoking scriptorium make fails.

When trying out the new Python system, running the following on a properly configured paper directory bombs out:
scriptorium make papers/thesis/main
The error produced indicates a failure to import a module.
Traceback (most recent call last):
  File "/usr/local/bin/scriptorium", line 11, in <module>
    load_entry_point('scriptorium==2.0.0', 'console_scripts', 'scriptorium')()
  File "/home/hakujin/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 565,
 in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/hakujin/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2598,
 in load_entry_point
    return ep.load()
  File "/home/hakujin/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2258,
 in load
    return self.resolve()
  File "/home/hakujin/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2264,
 in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
ImportError: No module named main

As far as I know, all python dependencies are satisfied at this point.

For reference, the command was invoked at the root of the scriptorium directory, in case that messes with the path logic.

Try the latest version of the branch, I think this is fixed now

After running setup.py again, everything worked like a charm. Good stuff


Compilation error

Hi! I am trying to use your lib in my project, but it won't compile:
   Compiling android_logger v0.11.1
error: type parameters must be declared prior to const parameters
   --> /home/caiiiycuk/.cargo/registry/src/github.com-1ecc6299db9ec823/android_logger-0.11.1/src/lib.rs:437:33
    |
437 | fn uninit_array<const N: usize, T>() -> [MaybeUninit<T>; N] {
    |                -----------------^- help: reorder the parameters: lifetimes, then types, then consts: <T, const N: usize>

@Nilstrieb Help

Earlier this year we changed it so that the order of generic parameters doesn't matter anymore. Previously, const generics had to come last. To fix the issue, update your compiler.
@Nercury In case you want to support these older compilers, you can just swap the order of the generics in the helper function.

Thanks for explanation. No we don't have hands available to support and test old compilers. It's always possible to use older crate version.


document --json in the book

#295 added the --json flag but it has not been documented in the book yet. It would be good to put it under the printers section

and note that it can be used to change the format of the logs as asked in knurling-rs/defmt#664

--json flag documented in  https://github.com/knurling-rs/defmt/pull/669 (updated page json output)

Merged and closed.


fix #2066 - wrong trivial accessor correction with instance_eval

The commit message should follow the project's style and refer the issue report. You also need to add a changelog entry.

@bbatsov I'm sorry that I didn't follow the pull request convention, I will modify the message and add changelog entry.


ModuleNotFoundError: No module named 'bark'

Any fix for this? I'm getting this issue in all notebooks.

looks like bark isn't found. did you install it correctly?

Nope, sorry about that.


We have tried to register a center with VBCR.lic file. but we got a error.

In center management section after click "Add new Center", we uploads VBCR.lic file(which is provided in root directory of source code), after that a new row comes in "center management" table with value Expires On=02-23-2031(3073), Code=VBCR019, Name=iMediXcare Hospital. After Clicking its edit button a error comes, that is "ERROR YOU ARE NOT AUTHORIZED TO ACCESS FORWARD", we needs to register few centers in our system, Please help us to solve this issue.

Kindly update the UserAccessControl.json file located at iMediXCare/iMediXcare/WEB-INF/classes/.


CallExpression assignments should be inlined when their variable is only used once.

Input:
function foo() {
  var a = b();
  a.c();
}

Output:
function foo(){var c=b();c.c()}

Expected Output:
function foo(){b().c()}

(Part of a series of issues that affect the optimal minification of twbs/bootstrap.)

Looks like uglify doesn't do this either?

Uglify doesn't. Closure does.

There is some discussion here about replacing side-effecty things. #221

$ echo 'function foo() { var a = b(); a.c(); }' | uglifyjs -m -c collapse_vars
WARN: Replacing variable a [-:1,30]
function foo(){b().c()}


Rereview project dependencies in solution

Provide a description of the new feature / enhancement
Recently i've tried to a normal build / F5 run a project via runner or the hosting app and just didn't run what was expected due to not doing a full rebuild.
We should valid someone can do a solid F5 and just run these.  This goes for tests as well.

Runner

-> Modules

->  Dependencies (example a plugin)

As far as I know, F5 doesn't trigger a rebuild, just a build of what has been modified, but it won't force to rebuild all the dependencies.

example here are PT Run plugins.  If i tweak something in PT Run plugin and just F5 with the runner set as default, the runner should see that change

Ah OK, so the ask is to have the Runner build equivalent to the solution build.
It has some pros and cons, it depends on what is the most frequent usage. Personally I always to a full clean build and after that I only build what I change and it would be annoying to have the runner check all 80+ projects every time.

No. My ask is projects need to appropriate build. I've caught in PT run a few instances where a plugin does not a dependent of Run which then when I tweaked something, it wasn't being reflected
This is to be sure our utilities are set up correctly, our tests are and the runner is as well.
Runner should only care about the utilities themselves. Those utilities bubble to their stuff
This way F5 works on the children as well as the runner.
This may primarily be a PT run issue.

I think the same issue applies to projects that are executables(e.g. KeboardManagerEngine, PowerLauncher...). Ideally, they should build if F5 is pressed as well.


move GeneralizeNamedOp pass

moves SPRIVGeneralizeNamedOp Pass to Common/GPU
Use it in LLVMGPU Pipeline

merged upstream and rebased


Create user

The application is orchestrating things in a way that I don’t think is optimum but to simplify things and answer what I think the original question is about, the change in this commit may be reasonable.
What I think is at least part of the original question is how can a plugin create an instance of a class that it can’t know about at compile time.  For example, how can a plugin create an instance of a class that is provided by the containing application.  In order to do that, somehow the plugin needs to be able to discover at runtime which class to create an instance of.  There are a number of ways this can be done.  This commit involves introducing support for the application to provide the name of a class in the configuration and the plugin can retrieve that value and use it.
This commit leaves out reasonable error handling as that would only complicate the discussion.   This code assumes that the appropriate property is defined in application.yml.

" I don’t think is optimum "... the goal is definitely not to make a suboptimal design work in spite of the fact that it's wrong.  The goal is to have a good design based on strategies that are generally useful for Grails plugins.
I would not have expected to use:
myapp:
   securityDomainClass: 'com.example.BookstoreUser'

but it's simple enough and easy to follow.
The createAndSaveUser() method is straightforward to call, so this looks like a good strategy to me.


Pass a destination buffer for HID comms

Description
This PR removes the forced usage of G_io_apdu_buffer for HID communication and allows passing manually a different destination buffer.
This behaviour is only active if HAVE_LOCAL_APDU_BUFFER is defined, which is only the case for the Rust SDK at the moment. Merging this PR would allow this Rust SDK to have ledger-secure-sdk as a submodule instead of manually upgrading the necessary files when upgrading OS versions.
Changes include

[x] New feature (non-breaking change that adds functionality)

@yhql j'imagine que tu as testé sur des apps non rust? :innocent:

@cbouvet-ledger oui, avec l'app btc.

@yhql this is breaking the build of two apps, is it expected?
https://github.com/LedgerHQ/ledger-secure-sdk/actions/runs/4617218814/jobs/8163224070?pr=188
https://github.com/LedgerHQ/ledger-secure-sdk/actions/runs/4617218814/jobs/8163225995?pr=188

@yhql this is breaking the build of two apps, is it expected? https://github.com/LedgerHQ/ledger-secure-sdk/actions/runs/4617218814/jobs/8163224070?pr=188 https://github.com/LedgerHQ/ledger-secure-sdk/actions/runs/4617218814/jobs/8163225995?pr=188

No, I 'll update the corresponding ccid prototype


[dlib] build failure on Windows

Operating system
Windows 11
Compiler
Microsoft Visual Studio Enterprise 2022 (64-bit) - Current Version 17.6.5
Steps to reproduce the behavior
`./vcpkg install dlib`

Failure logs
1>------ Build started: Project: mlp_ex, Configuration: Debug x64 ------
1>mlp_ex.cpp
1>LINK : fatal error LNK1104: cannot open file 'C:\Program Files (x86)\Intel\oneAPI\mkl\2021.1.1\lib\intel64\mkl_intel_lp64.lib'
1>Done building project "mlp_ex.vcxproj" -- FAILED.
Additional context
It worked previously. It seems Intel oneAPI is now expected. Within the Visual Studio project generated by CMake, a number of explicit non-existent paths are found:
C:\Program Files (x86)\Intel\oneAPI\mkl\2021.1.1\lib\intel64\mkl_intel_lp64.lib
C:\Program Files (x86)\Intel\oneAPI\mkl\2021.1.1\lib\intel64\mkl_core.lib
C:\Program Files (x86)\Intel\oneAPI\mkl\2021.1.1\lib\intel64\mkl_intel_thread.lib
C:\Program Files (x86)\Intel\oneAPI\compiler\2021.1.1\windows\compiler\lib\intel64_win\libiomp5md.lib

Here is the CMakeLists.txt file contents:
cmake_minimum_required(VERSION 3.7)

set(VCPKG_CMAKE "C:/vcpkg/scripts/buildsystems/vcpkg.cmake")
set(CMAKE_TOOLCHAIN_FILE ${VCPKG_CMAKE})

set(n mlp_ex)
project(${n})

add_executable(${n} ${n}.cpp)

find_package(dlib REQUIRED)

target_link_libraries(${n} dlib::dlib)
set_property(DIRECTORY PROPERTY VS_STARTUP_PROJECT ${n})

Srry I can't repro your issue.
G:\test_manifest\build>cmake ..
-- Building for: Visual Studio 17 2022
-- Selecting Windows SDK version 10.0.22621.0 to target Windows 10.0.19045.
-- The CXX compiler identification is MSVC 19.39.33522.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: C:/Program Files/Microsoft Visual Studio/2022/Enterprise/VC/Tools/MSVC/14.39.33519/bin/Hostx64/x64/cl.exe - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done (3.6s)
-- Generating done (0.0s)
CMake Warning (dev) in CMakeLists.txt:
  Directory property VS_STARTUP_PROJECT specifies target 'test_manifest' that
  does not exist.  Ignoring.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Build files have been written to: G:/test_manifest/build

G:\test_manifest\build>
G:\test_manifest\build>
G:\test_manifest\build>
G:\test_manifest\build>
G:\test_manifest\build>cmake --build .
MSBuild version 17.9.5+33de0b227 for .NET Framework

  1>Checking Build System
  Building Custom Rule G:/test_manifest/CMakeLists.txt
  main.cpp
  main.vcxproj -> G:\test_manifest\build\Debug\main.exe
  Building Custom Rule G:/test_manifest/CMakeLists.txt

main.cpp

#include <iostream>
#include "dlib/config.h"
using namespace std;
int main()
{
cout << "Hello CMake." << endl;
return 0;
}

CMakeLists.txt

cmake_minimum_required(VERSION 3.8)
set(CMAKE_TOOLCHAIN_FILE "G:/vcpkg/scripts/buildsystems/vcpkg.cmake")
project(test_manifest CXX)
add_executable(main main.cpp)
find_package(dlib CONFIG REQUIRED)
target_link_libraries(main PRIVATE dlib::dlib)
set_property(DIRECTORY PROPERTY VS_STARTUP_PROJECT test_manifest)

PS G:\vcpkg> ./vcpkg version
vcpkg package management program version 2024-03-14-7d353e869753e5609a1f1a057df3db8fd356e49d

See LICENSE.txt for license information.

Please confirm your current vcpkg version and try the following commands:
./vcpkg remove dlib lapack lapack-reference --recurse
./vcpkg install dlib

That is a problem which happens if MKL is installed but blas/lapack is not explicitly controlled. Try rebuilding with https://github.com/microsoft/vcpkg/pull/38100

We haven't been able to repro this; if more information comes up, or this issue appears again, please reopen.


fix logic to do cgm-loop stuff for g4-upload, not g4-local

@scottleibrand +1 on this one. I couldn't get my cgm loop uploading without a similar fix.  Can you merge this to dev and adj-target-when-high branch?

Done.


Enable dependency paths and native-lib paths work across Operating Systems

Purpose

To fix three test cases that were failing on Windows due to the issue in the toml parser.

Fixes
#21638,
#20933,
#20044
Approach

Describe how you are implementing the solutions along with the design details.

Samples

Provide high-level details about the samples related to this feature.

Remarks

List any other known issues, related PRs, TODO items, or any other notes related to the PR.

Check List

[ ] Read the Contributing Guide
[ ] Updated Change Log
[ ] Checked Tooling Support (#)
[ ] Added necessary tests

[ ] Unit Tests
[ ] Spec Conformance Tests
[ ] Integration Tests
[ ] Ballerina By Example Tests

[ ] Increased Test Coverage
[ ] Added necessary documentation

[ ] API documentation
[ ] Module documentation in Module.md files
[ ] Ballerina By Examples

Codecov Report

Merging #22742 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master   #22742   +/-   ##
=======================================
  Coverage   14.59%   14.59%
=======================================
  Files          51       51
  Lines        1411     1411
  Branches      219      219
=======================================
  Hits          206      206
  Misses       1189     1189
  Partials       16       16

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[dev] Needs more granular error handling

🐛 Bug Report

Environment
OSX 10.14.6
Node v12.15.0
Wrangler 1.8.4
Steps to reproduce
Using Workers sites, if you accidentally run wrangler dev before building your project (i.e. the bucket directory doesn't exist), Wrangler returns an unhelpful error message.  Downgrading Wrangler to 1.8.0 returned a helpful error message about the missing ./public bucket that allowed me to fix the problem.  It appears the new Could not upload your script error is clobbering more actionable errors from previous versions.
What did you expect to see?
An error message about the missing bucket.
What did you see instead?
✨  Built successfully, built project size is 491 KiB.
🌀  Using namespace for Workers Site "__blog-workers_sites_assets_preview"
Error: Could not upload your script. Check your internet connection or https://www.cloudflarestatus.com/ for rare incidents impacting the Cloudflare Workers API.

this is closed by #1251, thanks @mpint


[WIP] Add manual installation guide

Hmm, how should we do this? Alamofire has a great explanation on how to add their project as a git submodule, which are roughly the same steps needed for Result and Moya.
I don't think I've captured that the best I could; I'd love some feedback on how to make it better!
Fixes #780

@jaymutzafi: please check if this works for you, and let me know if you have any questions / improvements!

Do the same for Moya is a little sparse, what if we tried to copy more of Alamofire's docs?
almost exactly all of this, tweaked to work for Moya

Was considering that. And then make it "compatible" with all three frameworks?

          1 Warning

:warning:
PR is classed as Work in Progress

  Generated by :no_entry_sign: danger

Current coverage is 83.29% (diff: 100%)

Merging #833 into master will not change coverage

@@             master       #833   diff @@
==========================================
  Files            34         34
  Lines          2771       2771
  Methods           0          0
  Messages          0          0
  Branches          0          0
==========================================
  Hits           2308       2308
  Misses          463        463
  Partials          0          0

Powered by Codecov. Last update 8b1dc46...c2fbb73

@BasThomas that sounds good to me!

Updated them. If someone could try this and provide feedback, that'd be awesome!

Awesome!


Text under 'Optional Steps' regarding Jupyter Notebook not visible.

Can you send the link to the page?

Sure,
https://github.com/reshamas/fastai_deeplearn_part1/blob/master/tools/paperspace.md

This is what I see. Is it not the same for you?  What browser are you using?

Maybe this is what you meant:
"I was looking at the paperspace setup file and cannot read the text in Step 6 of Optional Steps at the end."
Is this what you mean?  I would try some different browsers.
https://github.com/reshamas/fastai_deeplearn_part1/blob/master/tools/paperspace.md#step-6-start-jupyter-notebook--after-logging-into-paperspace-computer-via-ssh-from-your-local-computer

Ah, I see. My mistake, I was confused by the heading sizes under Optional Steps. I didn't realise that "Setup: Simplifying Logging in to Paperspace " was a subheading under "Skip Password and Updating IP Address...".
It was all a misunderstanding, apologies.


Arrays with minimum sizes and tuples are not preserved by Array.map

Bug Report

🔎 Search Terms
Array size, map, tuple

🕗 Version & Regression Information
tsc --version #Version 4.2.4

Most likely this bug has been in TS for a long time

This is the behavior in every version I tried, and I reviewed the FAQ for entries about arrays

⏯ Playground Link

Playground link with relevant code
💻 Code

type Input = [number, ...number[]];

const test = (inp: Input): Input => inp.map( i => i+1 );

With a Tuple:
type Tuple = [number, number]

const run = (input: Tuple): Tuple => input.map(i => i);

🙁 Actual behavior
TS gives an error, saying that number[] is not the same as [number, ...number[]];. In older versions the message says that key 0 is missing, which is basically the same.

🙂 Expected behavior
No errors
And something like this should also work:
type Input = [number, ...number[]];
type Output = [string, ...string[]];

const test = (inp: Input): Output => inp.map( i => i.toString() );

Duplicate of https://github.com/microsoft/TypeScript/issues/29841
My search terms were Array map tuple


Add files via upload

java and Angular side code for given task

java and angular code

java and angular code


Use late static binding on JWTUser

use late static binding on JWTUser so I as a developer can extend this class (createFromPayload can now return instance of class extending this class)
https://www.php.net/manual/en/language.oop5.late-static-bindings.php

Good catch, thanks @kaznovac.


feat: add technology labels to templates

The purpose of this pull request is to address the fact that we currently have templates that are not supported by Kubernetes. We need to find a way to inform users which templates are compatible with which technology.

Codecov Report
Base: 17.55% // Head: 17.56% // Increases project coverage by +0.00% :tada:

Coverage data is based on head (fc7c394) compared to base (5c58259).
Patch coverage: 0.00% of modified lines in pull request are covered.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more
Additional details and impacted files
@@           Coverage Diff            @@
##           develop     #472   +/-   ##
========================================
  Coverage    17.55%   17.56%
========================================
  Files           57       57
  Lines         6089     6087    -2
========================================
  Hits          1069     1069
+ Misses        4938     4936    -2
  Partials        82       82

Impacted Files
Coverage Δ

golang/internal/mapper/grpc.go
69.04% <0.00%> (+0.36%)
:arrow_up:

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Helm updrade from 1.0.4 to 1.1.snapshot.5 fails

Describe the bug
When upgrading from 1.0.4 to 1.1.0.snapshot 5, we encountered this error:
Error: UPGRADE FAILED: Service "istio-egressgateway" is invalid: [spec.ports[0].nodePort: Forbidden: may not be used when `type` is 'ClusterIP', spec.ports[1].nodePort: Forbidden: may not be used when `type` is 'ClusterIP']

This is the helm history:
REVISION        UPDATED                         STATUS          CHART           DESCRIPTION
1               Wed Jan 30 04:55:52 2019        DEPLOYED        istio-1.0.4     Install complete
2               Wed Jan 30 04:57:46 2019        FAILED          istio-1.1.0     Upgrade "istio" failed: Service "istio-egressgateway" is ...

Expected behavior
The upgrade should be successful
Steps to reproduce the bug
Install istio 1.0.4 using Helm and Tiller. And then run
helm upgrade istio istio-1.1.0-snapshot.5/install/kubernetes/helm/istio --namespace istio-system
Version
k8s version:
Client Version: version.Info{Major:"1", Minor:"11", GitVersion:"v1.11.1", GitCommit:"b1b29978270dc22fecc592ac55d903350454310a", GitTreeState:"clean", BuildDate:"2018-07-17T18:53:20Z", GoVersion:"go1.10.3", Compiler:"gc", Platform:"linux/amd64"}
Server Version: version.Info{Major:"1", Minor:"11", GitVersion:"v1.11.1", GitCommit:"b1b29978270dc22fecc592ac55d903350454310a", GitTreeState:"clean", BuildDate:"2018-07-17T18:43:26Z", GoVersion:"go1.10.3", Compiler:"gc", Platform:"linux/amd64"}

Installation
Using Helm and Tiller
Environment
Baremetal, kernel: 4.4.110-1.el7.elrepo.x86_64

@ostromart can you take a stab at this?  or failfast and tell me to find someone else?

Yes, I'll take it.

I tried to repro but it works for me when starting from a clean slate.
I need some more info to see what's happening in your case:
helm repo list
kc get deployment istio-egressgateway -o yaml
kc get service istio-egressgateway -o yaml
What options do you pass to helm install (if any)?

These are two similar issues.
https://github.com/istio/istio/issues/11865
https://github.com/istio/istio/issues/11868

Since there's no update, I'm going to make a guess that this was due to a missing helm repo.
I verified that 1.0.4->1.1.0-rc.0 works.
@iandyh if you want to try it again, could you try with rc0 and the new & improved upgrade instructions on preliminary.istio.io? Make sure you have the correct helm repo installed.
If you hit a problem, please open a new bug.

@ostromart Sorry for the inactivity. Was busy with checking other issues...
I believe this is due to a invalid configuration in my local and I'll keep an eye on this.


Corrected description of Deno benefits and added link to hosting section

Let's wait for @roj1512 to decide if it's ready. If he has comments, it'd be too early to translate

@KnorpelSenf That is, labels for such PRs are added only after agreement? OK, I'll know.

@KnorpelSenf That is, labels for such PRs are added only after agreement? OK, I'll know.

Yep :)

Only ready for translation actually. You can add 🇺🇦 yourself as soon as some Ukrainian translation is completed. If something isn't translatable, you can also add this label yourself.

Added a new commit. Did I do the right thing about the commit?

Yes, thanks. My comment was just late. @roj1512 will approve soon and then translation can happen.

https://github.com/grammyjs/website/pull/641

https://github.com/grammyjs/website/pull/646


ci: add specfic image-type for aarch64

default image-type(aka clearlinux) couldn't work in aarch64, so we add specifc image-type to avoid jenkins set-up failure.
Fixes: #461
Signed-off-by: Penny Zheng<EMAIL_ADDRESS>Signed-off-by: Jianyong Wu<EMAIL_ADDRESS>

lgtm, I think would be nice to follow image-type-x86_64 to follow the same conversion. But that can be done in a follow up PR because will need to modify CI scripts as well.

ptal 😊@jodh-intel @jcvenegas

@jodh-intel will be off for 2 weeks, let's merge this without waiting for his feedback here.

\o/ - nice! ;)

@egernst clearly not a breaking change, but not a bug fix either. Should we backport it?


Parser support library

This PR provides parser support for the library keyword. Runtime support will need to be implemented at a later time (tracked by #217)
Fixes #174

@sjbarag I just got this branch up-to-date from master

Thanks for keeping this up to date and dealing with my absence over the past few months, @TwitchBronBron!

@sjbarag this is ready for your review again.


Pay with Amazon button triggers Adobe Flash plugin

Our checkout process has been requiring Adobe Flash, which triggers a browser warning if a customer's Flash plugin is out-of-date. After further investigation, I found that the code associated with the "Pay with Amazon" button is triggering the plugin.
Here's an example on one of our sites: http://www.united-states-flag.com/checkout/cart/
To demonstrate this button as the cause, paste the code below in an empty .html file and replace the [SELLER_ID] with your own. This code was generated by the Magento Amazon Payments plugin:

If you open up this code in FireFox, you should see the plugin icon appear next to the url. Or, if your Flash player is out-of-date, you'll see a warning.
Is it possible to generate the Pay with Amazon button without using the Flash plugin so that flash does not appear during our checkout process?

Where is the plugin icon you are referring to? I don't see it on your site or on my test site. The plug-in does not use Flash.

I am non-repro with the above code sample. The image renders as expected.

in Firefox.

@cdietzols is there some toolbar or other firefox plugin causing this in your browser? can you try a different browser?

@dbrent-amazon  @ngrices  thank you both for the quick replies.
To be more specific, there's an icon that appears next to the globe when running a page with flash:

Further, if someone is running an out-of-date version, the icon becomes red and a message is displayed:

The button rendering and functionality works fine in all cases. If flash is disabled, it continues to work fine. Our concern is regarding the flash messages--we would not want a customer to become distracted or turn away from checkout because of the warning messages.
In the code, the line with "OffAmazonPayments.Button()" triggers the plugin. If I comment that line only, the icon disappears.
We ran some further tests this morning, and it looks like we were only able to get the plugin icon to show in FireFox on a Windows machine. IE, Chrome, and Safari don't seem to offer any indications as to whether a page has required the flash plugin, and FireFox on Mac does not show any plugin icon. Also, if any of these browsers lack a flash plugin, then no warnings or icons are shown.

Thanks for reporting.
This is not related to the Magento plugin and no fix is possible in this project.
This needs to be addressed at a higher level and will then be effective for this solution automatically.
Resolving as not fixable within this plugin.


Implement more things for FileName

This adds a couple relatively small changes to make interoperating between FileName and Path/PathBuf a bit easier:

Derive Hash so FileName can be used as the key in things like HashMap
From<FileName> for Path and PathBuf (only requires an allocation in the Cow::Borrowed case)
AsRef<Path> (useful for things like File::open(...))
PartialEq<PathBuf>/PartialEq<Path> for comparing a FileName to Path and PathBuf

Thanks!


Issue with Mod Spamming "blockActivateMethodName is null!" to Console

Hi,
I have been using your mod recently and noticed that there appears to be an issue with the mod outputting numerous lines of info every single tick.

Above is a screenshot from the ATLauncher console. When I have this mod enabled and I have a block highlighted, this information is constantly spammed to the console causing some micro stuttering.
The message reads:
blockActivateMethodName is null!
Unable to find block net.minecraft.class_2248 activate method
I am using the latest version of the mod from your GitHub (1.2.4).
I am also using Fabric 0.15.11 along with Fabric API 0.100.4+1.21.
If there is anymore information that you need in order to recreate this, please reach out.
I hope this is helpful.
Kind Regards.

@ProSabre this is fixed in the latest release, v1.2.5.
Thanks for reporting it!


The link to contribution guide in README.md is broken.

The contribution guide link in README.md is broken.
If you're interested in being a contributor, read [the contribution guide](docs/contribution/README.md).

So I'll send PR to fix it.

Thanks @aimof . We recently moved the file.