Added the "fpm restard" command to shell completion

Additionally,

Removed unused imports in all fpm subcommands.
Made all fpm subcommands explicitly extend VirtualCommand.
Made VirtualCommand::execute() final in order to make sure the extending commands do not implement any other handling (this is the purpose of virtual command).
Cleaned up imports and annotations in VirtualCommand.

Coverage decreased (-0.6%) to 52.012% when pulling b1ed6ece13d7197f35ea2e66ef4d376bab0ae991 on morozov:fpm-restart-completion into 221fc6f433235ad794aee2de9f9f982807502ab1 on phpbrew:master.

Looks good to me


In-progress delegation needs to show that it's my DRep

Context & versions
staging.sanchonet
Steps to reproduce

Delegate to a Drep
While in progress, go to the DRep detail page

Video:
https://www.loom.com/share/a9e92e0f0f7f4e5891399d8431b2faa0?sid=a60bce23-b6dd-44d9-afcd-cde0fb5a9509
Actual behavior
There is no indication that you are delegating to this dRep
Expected behavior
The Drep page should show that this is the Drep that you are delegating to, as per design in Figma

Noticed in issue

Drep details labels showing DRep delegation needs to be added accordingly to reflect actual status of delegation - TBC.

OH No @pmbinapps There are two designs for this. I will sort it out somehow.

@pmbinapps I have found a third version. :(. https://www.figma.com/design/mJTBiUofLfb74Xc3W2U59o/Voltaire---GOV-TOOL?m=auto&node-id=9660%3A175716&t=7rsYaYcuCkBafa4l-1

@m-i-k-e You will have to pick one alternative, branch it somehow and merge it. You have written to @BojanKocijan  to see how branching can be used when something is subtracted.

@m-i-k-e You will have to pick one alternative, branch it somehow and merge it. You have written to @BojanKocijan to see how branching can be used when something is subtracted.

Unfortunately I don't understand that message, is that means something that we should do? 👀 (decide on the alternative)?

@MSzalowski That cryptic message was for myself. Sorry it was confusing!

This works now on staging. Closing


Fix three threading+callback issues

Testcase is available at #2172 , fixes also #2149 and an unreported mistake in the original code I copied the fix from.

This is a superset of https://github.com/bytecodealliance/wasm-micr4o-runtime/pull/2170 and misses the mentioned future refactor and both cleanup codes (including the one included there).

I closed the other PR, let's discuss here instead. For https://github.com/bytecodealliance/wasm-micro-runtime/pull/2170#discussion_r1184676549, yes, no need for the additional free, it's done already in https://github.com/bytecodealliance/wasm-micro-runtime/blob/47fcb8506f7f1ee66fadeef4de8a3481b44633a7/core/iwasm/interpreter/wasm_runtime.c#L2265

LGTM


Deselecting options with multiple: true raises TypeError: cannot read property 'query' of null

I'm defining my column for multiple select2 like this:
{
    name: "location",
    label: "Location",
    cell: Backgrid.Extension.Select2Cell.extend({
        multiple: true,
        optionValues: [["Boston", 1], ["Greater Boston Area", 2], ["Alto", 3]]
    })
}

When the cell goes in edit mode selected option show just fine. But when I click on 'x' to deselect an option, console goes red with:

Uncaught TypeError: Cannot read property 'query' of null

I had the same error.


404  org-dartlang-sdk:///sdk/lib/_internal/js_runtime/lib/js_primitives.dart

Steps to Reproduce

flutter channel beta
Run flutter create bug. Write some code
flutter build web
host the build/web folder

Expected results:
no 404 message. Content visible on browser window
Actual results:
404 message in console. Blank widget after first page.
Note: if someone from dev team would like, I can give the access to Git repo as well as info about the website where it is hosted.

Hi @imrhk
can you please provide your flutter doctor -v and flutter build web --verbose?
Thank you

flutter doctor -v
`[✓] Flutter (Channel beta, v1.14.6, on Mac OS X 10.15.2 19C57, locale en-IN)
• Flutter version 1.14.6 at /Users/rahul/Library/flutter/flutter
• Framework revision fabeb2a16f (5 weeks ago), 2020-01-28 07:56:51 -0800
• Engine revision c4229bfbba
• Dart version 2.8.0 (build 2.8.0-dev.5.0 fc3af737c7)

[✓] Android toolchain - develop for Android devices (Android SDK version 29.0.2)
• Android SDK at /Users/rahul/Library/Android/sdk
• Android NDK location not configured (optional; useful for native profiling support)
• Platform android-29, build-tools 29.0.2
• ANDROID_HOME = /Users/rahul/Library/Android/sdk
• Java binary at: /Applications/Android Studio.app/Contents/jre/jdk/Contents/Home/bin/java
• Java version OpenJDK Runtime Environment (build 1.8.0_202-release-1483-b49-5587405)
• All Android licenses accepted.
[✓] Xcode - develop for iOS and macOS (Xcode 11.3.1)
• Xcode at /Applications/Xcode.app/Contents/Developer
• Xcode 11.3.1, Build version 11C504
• CocoaPods version 1.8.4
[✓] Chrome - develop for the web
• Chrome at /Applications/Google Chrome.app/Contents/MacOS/Google Chrome
[✓] Android Studio (version 3.5)
• Android Studio at /Applications/Android Studio.app/Contents
• Flutter plugin version 42.1.1
• Dart plugin version 191.8593
• Java version OpenJDK Runtime Environment (build 1.8.0_202-release-1483-b49-5587405)
[!] Android Studio
• Android Studio at /Applications/Android Studio 4.0 Preview.app/Contents
✗ Flutter plugin not installed; this adds Flutter specific functionality.
✗ Dart plugin not installed; this adds Dart specific functionality.
• Java version OpenJDK Runtime Environment (build 1.8.0_212-release-1586-b4-5784211)
[!] IntelliJ IDEA Community Edition (version 2019.3)
• IntelliJ at /Applications/IntelliJ IDEA CE.app
✗ Flutter plugin not installed; this adds Flutter specific functionality.
✗ Dart plugin not installed; this adds Dart specific functionality.
• For information about installing plugins, see
https://flutter.dev/intellij-setup/#installing-the-plugins
[✓] VS Code (version 1.42.1)
• VS Code at /Applications/Visual Studio Code.app/Contents
• Flutter extension version 3.8.1
[✓] Connected device (3 available)
• Android SDK built for x86 • emulator-5554 • android-x86    • Android 10 (API 29) (emulator)
• Chrome                    • chrome        • web-javascript • Google Chrome 80.0.3987.122
• Web Server                • web-server    • web-javascript • Flutter Tools
! Doctor found issues in 2 categories.`

flutter clean && flutter build web --verbose

Rahuls-MacBook-Pro-2:app rahul$ flutter clean
Cleaning Xcode workspace...                                         4.0s
Deleting build...                                                  560ms
Deleting .dart_tool...                                             281ms
Rahuls-MacBook-Pro-2:app rahul$ flutter build web --verbose
[  +26 ms] executing: [/Users/rahul/Library/flutter/flutter/] git -c log.showSignature=false log -n 1 --pretty=format:%H
[  +40 ms] Exit code 0 from: git -c log.showSignature=false log -n 1 --pretty=format:%H
[        ] fabeb2a16f1d008ab8230f450c49141d35669798
[        ] executing: [/Users/rahul/Library/flutter/flutter/] git describe --match v*.*.* --first-parent --long --tags
[  +20 ms] Exit code 0 from: git describe --match v*.*.* --first-parent --long --tags
[        ] v1.14.6-0-gfabeb2a16
[   +8 ms] executing: [/Users/rahul/Library/flutter/flutter/] git rev-parse --abbrev-ref --symbolic @{u}
[  +10 ms] Exit code 0 from: git rev-parse --abbrev-ref --symbolic @{u}
[        ] origin/beta
[        ] executing: [/Users/rahul/Library/flutter/flutter/] git ls-remote --get-url origin
[  +10 ms] Exit code 0 from: git ls-remote --get-url origin
[        ] https://github.com/flutter/flutter.git
[  +52 ms] executing: [/Users/rahul/Library/flutter/flutter/] git rev-parse --abbrev-ref HEAD
[  +11 ms] Exit code 0 from: git rev-parse --abbrev-ref HEAD
[        ] beta
[   +4 ms] executing: sw_vers -productName
[  +14 ms] Exit code 0 from: sw_vers -productName
[        ] Mac OS X
[        ] executing: sw_vers -productVersion
[  +14 ms] Exit code 0 from: sw_vers -productVersion
[        ] 10.15.2
[        ] executing: sw_vers -buildVersion
[  +13 ms] Exit code 0 from: sw_vers -buildVersion
[        ] 19C57
[  +27 ms] Artifact Instance of 'AndroidMavenArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'AndroidGenSnapshotArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'AndroidInternalBuildArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'IOSEngineArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'FlutterWebSdk' is not required, skipping update.
[   +2 ms] Artifact Instance of 'WindowsEngineArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'MacOSEngineArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'LinuxEngineArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'LinuxFuchsiaSDKArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'MacOSFuchsiaSDKArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'FlutterRunnerSDKArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'FlutterRunnerDebugSymbols' is not required, skipping update.
[   +6 ms] Artifact Instance of 'MaterialFonts' is not required, skipping update.
[        ] Artifact Instance of 'GradleWrapper' is not required, skipping update.
[        ] Artifact Instance of 'AndroidMavenArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'AndroidGenSnapshotArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'AndroidInternalBuildArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'IOSEngineArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'FlutterSdk' is not required, skipping update.
[        ] Artifact Instance of 'WindowsEngineArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'MacOSEngineArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'LinuxEngineArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'LinuxFuchsiaSDKArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'MacOSFuchsiaSDKArtifacts' is not required, skipping update.
[   +1 ms] Artifact Instance of 'FlutterRunnerSDKArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'FlutterRunnerDebugSymbols' is not required, skipping update.
[        ] Artifact Instance of 'IosUsbArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'IosUsbArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'IosUsbArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'IosUsbArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'IosUsbArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'IosUsbArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'IosUsbArtifacts' is not required, skipping update.
[        ] Artifact Instance of 'FontSubsetArtifacts' is not required, skipping update.
[  +93 ms] Found plugin path_provider at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/path_provider-1.6.4/
[   +5 ms] Found plugin path_provider_macos at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/path_provider_macos-0.0.4/
[   +9 ms] Found plugin shared_preferences at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences-0.5.6+2/
[   +1 ms] Found plugin shared_preferences_macos at
/Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences_macos-0.0.1+6/
[   +6 ms] Found plugin shared_preferences_web at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences_web-0.1.2+4/
[  +13 ms] Found plugin url_launcher at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher-5.4.2/
[   +1 ms] Found plugin url_launcher_macos at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher_macos-0.0.1+4/
[   +3 ms] Found plugin url_launcher_web at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher_web-0.1.1+1/
[  +85 ms] Found plugin path_provider at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/path_provider-1.6.4/
[   +1 ms] Found plugin path_provider_macos at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/path_provider_macos-0.0.4/
[   +7 ms] Found plugin shared_preferences at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences-0.5.6+2/
[   +1 ms] Found plugin shared_preferences_macos at
/Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences_macos-0.0.1+6/
[   +2 ms] Found plugin shared_preferences_web at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences_web-0.1.2+4/
[   +8 ms] Found plugin url_launcher at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher-5.4.2/
[   +1 ms] Found plugin url_launcher_macos at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher_macos-0.0.1+4/
[   +2 ms] Found plugin url_launcher_web at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher_web-0.1.1+1/
[  +53 ms] Generating /Users/rahul/app/pathika/app/android/app/src/main/java/io/flutter/plugins/GeneratedPluginRegistrant.java
[  +39 ms] executing: /usr/bin/xcodebuild -version
[ +717 ms] Exit code 0 from: /usr/bin/xcodebuild -version
[   +1 ms] Xcode 11.3.1
           Build version 11C504
[  +42 ms] Found plugin path_provider at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/path_provider-1.6.4/
[        ] Found plugin path_provider_macos at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/path_provider_macos-0.0.4/
[   +4 ms] Found plugin shared_preferences at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences-0.5.6+2/
[   +1 ms] Found plugin shared_preferences_macos at
/Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences_macos-0.0.1+6/
[   +1 ms] Found plugin shared_preferences_web at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences_web-0.1.2+4/
[   +6 ms] Found plugin url_launcher at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher-5.4.2/
[        ] Found plugin url_launcher_macos at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher_macos-0.0.1+4/
[   +1 ms] Found plugin url_launcher_web at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher_web-0.1.1+1/
[  +14 ms] Found plugin path_provider at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/path_provider-1.6.4/
[        ] Found plugin path_provider_macos at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/path_provider_macos-0.0.4/
[   +3 ms] Found plugin shared_preferences at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences-0.5.6+2/
[        ] Found plugin shared_preferences_macos at
/Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences_macos-0.0.1+6/
[   +1 ms] Found plugin shared_preferences_web at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/shared_preferences_web-0.1.2+4/
[   +5 ms] Found plugin url_launcher at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher-5.4.2/
[        ] Found plugin url_launcher_macos at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher_macos-0.0.1+4/
[   +2 ms] Found plugin url_launcher_web at /Users/rahul/.pub-cache/hosted/pub.dartlang.org/url_launcher_web-0.1.1+1/
[   +5 ms] Generating /Users/rahul/app/pathika/app/android/app/src/main/java/io/flutter/plugins/GeneratedPluginRegistrant.java
[  +10 ms] Compiling lib/main.dart for the Web...
[  +13 ms] Initializing file store
[  +31 ms] invalidated build due to missing files:
/Users/rahul/app/pathika/app/packages/flutter_tools/lib/src/build_system/targets/web.dart
[        ] web_entrypoint: Starting due to {InvalidatedReason.inputMissing}
[   +3 ms] web_entrypoint: Complete
[  +19 ms] dart2js: Starting due to {}
[+20197 ms] dart2js: Complete
[+1824 ms] web_release_bundle: Starting due to {}
[ +111 ms] web_release_bundle: Complete
[ +407 ms] web_service_worker: Starting due to {}
[  +31 ms] web_service_worker: Complete
[  +39 ms] Persisting file store
[   +5 ms] Done persisting file store
[  +14 ms] Compiling lib/main.dart for the Web... (completed in 22.7s)
[   +2 ms] "flutter web" took 23,969ms.

I also have this log in console multiple time (almost 25 times)
Another exception was thrown: Instance of 'minified:aU<void>' on js_primitives.dart:49

I tried running the app in debug mode (web) and found out the crash logs along with lines.
Here is the crash log for web
Restarted application in 1,329ms.
Reloaded application in 901ms.
════════ Exception caught by rendering library ═════════════════════════════════
The following NoSuchMethodError was thrown during performLayout():
'<Unexpected Null Value>'
method not found
Receiver: null
Arguments: []

When the exception was thrown, this was the stack
throw_ (package:dart-sdk/lib/_internal/js_dev_runtime/private/ddc_runtime/errors.dart:196:49)
throwNullValueError (package:dart-sdk/lib/_internal/js_dev_runtime/private/ddc_runtime/errors.dart:37:3)
_notNull (package:dart-sdk/lib/_internal/js_dev_runtime/private/ddc_runtime/operations.dart:464:39)
build
build
...
The following RenderObject was being processed when the exception was fired: RenderParagraph#d0726 relayoutBoundary=up4 NEEDS-LAYOUT NEEDS-PAINT NEEDS-COMPOSITING-BITS-UPDATE
RenderObject: RenderParagraph#d0726 relayoutBoundary=up4 NEEDS-LAYOUT NEEDS-PAINT NEEDS-COMPOSITING-BITS-UPDATE
    parentData: offset=Offset(0.0, 0.0); flex=null; fit=null (can use size)
    constraints: BoxConstraints(0.0<=w<=814.0, 0.0<=h<=Infinity)
    semantic boundary
    size: MISSING
    textAlign: start
    textDirection: ltr
    softWrap: wrapping at box width
    overflow: clip
    locale: en_US
    maxLines: unlimited
    text: TextSpan
        inherit: true
        style: italic
        WidgetSpan#f4488
            alignment: bottom
        TextSpan
            debugLabel: (englishLike caption 2014).merge(blackMountainView caption)
            inherit: false
            color: Color(0x8a000000)
            family: Roboto
            size: 12.0
            weight: 400
            baseline: alphabetic
            decoration: TextDecoration.none
            " If you believe there is translation issue or any other issue with the content, please report "
        TextSpan
            debugLabel: ((englishLike caption 2014).merge(blackMountainView caption)).apply
            inherit: false
            color: Color(0x8a000000)
            family: Roboto
            size: 12.0
            weight: 400
            baseline: alphabetic
            decoration: TextDecoration.underline
            "here"
            recognizer: TapGestureRecognizer
                state: ready
════════════════════════════════════════════════════════════════════════════════

════════ Exception caught by rendering library ═════════════════════════════════
Assertion failed: org-dartlang-app:///packages/flutter/src/rendering/box.dart:1694:12
hasSize
"RenderBox was not laid out: RenderParagraph#d0726 relayoutBoundary=up4 NEEDS-PAINT NEEDS-COMPOSITING-BITS-UPDATE"
════════════════════════════════════════════════════════════════════════════════

════════ Exception caught by rendering library ═════════════════════════════════
Assertion failed: org-dartlang-app:///packages/flutter/src/rendering/box.dart:1694:12
hasSize
"RenderBox was not laid out: RenderFlex#3e5b6 relayoutBoundary=up3 NEEDS-PAINT NEEDS-COMPOSITING-BITS-UPDATE"
════════════════════════════════════════════════════════════════════════════════

════════ Exception caught by rendering library ═════════════════════════════════
Assertion failed: org-dartlang-app:///packages/flutter/src/rendering/box.dart:1694:12
hasSize
"RenderBox was not laid out: RenderPadding#b6e6b relayoutBoundary=up2 NEEDS-PAINT NEEDS-COMPOSITING-BITS-UPDATE"
════════════════════════════════════════════════════════════════════════════════

════════ Exception caught by rendering library ═════════════════════════════════
NoSuchMethodError: invalid member on null: 'debugAssertIsValid'
════════════════════════════════════════════════════════════════════════════════

════════ Exception caught by rendering library ═════════════════════════════════
NoSuchMethodError: invalid member on null: 'visible'
════════════════════════════════════════════════════════════════════════════════

════════ Exception caught by rendering library ═════════════════════════════════
NoSuchMethodError: invalid member on null: 'debugAssertIsValid'
════════════════════════════════════════════════════════════════════════════════

════════ Exception caught by rendering library ═════════════════════════════════
NoSuchMethodError: invalid member on null: 'visible'
════════════════════════════════════════════════════════════════════════════════

The widget causing this was
WidgetSpan(
                        child: Icon(Icons.info_outline,
                            size: 14,
                            color: Theme.of(context).textTheme.caption.color),
                      ),

This widget was placed like below in hierarchy
CustomScrollView ->SliverToBoxAdapter->Container->Column->RichText->TextSpan->WidgetSpan
I hope this helps.

Hi @imrhk
To better address the issue, would be helpful
if you could post a minimal code sample to reproduce the problem with this
CustomScrollView ->SliverToBoxAdapter->Container->Column->RichText->TextSpan->WidgetSpan
Thank you

import 'package:flutter/material.dart';

void main() => runApp(MyApp());

class MyApp extends StatelessWidget {
  @override
  Widget build(BuildContext context) {
    return MaterialApp(
      title: 'Flutter Issue #51894',
      theme: ThemeData(
        primarySwatch: Colors.blue,
      ),
      home: MyHomePage(title: 'Flutter Demo Home Page'),
    );
  }
}

class MyHomePage extends StatelessWidget {
  MyHomePage({Key key, this.title}) : super(key: key);

  final String title;

  @override
  Widget build(BuildContext context) {
    return Scaffold(
      appBar: AppBar(title: Text(title)),
      body: CustomScrollView(
        slivers: <Widget>[
          SliverToBoxAdapter(
            child: Container(
              child: Column(
                children: <Widget>[
                  RichText(
                    text: TextSpan(
                      children: [
                        WidgetSpan(
                          child: Icon(Icons.info_outline,
                              size: 14,
                              color: Theme.of(context).textTheme.caption.color),
                        ),
                      ],
                    ),
                  ),
                ],
              ),
            ),
          )
        ],
      ),
    );
  }
}

Debug Console
Launching lib/main.dart on Chrome in debug mode...
Debug service listening on ws://<IP_ADDRESS>:63447/FppeOCxRr7s=
══╡ EXCEPTION CAUGHT BY RENDERING LIBRARY ╞═════════════════════════════════════════════════════════
The following NoSuchMethodError was thrown during performLayout():
'<Unexpected Null Value>'
method not found
Receiver: null
Arguments: []
The relevant error-causing widget was:
RichText org-dartlang-app:///packages/bug_repro/main.dart:33:19
When the exception was thrown, this was the stack:
throw_ (package:dart-sdk/lib/_internal/js_dev_runtime/private/ddc_runtime/errors.dart:196:49)
throwNullValueError (package:dart-sdk/lib/_internal/js_dev_runtime/private/ddc_runtime/errors.dart:37:3)
_notNull (package:dart-sdk/lib/_internal/js_dev_runtime/private/ddc_runtime/operations.dart:464:39)
build
package:flutter/…/widgets/widget_span.dart:108
build
package:flutter/…/painting/text_span.dart:211
layout
[_layoutText]
package:flutter/…/rendering/paragraph.dart:477
[_layoutTextWithConstraints]
package:flutter/…/rendering/paragraph.dart:500
performLayout
package:flutter/…/rendering/paragraph.dart:567
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/flex.dart:744
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/sliver.dart:1816
layout
package:flutter/…/rendering/object.dart:1767
layoutChildSequence
package:flutter/…/rendering/viewport.dart:452
[_attemptLayout]
package:flutter/…/rendering/viewport.dart:1444
performLayout
package:flutter/…/rendering/viewport.dart:1353
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
layoutChild
package:flutter/…/rendering/custom_layout.dart:171
performLayout
package:flutter/…/material/scaffold.dart:477
[_callPerformLayout]
package:flutter/…/rendering/custom_layout.dart:240
performLayout
package:flutter/…/rendering/custom_layout.dart:399
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
performLayout
package:flutter/…/rendering/proxy_box.dart:1247
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
performLayout
package:flutter/…/rendering/proxy_box.dart:3219
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/widgets/overlay.dart:700
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/proxy_box.dart:110
layout
package:flutter/…/rendering/object.dart:1767
performLayout
package:flutter/…/rendering/view.dart:167
[_layoutWithoutResize]
package:flutter/…/rendering/object.dart:1628
flushLayout
package:flutter/…/rendering/object.dart:888
drawFrame
package:flutter/…/rendering/binding.dart:401
drawFrame
package:flutter/…/widgets/binding.dart:797
[_handlePersistentFrameCallback]
package:flutter/…/rendering/binding.dart:283
[_invokeFrameCallback]
package:flutter/…/scheduler/binding.dart:1109
handleDrawFrame
package:flutter/…/scheduler/binding.dart:1048
<fn>
package:flutter/…/scheduler/binding.dart:857
internalCallback (package:dart-sdk/lib/_internal/js_dev_runtime/private/isolate_helper.dart:50:19)
The following RenderObject was being processed when the exception was fired: RenderParagraph#d5214 relayoutBoundary=up3 NEEDS-LAYOUT NEEDS-PAINT NEEDS-COMPOSITING-BITS-UPDATE:
creator: RichText ← Column ← Container ← SliverToBoxAdapter ← Viewport ←
IgnorePointer-[GlobalKey#a542e] ← Semantics ← _PointerListener ← Listener ← _GestureSemantics ←
RawGestureDetector-[LabeledGlobalKey<RawGestureDetectorState>#33edb] ← _PointerListener ← ⋯
parentData: offset=Offset(0.0, 0.0); flex=null; fit=null (can use size)
constraints: BoxConstraints(0.0<=w<=1389.0, 0.0<=h<=Infinity)
size: MISSING
textAlign: start
textDirection: ltr
softWrap: wrapping at box width
overflow: clip
locale: en_US
maxLines: unlimited
This RenderObject had the following descendants (showing up to depth 5):
text: TextSpan
WidgetSpan#7a448
════════════════════════════════════════════════════════════════════════════════════════════════════
Another exception was thrown: Assertion failed: org-dartlang-app:///packages/flutter/src/rendering/box.dart:1694:12
Another exception was thrown: Assertion failed: org-dartlang-app:///packages/flutter/src/rendering/box.dart:1694:12
Another exception was thrown: NoSuchMethodError: invalid member on null: 'debugAssertIsValid'
Another exception was thrown: NoSuchMethodError: invalid member on null: 'visible'

Any update on this?

There seems to be an issue in stack trace formatting. It's stripping out information about the location of the build methods. We should fix that. @jonahwilliams could this be related to the latest stack trace/dwds changes?
According to the last stack trace the issue is with WidgetSpan. It's a known issue: https://github.com/flutter/flutter/issues/42086. Please feel free to follow that one.

@imrhk Can you please try the latest master channel? You are using the beta channel right now.

I did. Still the same.
Flutter doctor
Running flutter doctor...
Doctor summary (to see all details, run flutter doctor -v):
[✓] Flutter (Channel master, v1.16.2-pre.15, on Mac OS X 10.15.2 19C57, locale en-IN)
[✓] Android toolchain - develop for Android devices (Android SDK version 29.0.2)
[✓] Xcode - develop for iOS and macOS (Xcode 11.3.1)
[✓] Chrome - develop for the web
[✓] Android Studio (version 3.5)
[!] Android Studio
    ✗ Flutter plugin not installed; this adds Flutter specific functionality.
    ✗ Dart plugin not installed; this adds Dart specific functionality.
[!] IntelliJ IDEA Community Edition (version 2019.3)
    ✗ Flutter plugin not installed; this adds Flutter specific functionality.
    ✗ Dart plugin not installed; this adds Dart specific functionality.
[✓] VS Code (version 1.43.1)
[✓] Connected device (3 available)

! Doctor found issues in 2 categories.

Chome console
══╡ EXCEPTION CAUGHT BY RENDERING LIBRARY ╞═════════════════════════════════════════════════════════
js_primitives.dart:32 The following NoSuchMethodError was thrown during performLayout():
js_primitives.dart:32 '<Unexpected Null Value>'
js_primitives.dart:32 method not found
js_primitives.dart:32 Receiver: null
js_primitives.dart:32 Arguments: []
js_primitives.dart:32
js_primitives.dart:32 The relevant error-causing widget was:
js_primitives.dart:32   RichText file:///Users/rahul/dev/flutter-playground/bug_repro/lib/main.dart:33:19
js_primitives.dart:32
js_primitives.dart:32 When the exception was thrown, this was the stack:
js_primitives.dart:32 dart-sdk/lib/_internal/js_dev_runtime/private/ddc_runtime/errors.dart 196:49      throw_
js_primitives.dart:32 dart-sdk/lib/_internal/js_dev_runtime/private/ddc_runtime/errors.dart 37:3        throwNullValueError
js_primitives.dart:32 dart-sdk/lib/_internal/js_dev_runtime/private/ddc_runtime/operations.dart 446:39  _notNull
js_primitives.dart:32 packages/flutter/src/widgets/widget_span.dart 108:37                              build
js_primitives.dart:32 packages/flutter/src/painting/text_span.dart 211:14                               build
js_primitives.dart:32 packages/flutter/src/painting/text_painter.dart 558:13                            layout
js_primitives.dart:32 packages/flutter/src/rendering/paragraph.dart 490:18                              [_layoutText]
js_primitives.dart:32 packages/flutter/src/rendering/paragraph.dart 513:5                               [_layoutTextWithConstraints]
js_primitives.dart:32 packages/flutter/src/rendering/paragraph.dart 581:5                               performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/flex.dart 746:14                                   performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/sliver.dart 1820:11                                performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/viewport.dart 452:12                               layoutChildSequence
js_primitives.dart:32 packages/flutter/src/rendering/viewport.dart 1444:12                              [_attemptLayout]
js_primitives.dart:32 packages/flutter/src/rendering/viewport.dart 1353:20                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/custom_layout.dart 171:10                          layoutChild
js_primitives.dart:32 packages/flutter/src/material/scaffold.dart 484:7                                 performLayout
js_primitives.dart:32 packages/flutter/src/rendering/custom_layout.dart 240:7                           [_callPerformLayout]
js_primitives.dart:32 packages/flutter/src/rendering/custom_layout.dart 399:14                          performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 1247:11                             performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 3224:13                             performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/widgets/overlay.dart 700:14                                  performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/proxy_box.dart 110:13                              performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1767:7                                 layout
js_primitives.dart:32 packages/flutter/src/rendering/view.dart 167:48                                   performLayout
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 1630:7                                 [_layoutWithoutResize]
js_primitives.dart:32 packages/flutter/src/rendering/object.dart 887:17                                 flushLayout
js_primitives.dart:32 packages/flutter/src/rendering/binding.dart 401:19                                drawFrame
js_primitives.dart:32 packages/flutter/src/widgets/binding.dart 884:13                                  drawFrame
js_primitives.dart:32 packages/flutter/src/rendering/binding.dart 283:5                                 [_handlePersistentFrameCallback]
js_primitives.dart:32 packages/flutter/src/scheduler/binding.dart 1108:15                               [_invokeFrameCallback]
js_primitives.dart:32 packages/flutter/src/scheduler/binding.dart 1047:9                                handleDrawFrame
js_primitives.dart:32 packages/flutter/src/scheduler/binding.dart 856:7                                 <fn>
js_primitives.dart:32 dart-sdk/lib/_internal/js_dev_runtime/private/isolate_helper.dart 50:19           internalCallback
js_primitives.dart:32
js_primitives.dart:32 The following RenderObject was being processed when the exception was fired: RenderParagraph#0d69c relayoutBoundary=up3 NEEDS-LAYOUT NEEDS-PAINT NEEDS-COMPOSITING-BITS-UPDATE:
js_primitives.dart:32   creator: RichText ← Column ← Container ← SliverToBoxAdapter ← Viewport ←
js_primitives.dart:32     IgnorePointer-[GlobalKey#7e326] ← Semantics ← _PointerListener ← Listener ← _GestureSemantics ←
js_primitives.dart:32     RawGestureDetector-[LabeledGlobalKey<RawGestureDetectorState>#58513] ← _PointerListener ← ⋯
js_primitives.dart:32   parentData: offset=Offset(0.0, 0.0); flex=null; fit=null (can use size)
js_primitives.dart:32   constraints: BoxConstraints(0.0<=w<=1389.0, 0.0<=h<=Infinity)
js_primitives.dart:32   size: MISSING
js_primitives.dart:32   textAlign: start
js_primitives.dart:32   textDirection: ltr
js_primitives.dart:32   softWrap: wrapping at box width
js_primitives.dart:32   overflow: clip
js_primitives.dart:32   locale: en_US
js_primitives.dart:32   maxLines: unlimited
js_primitives.dart:32 This RenderObject had the following descendants (showing up to depth 5):
js_primitives.dart:32     text: TextSpan
js_primitives.dart:32       WidgetSpan#ac97a
js_primitives.dart:32 ════════════════════════════════════════════════════════════════════════════════════════════════════
js_primitives.dart:32 Another exception was thrown: Assertion failed: file:///Users/rahul/Library/flutter/flutter/packages/flutter/lib/src/rendering/box.dart:1694:12
js_primitives.dart:32 Another exception was thrown: Assertion failed: file:///Users/rahul/Library/flutter/flutter/packages/flutter/lib/src/rendering/box.dart:1694:12
js_primitives.dart:32 Another exception was thrown: NoSuchMethodError: invalid member on null: 'debugAssertIsValid'
js_primitives.dart:32 Another exception was thrown: NoSuchMethodError: invalid member on null: 'visible'
viewport.dart:636 Uncaught TypeError: Cannot read property 'visible' of null
    at viewport.RenderViewport.new.hitTestChildren (viewport.dart:636)
    at viewport.RenderViewport.new.hitTest (box.dart:2142)
    at proxy_box.RenderIgnorePointer.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderIgnorePointer.new.hitTest (box.dart:2142)
    at proxy_box.RenderIgnorePointer.new.hitTest (proxy_box.dart:3120)
    at proxy_box.RenderSemanticsAnnotations.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderSemanticsAnnotations.new.hitTest (box.dart:2142)
    at proxy_box.RenderPointerListener.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderPointerListener.new.hitTest (proxy_box.dart:166)
    at proxy_box.RenderSemanticsGestureHandler.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderSemanticsGestureHandler.new.hitTest (box.dart:2142)
    at proxy_box.RenderPointerListener.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderPointerListener.new.hitTest (proxy_box.dart:166)
    at scrollable$._RenderScrollSemantics.new.hitTestChildren (proxy_box.dart:119)
    at scrollable$._RenderScrollSemantics.new.hitTest (box.dart:2142)
    at proxy_box.RenderRepaintBoundary.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderRepaintBoundary.new.hitTest (box.dart:2142)
    at custom_paint.RenderCustomPaint.new.hitTestChildren (proxy_box.dart:119)
    at custom_paint.RenderCustomPaint.new.hitTestChildren (custom_paint.dart:508)
    at custom_paint.RenderCustomPaint.new.hitTest (box.dart:2142)
    at proxy_box.RenderRepaintBoundary.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderRepaintBoundary.new.hitTest (box.dart:2142)
    at box.dart:2495
    at box.BoxHitTestResult.wrap.addWithRawTransform (box.dart:808)
    at box.BoxHitTestResult.wrap.addWithPaintOffset (box.dart:765)
    at custom_layout.RenderCustomMultiChildLayoutBox.new.defaultHitTestChildren (box.dart:2490)
    at custom_layout.RenderCustomMultiChildLayoutBox.new.hitTestChildren (custom_layout.dart:409)
    at custom_layout.RenderCustomMultiChildLayoutBox.new.hitTest (box.dart:2142)
    at material._RenderInkFeatures.new.hitTestChildren (proxy_box.dart:119)
    at material._RenderInkFeatures.new.hitTest (box.dart:2142)
    at proxy_box.RenderPhysicalModel.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderPhysicalModel.new.hitTest (box.dart:2142)
    at proxy_box.RenderPhysicalModel.new.hitTest (proxy_box.dart:1766)
    at proxy_box.RenderSemanticsAnnotations.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderSemanticsAnnotations.new.hitTest (box.dart:2142)
    at proxy_box.RenderRepaintBoundary.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderRepaintBoundary.new.hitTest (box.dart:2142)
    at proxy_box.RenderIgnorePointer.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderIgnorePointer.new.hitTest (box.dart:2142)
    at proxy_box.RenderIgnorePointer.new.hitTest (proxy_box.dart:3120)
    at proxy_box.RenderAnimatedOpacity.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderAnimatedOpacity.new.hitTest (box.dart:2142)
    at proxy_box.RenderFractionalTranslation.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.dart:2504
    at box.BoxHitTestResult.wrap.addWithRawTransform (box.dart:808)
    at box.BoxHitTestResult.wrap.addWithPaintOffset (box.dart:765)
    at proxy_box.RenderFractionalTranslation.new.hitTestChildren (proxy_box.dart:2498)
    at proxy_box.RenderFractionalTranslation.new.hitTest (proxy_box.dart:2484)
    at proxy_box.RenderRepaintBoundary.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderRepaintBoundary.new.hitTest (box.dart:2142)
    at proxy_box.RenderSemanticsAnnotations.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderSemanticsAnnotations.new.hitTest (box.dart:2142)
    at proxy_box.RenderOffstage.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderOffstage.new.hitTest (box.dart:2142)
    at proxy_box.RenderOffstage.new.hitTest (proxy_box.dart:3230)
    at overlay.dart:722
    at box.BoxHitTestResult.wrap.addWithRawTransform (box.dart:808)
    at box.BoxHitTestResult.wrap.addWithPaintOffset (box.dart:765)
    at overlay$._RenderTheatre.new.hitTestChildren (overlay.dart:717)
    at overlay$._RenderTheatre.new.hitTest (box.dart:2142)
    at proxy_box.RenderSemanticsAnnotations.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderSemanticsAnnotations.new.hitTest (box.dart:2142)
    at proxy_box.RenderAbsorbPointer.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderAbsorbPointer.new.hitTest (box.dart:2142)
    at proxy_box.RenderAbsorbPointer.new.hitTest (proxy_box.dart:3328)
    at proxy_box.RenderPointerListener.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderPointerListener.new.hitTest (proxy_box.dart:166)
    at custom_paint.RenderCustomPaint.new.hitTestChildren (proxy_box.dart:119)
    at custom_paint.RenderCustomPaint.new.hitTestChildren (custom_paint.dart:508)
    at custom_paint.RenderCustomPaint.new.hitTest (box.dart:2142)
    at proxy_box.RenderSemanticsAnnotations.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderSemanticsAnnotations.new.hitTest (box.dart:2142)
    at proxy_box.RenderSemanticsAnnotations.new.hitTestChildren (proxy_box.dart:119)
    at proxy_box.RenderSemanticsAnnotations.new.hitTest (box.dart:2142)
    at view.RenderView.new.hitTest (view.dart:187)
    at binding$5.WidgetsFlutterBinding.new.hitTest (binding.dart:427)
    at binding$5.WidgetsFlutterBinding.new.[_handlePointerEvent] (binding.dart:128)
    at binding$5.WidgetsFlutterBinding.new.[_flushPointerEventQueue] (binding.dart:102)
    at binding$5.WidgetsFlutterBinding.new.[_handlePointerDataPacket] (binding.dart:86)
    at _engine.PointerBinding.__.[_onPointerData] (pointer_binding.dart:130)
    at pointer_binding.dart:434
    at pointer_binding.dart:419
    at HTMLElement.<anonymous> (pointer_binding.dart:196)
hitTestChildren @ viewport.dart:636
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTest @ proxy_box.dart:3120
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ proxy_box.dart:166
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ proxy_box.dart:166
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTestChildren @ custom_paint.dart:508
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
(anonymous) @ box.dart:2495
addWithRawTransform @ box.dart:808
addWithPaintOffset @ box.dart:765
defaultHitTestChildren @ box.dart:2490
hitTestChildren @ custom_layout.dart:409
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTest @ proxy_box.dart:1766
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTest @ proxy_box.dart:3120
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
(anonymous) @ proxy_box.dart:2504
addWithRawTransform @ box.dart:808
addWithPaintOffset @ box.dart:765
hitTestChildren @ proxy_box.dart:2498
hitTest @ proxy_box.dart:2484
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTest @ proxy_box.dart:3230
(anonymous) @ overlay.dart:722
addWithRawTransform @ box.dart:808
addWithPaintOffset @ box.dart:765
hitTestChildren @ overlay.dart:717
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTest @ proxy_box.dart:3328
hitTestChildren @ proxy_box.dart:119
hitTest @ proxy_box.dart:166
hitTestChildren @ proxy_box.dart:119
hitTestChildren @ custom_paint.dart:508
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTestChildren @ proxy_box.dart:119
hitTest @ box.dart:2142
hitTest @ view.dart:187
hitTest @ binding.dart:427
[_handlePointerEvent] @ binding.dart:128
[_flushPointerEventQueue] @ binding.dart:102
[_handlePointerDataPacket] @ binding.dart:86
[_onPointerData] @ pointer_binding.dart:130
(anonymous) @ pointer_binding.dart:434
(anonymous) @ pointer_binding.dart:419
(anonymous) @ pointer_binding.dart:196
Show 53 more frames
DevTools failed to parse SourceMap: http://localhost:57756/dwds/src/injected/client.dart.js.map

Ok, so the stack traces look good now. For the WidgetSpan issue, let's track it in #42086.


Cannot call ref for methods on < MapView /> when using Function Components + Hooks

Question

I found this StackOverflow post with similar information on how this could be figured out and resolved, however I tried with both the useRef and createRef hooks and neither was able to capture a reference to the map in the way I can actually call a method on it.
https://stackoverflow.com/questions/41048546/how-can-i-attach-to-a-stateless-components-ref-in-react
One example:
import React, { createRef }, from "react"

<ommitted>

const ServiceMap = ({service, driver}) => {

let mapRef = createRef();

return (
<MapView
ref={mapref}
>

</MapView>
)

}

No matter what when I use the patterns and proposed solutions I get the following value from my "mapRef":
Object {
  "current": null,
}

Then when I try to call one of the methods on it, I am told that it is undefined. When I look up all of the documentation about how to use Refs, then I am never shown with this format, however this is the consistent way I am building my entire application with hooks. I would want to stay consistent with this approach.
When I read this article: https://www.robinwieruch.de/react-function-component I find that "React Function Components cannot have refs. However, if you need to pass a ref to a Function Component -- because you have to measure the size of a function component's DOM node, for example, or like in this case to focus an input field from the outside -- you can forward the ref:"
So then let me try to forward the ref, ok. Hold on, I cannot because I did not create the component and I cannot modify the "" component itself, I am importing it from this library!
Is there a solution here? Does this mean it is impossible to call methods on the components if I am using this approach? To clarify I can display the map, markers, etc. all just fine.

Hey @mvuk.
So in  you attach the ref as mapref, but you've defined it as mapRef further above. Fix the typo where you attach the ref in MapView and you're good to go.  It should work.
Now, it's true that functional components cannot have refs, in the sense that you can't attach a ref to them. This is not what you're doing here. You're attaching a ref to  which is not a functional component, it's a class component. So you shouldn't worry about that.
As for createRef() vs useRef(), you should generally prefer useRef() in functional components since you probably want to maintain the reference across updates.

Same thing here. I can't have acces to any method in my MapView's ref.
Code is almost the same, the "major" difference here is that I use useRef.
Code example :
import React, { useRef } from 'react';
import MapView from 'react-native-maps';

const MyComp = () => {
    const mapRef = useRef(null);
    return (
      <MapView ref={mapRef} onMapReady={() => console.log(mapRef)}>[...myMarkers...]</MapView>
    );
}

I am using expo v35, and react-native-maps v0.25.0

@dragma How are you trying to access the methods? Can you show us what you’re trying to do and what error you’re getting?
FYI,  make sure you’re accessing the methods through the .current property, i.e as mapRef.current.methodName

I am trying to access the method by the mapRef variable.
The output I get with this code
import React, { useRef } from 'react';
import MapView from 'react-native-maps';

const MyComp = () => {
    const mapRef = useRef(null);
    return (
    <MapView
        ref={mapRef}
        onMapReady={() => {
            console.log('==> REF CURRENT OBJECT KEYS');
            console.log(Object.keys(mapRef.current));
            console.log('==> TYPE OF EACH METHODS');
            console.log('mapRef.current.getCamera => ', typeof mapRef.current.getCamera);
            console.log('mapRef.current.animateCamera => ', typeof mapRef.current.animateCamera);
            console.log('mapRef.current.setCamera => ', typeof mapRef.current.setCamera);
            console.log('mapRef.current.animateToRegion => ', typeof mapRef.current.animateToRegion);
            console.log('mapRef.current.animateToNavigation => ', typeof mapRef.current.animateToNavigation);
            console.log('mapRef.current.animateToCoordinate => ', typeof mapRef.current.animateToCoordinate);
            console.log('mapRef.current.animateToBearing => ', typeof mapRef.current.animateToBearing);
            console.log('mapRef.current.animateToViewingAngle => ', typeof mapRef.current.animateToViewingAngle);
            console.log('mapRef.current.getMapBoundaries => ', typeof mapRef.current.getMapBoundaries);
            console.log('mapRef.current.setMapBoundaries => ', typeof mapRef.current.setMapBoundaries);
            console.log('mapRef.current.setIndoorActiveLevelIndex => ', typeof mapRef.current.setIndoorActiveLevelIndex);
            console.log('mapRef.current.fitToElements => ', typeof mapRef.current.fitToElements);
            console.log('mapRef.current.fitToSuppliedMarkers => ', typeof mapRef.current.fitToSuppliedMarkers);
            console.log('mapRef.current.fitToCoordinates => ', typeof mapRef.current.fitToCoordinates);
            console.log('mapRef.current.pointForCoordinate => ', typeof mapRef.current.pointForCoordinate);
            console.log('mapRef.current.coordinateForPoint => ', typeof mapRef.current.coordinateForPoint);
            console.log('mapRef.current.getMarkersFrames => ', typeof mapRef.current.getMarkersFrames);
            console.log('==> TEST GET CAMERA');
            mapRef.current.getCamera();
        }} />
    );
}

is this one
==> REF CURRENT OBJECT KEYS
Array [
  "props",
  "context",
  "refs",
  "updater",
  "state",
  "_onMapReady",
  "_onMarkerPress",
  "_onChange",
  "_onLayout",
  "_reactInternalFiber",
  "_reactInternalInstance",
  "__reactInternalMemoizedMergedChildContext",
  "map",
  "__reactInternalSnapshotBeforeUpdate",
]
==> TYPE OF EACH METHODS
mapRef.current.getCamera =>  function
mapRef.current.animateCamera =>  function
mapRef.current.setCamera =>  function
mapRef.current.animateToRegion =>  function
mapRef.current.animateToNavigation =>  function
mapRef.current.animateToCoordinate =>  function
mapRef.current.animateToBearing =>  function
mapRef.current.animateToViewingAngle =>  function
mapRef.current.getMapBoundaries =>  function
mapRef.current.setMapBoundaries =>  function
mapRef.current.setIndoorActiveLevelIndex =>  function
mapRef.current.fitToElements =>  function
mapRef.current.fitToSuppliedMarkers =>  function
mapRef.current.fitToCoordinates =>  function
mapRef.current.pointForCoordinate =>  function
mapRef.current.coordinateForPoint =>  function
mapRef.current.getMarkersFrames =>  function
==> TEST GET CAMERA

TypeError: TypeError: null is not an object (evaluating '_reactNative.NativeModules.AirMapModule.getCamera')
- node_modules/react-native-maps/lib/components/MapView.js:630:40 in getCamera
* src/views/HomeScreen/components/Map.js:149:12 in onMapReady
- node_modules/react-native-maps/lib/components/MapView.js:586:18 in <unknown>
- node_modules/react-native/Libraries/Renderer/oss/ReactNativeRenderer-dev.js:13857:16 in callCallback
- ... 22 more stack frames from framework internals

Any clue ?

I must say that i get this error only on android.
react-native-maps: v0.25
expo: SDK35

@dragma that error is related to #3099

I have a similar problem trying to get callouts to work with useRef hooks. There seems to be either ridiculously involved examples or nothing explaining how this works, the getCallout() always throws an error as not defined when using hooks. There is no clear example on how to do this.

Hello All,
having same issue. Cant access methods animateToRegion when add reference with useRef().
Does anybody has working example with hooks?

Hello All,
having same issue. Cant access methods animateToRegion when add reference with useRef().
Does anybody has working example with hooks?

Please try ref.current
const mapRef = useRef(null);
mapRef.current.animateToRegion

Hello All,
having same issue. Cant access methods animateToRegion when add reference with useRef().
Does anybody has working example with hooks?

Please try ref.current
const mapRef = useRef(null);
mapRef.current.animateToRegion

I'm doing this with a functional component that is a wrapper to my MapView. However, I'm still having the warning that "Function components cannot be given refs". Can anyone help a react beginner out please?

the problem for me is that onMapReady does not send the map ref as an argument, so we cannot set the ref outside the render. Setting refs on render are not recommended by the React docs:
Unless you’re doing lazy initialization, avoid setting refs during rendering — this can lead to surprising behavior. Instead, typically you want to modify refs in event handlers and effects```
source: https://reactjs.org/docs/hooks-faq.html#is-there-something-like-instance-variables

Not sure how hard would be to fix that

For me this is working partially.
I have a component <MapView ref={map} /> and a const map = useRef(null); declaration in a FunctionComponent. From within a useEffect effect callback I can call map.current.fitToCoordinates() for instance, which is working great. But from within an onChangeText handler of a <TextInput/> in the same component, the map.current reference is null.
Does anyone have any idea how to fix this?

Something is definitely wrong with what is exposed explicitly in the JS side (at least on iOS).

Same problem if you do some defensing programming like I were doing
if (mapRef.current && mapRef.current.animateToRegion) {
  mapRef.current.animateToRegion( ... )
}

This code just never call the method because the test doesn't pass. That said, if you change your code to
if (mapRef.current) {
  mapRef.current.animateToRegion( ... )
}

It works (with a risk of failure, but it works).

@MoOx
I fixed this by passing this into onMapReady cb into this module using patch-package
--- a/node_modules/react-native-maps/lib/components/MapView.js
+++ b/node_modules/react-native-maps/lib/components/MapView.js
@@ -596,7 +596,7 @@ class MapView extends React.Component {
     this._updateStyle(this.props);
     this.setState({ isReady: true }, () => {
       if (onMapReady) {
-        onMapReady();
+        onMapReady(this);
       }
     });
   }

you can read further details about this here: https://github.com/react-native-maps/react-native-maps/pull/1369#discussion_r429042230

mapRef.current.routeBetween

mapRef.current.routeBetween
У меня выдается что это undefined, хотя я все делал по инструкции.

TypeError: mapRef.current.routeBetween is not a function (it is undefined), js engine: hermes
I get an undefined message, even though I did everything according to the instructions.
Does this method still exist?


Start crond when container boots

CRL's expire otherwise

already present: https://github.com/WLCG-Lightweight-Sites/wlcg_lightweight_site_ce_cream/blob/master/yaim/ce-config/init.sh#L32
Closing issue


Style - Improve Card

Hi, I am a contributor in GSSOC'23.
I want to work on Improving the alignment of card elements.
please assign me this task undel label gssoc'23

it was meant to be like that


please add clover to the action name

since only clover is supported, to make finding the best action easier for other users :D

Hi @a7madgamal
I'm planning to support multiple code coverage report formats in the future.
Do you have any requests for a format that should be supported next?


Expose envoy prom port for metrics scraping instead of using annotations

This PR moves away from an annotation-based discovery for individual envoy prometheus scrape
targets. Instead, it exposes the http-envoy-prom port in the podSpec for the injected
containers and adds config to the Prometheus addon to look for pods with a matching port
name for metrics ingest.
This PR is needed to prevent collisions between pods that have existing annotations for prometheus
scraping of a workload target and annotations for envoy scraping. Istio should not monopolize
the prometheus annotations and prevent existing use cases.

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@douglas-reid: The following test failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/istio-pilot-multicluster-e2e.sh
555a692edd5e3b96469231c01503999cc3680e62
link
/test istio-pilot-multicluster-e2e

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/lgtm

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This pull-request has been approved by: mandarjog
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this PR broke postsubmit


White Page Is Displayed When Signing in for the First Time

When a user creates a new account on AgoraCloud, the account created has no workspaces attached to it. In the UI, when the user signs in for the first time, the user should be guided to the create workspace page, as the user has no workspaces and the user should create a workspace to be able to use the AgoraCloud platform.
Currently, there is a bug that causes the user to be greeted with a white page when they sign in for the first time, instead of being directed to the create workspace page.

Fixed by @MarcDAFrame via the package integration in #66


error running 5 Sequel-IIe samples with docker

HI again,
I ran my first 5 real samples using your nice tool in docker mode (the example run succeeded before this one)
The samples are 5 identical Zymo DNA community standard D6305 run with different barcodes in 5 different 16S experiments
I ran this command in the pb-16S-nf folder with more cpu attributed to the jobs since I have 88 threads and 512GB RAM available:
nextflow run main.nf \
  --input /data/analyses/Zymo-SequelIIe-Hifi/run_samples.tsv \
  --metadata /data/analyses/Zymo-SequelIIe-Hifi/run_metadata.tsv \
  --outdir /data/analyses/Zymo-SequelIIe-Hifi/results \
  --dada2_cpu 24 \
  --vsearch_cpu 24 \
  --cutadapt_cpu 48 \
  -profile docker

My input files are attached and inspired from the example files
inputs.tgz
An archive of the work folder with logs is also attached
7545b2ea952a3f15532c70d815c2bc.tgz
Can you please help me correct this issue and run my first real analysis?
Thanks in advance
nextflow run main.nf --input /data/analyses/Zymo-SequelIIe-Hifi/run_samples.tsv --metadata /data/analyses/Zymo-SequelIIe-Hifi/run_metadata.tsv --outdir /data/analyses/Zymo-SequelIIe-Hifi/results -profile docker --dada2_cpu 24 --vsearch_cpu 24 --cutadapt_cpu 48
N E X T F L O W  ~  version 22.10.0
Launching `main.nf` [awesome_chandrasekhar] DSL2 - revision: 6c347af324

  Parameters set for pb-16S-nf pipeline for PacBio HiFi 16S
  =========================================================
  Number of samples in samples TSV: 5
  Filter input reads above Q: 20
  Trim primers with cutadapt: Yes
  Forward primer: AGRGTTYGATYMTGGCTCAG
  Reverse primer: AAGTCGTAACAAGGTARCY
  Minimum amplicon length filtered in DADA2: 1000
  Maximum amplicon length filtered in DADA2: 1600
  maxEE parameter for DADA2 filterAndTrim: 2
  minQ parameter for DADA2 filterAndTrim: 0
  Pooling method for DADA2 denoise process: pseudo
  Minimum number of samples required to keep any ASV: 1
  Minimum number of reads required to keep any ASV: 5
  Taxonomy sequence database for VSEARCH: /opt/biotools/pb-16S-nf/databases/GTDB_ssu_all_r207.qza
  Taxonomy annotation database for VSEARCH: /opt/biotools/pb-16S-nf/databases/GTDB_ssu_all_r207.taxonomy.qza
  Skip Naive Bayes classification: false
  SILVA database for Naive Bayes classifier: /opt/biotools/pb-16S-nf/databases/silva_nr99_v138.1_wSpecies_train_set.fa.gz
  GTDB database for Naive Bayes classifier: /opt/biotools/pb-16S-nf/databases/GTDB_bac120_arc53_ssu_r207_fullTaxo.fa.gz
  RefSeq + RDP database for Naive Bayes classifier: /opt/biotools/pb-16S-nf/databases/RefSeq_16S_6-11-20_RDPv16_fullTaxo.fa.gz
  VSEARCH maxreject: 100
  VSEARCH maxaccept: 100
  VSEARCH perc-identity: 0.97
  QIIME 2 rarefaction curve sampling depth: null
  Number of threads specified for cutadapt: 48
  Number of threads specified for DADA2: 24
  Number of threads specified for VSEARCH: 24
  Script location for HTML report generation: /opt/biotools/pb-16S-nf/scripts/visualize_biom.Rmd
  Container enabled via docker/singularity: true
  Version of Nextflow pipeline: 0.4

executor >  Local (27)
[52/8a912a] process > pb16S:write_log                      [100%] 1 of 1 ✔
[0d/17c679] process > pb16S:QC_fastq (3)                   [100%] 5 of 5 ✔
[f6/6875c2] process > pb16S:cutadapt (5)                   [100%] 5 of 5 ✔
[55/756ad4] process > pb16S:QC_fastq_post_trim (5)         [100%] 5 of 5 ✔
[11/735784] process > pb16S:collect_QC                     [100%] 1 of 1 ✔
[14/9c8073] process > pb16S:prepare_qiime2_manifest        [100%] 1 of 1 ✔
[fa/9d21ec] process > pb16S:import_qiime2                  [100%] 1 of 1 ✔
[ea/244ecc] process > pb16S:demux_summarize                [100%] 1 of 1 ✔
[4f/2ddff8] process > pb16S:dada2_denoise                  [100%] 1 of 1 ✔
[c5/ed6aaa] process > pb16S:filter_dada2                   [100%] 1 of 1 ✔
[a1/058f87] process > pb16S:dada2_qc (1)                   [100%] 1 of 1 ✔
[eb/131db8] process > pb16S:qiime2_phylogeny_diversity (1) [  0%] 0 of 1
[46/7545b2] process > pb16S:dada2_rarefaction (1)          [  0%] 0 of 1
[26/81a70d] process > pb16S:class_tax                      [  0%] 0 of 1
[02/09068c] process > pb16S:dada2_assignTax                [  0%] 0 of 1
[-        ] process > pb16S:export_biom                    -
executor >  Local (27)
[52/8a912a] process > pb16S:write_log                      [100%] 1 of 1 ✔
[0d/17c679] process > pb16S:QC_fastq (3)                   [100%] 5 of 5 ✔
[f6/6875c2] process > pb16S:cutadapt (5)                   [100%] 5 of 5 ✔
[55/756ad4] process > pb16S:QC_fastq_post_trim (5)         [100%] 5 of 5 ✔
[11/735784] process > pb16S:collect_QC                     [100%] 1 of 1 ✔
[14/9c8073] process > pb16S:prepare_qiime2_manifest        [100%] 1 of 1 ✔
[fa/9d21ec] process > pb16S:import_qiime2                  [100%] 1 of 1 ✔
[ea/244ecc] process > pb16S:demux_summarize                [100%] 1 of 1 ✔
[4f/2ddff8] process > pb16S:dada2_denoise                  [100%] 1 of 1 ✔
[c5/ed6aaa] process > pb16S:filter_dada2                   [100%] 1 of 1 ✔
[a1/058f87] process > pb16S:dada2_qc (1)                   [100%] 1 of 1 ✔
[-        ] process > pb16S:qiime2_phylogeny_diversity (1) -
[46/7545b2] process > pb16S:dada2_rarefaction (1)          [100%] 1 of 1, failed: 1 ✘
[-        ] process > pb16S:class_tax                      -
[-        ] process > pb16S:dada2_assignTax                -
[-        ] process > pb16S:export_biom                    -
[-        ] process > pb16S:barplot_nb                     -
[-        ] process > pb16S:barplot                        -
[-        ] process > pb16S:html_rep                       -
[-        ] process > pb16S:krona_plot                     -
Error executing process > 'pb16S:dada2_rarefaction (1)'

Caused by:
  Process `pb16S:dada2_rarefaction (1)` terminated with an error exit status (1)

Command executed:

  qiime diversity alpha-rarefaction --i-table dada2-ccs_table_filtered.qza     --m-metadata-file run_metadata.tsv     --o-visualization alpha-rarefaction-curves.qzv     --p-min-depth 10 --p-max-depth 36322

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
  Plugin error from diversity:

    All metadata filtered after dropping columns that contained non-categorical data.

  Debug info has been saved to /tmp/qiime2-q2cli-err-nq73n8tw.log

Work dir:
  /opt/biotools/pb-16S-nf/work/46/7545b2ea952a3f15532c70d815c2bc

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Hi Stephane, condition should not be a continuous variable as the error suggests. Can you change the condition into categorical variables such as "control"? There might be a parameter in QIIME I can make use to fix this and I will take a look. Thanks.

Indeed, I had used the experiment numbers in the condition column, not realizing they were numbers and not strings, I replaced them by control and ran it again, leading to a new issue detailed below.
In my command I have my inputs and outputs on a partition /data/analyses/Zymo-SequelIIe-Hifi distinct from the nextflow partition /opt/biotools/pb-16S-nf.
The new run with conditions set to control went well until the end and failed while generating the html report from the Rmd template and final results.
The failure was
cp: cannot stat '/opt/biotools/pb-16S-nf/scripts/visualize_biom.Rmd': No such file or directory

while copying the visualize_biom.Rmd template from the scripts folder of nextflow to the result folder
nextflow run main.nf --input /data/analyses/Zymo-SequelIIe-Hifi/run_samples.tsv --metadata /data/analyses/Zymo-SequelIIe-Hifi/run_metadata.tsv --outdir /data/analyses/Zymo-SequelIIe-Hifi/results4 -profile docker --dada2_cpu 64 --vsearch_cpu 64 --cutadapt_cpu 64
N E X T F L O W  ~  version 22.10.0
Launching `main.nf` [sleepy_hugle] DSL2 - revision: 6c347af324

  Parameters set for pb-16S-nf pipeline for PacBio HiFi 16S
  =========================================================
  Number of samples in samples TSV: 5
  Filter input reads above Q: 20
  Trim primers with cutadapt: Yes
  Forward primer: AGRGTTYGATYMTGGCTCAG
  Reverse primer: AAGTCGTAACAAGGTARCY
  Minimum amplicon length filtered in DADA2: 1000
  Maximum amplicon length filtered in DADA2: 1600
  maxEE parameter for DADA2 filterAndTrim: 2
  minQ parameter for DADA2 filterAndTrim: 0
  Pooling method for DADA2 denoise process: pseudo
  Minimum number of samples required to keep any ASV: 1
  Minimum number of reads required to keep any ASV: 5
  Taxonomy sequence database for VSEARCH: /opt/biotools/pb-16S-nf/databases/GTDB_ssu_all_r207.qza
  Taxonomy annotation database for VSEARCH: /opt/biotools/pb-16S-nf/databases/GTDB_ssu_all_r207.taxonomy.qza
  Skip Naive Bayes classification: false
  SILVA database for Naive Bayes classifier: /opt/biotools/pb-16S-nf/databases/silva_nr99_v138.1_wSpecies_train_set.fa.gz
  GTDB database for Naive Bayes classifier: /opt/biotools/pb-16S-nf/databases/GTDB_bac120_arc53_ssu_r207_fullTaxo.fa.gz
  RefSeq + RDP database for Naive Bayes classifier: /opt/biotools/pb-16S-nf/databases/RefSeq_16S_6-11-20_RDPv16_fullTaxo.fa.gz
  VSEARCH maxreject: 100
  VSEARCH maxaccept: 100
  VSEARCH perc-identity: 0.97
  QIIME 2 rarefaction curve sampling depth: null
  Number of threads specified for cutadapt: 64
  Number of threads specified for DADA2: 64
  Number of threads specified for VSEARCH: 64
  Script location for HTML report generation: /opt/biotools/pb-16S-nf/scripts/visualize_biom.Rmd
  Container enabled via docker/singularity: true
  Version of Nextflow pipeline: 0.4

executor >  Local (32)
[b4/955cb3] process > pb16S:write_log                      [100%] 1 of 1 ✔
[a9/80429e] process > pb16S:QC_fastq (3)                   [100%] 5 of 5 ✔
[4f/645346] process > pb16S:cutadapt (5)                   [100%] 5 of 5 ✔
[ac/6fb92a] process > pb16S:QC_fastq_post_trim (5)         [100%] 5 of 5 ✔
[e5/e9de98] process > pb16S:collect_QC                     [100%] 1 of 1 ✔
[28/aa66c5] process > pb16S:prepare_qiime2_manifest        [100%] 1 of 1 ✔
[cf/81dca4] process > pb16S:import_qiime2                  [100%] 1 of 1 ✔
[d5/bdff12] process > pb16S:demux_summarize                [100%] 1 of 1 ✔
executor >  Local (32)
[b4/955cb3] process > pb16S:write_log                      [100%] 1 of 1 ✔
[a9/80429e] process > pb16S:QC_fastq (3)                   [100%] 5 of 5 ✔
[4f/645346] process > pb16S:cutadapt (5)                   [100%] 5 of 5 ✔
[ac/6fb92a] process > pb16S:QC_fastq_post_trim (5)         [100%] 5 of 5 ✔
[e5/e9de98] process > pb16S:collect_QC                     [100%] 1 of 1 ✔
[28/aa66c5] process > pb16S:prepare_qiime2_manifest        [100%] 1 of 1 ✔
[cf/81dca4] process > pb16S:import_qiime2                  [100%] 1 of 1 ✔
[d5/bdff12] process > pb16S:demux_summarize                [100%] 1 of 1 ✔
[d6/e9dd53] process > pb16S:dada2_denoise                  [100%] 1 of 1 ✔
[77/59bcbb] process > pb16S:filter_dada2                   [100%] 1 of 1 ✔
[45/e4ea1e] process > pb16S:dada2_qc (1)                   [100%] 1 of 1 ✔
[fa/cf7381] process > pb16S:qiime2_phylogeny_diversity (1) [100%] 1 of 1 ✔
[77/cf0097] process > pb16S:dada2_rarefaction (1)          [100%] 1 of 1 ✔
[49/a20b2d] process > pb16S:class_tax                      [100%] 1 of 1 ✔
[fc/bfbfc2] process > pb16S:dada2_assignTax                [100%] 1 of 1 ✔
[-        ] process > pb16S:export_biom                    -
[ba/7a7dbd] process > pb16S:barplot_nb (1)                 [100%] 1 of 1 ✔
[-        ] process > pb16S:barplot (1)                    -
[39/434c7f] process > pb16S:html_rep (1)                   [100%] 1 of 1, failed: 1 ✘
[-        ] process > pb16S:krona_plot                     -
Error executing process > 'pb16S:html_rep (1)'

Caused by:
  Process `pb16S:html_rep (1)` terminated with an error exit status (1)

Command executed:

  export R_LIBS_USER="/opt/conda/envs/pb-16S-vis/lib/R/library"
  cp /opt/biotools/pb-16S-nf/scripts/visualize_biom.Rmd visualize_biom.Rmd
  cp /opt/biotools/pb-16S-nf/scripts/import_biom.R import_biom.R
  Rscript -e 'rmarkdown::render("visualize_biom.Rmd", params=list(merged_tax_tab_file="/opt/biotools/pb-16S-nf/work/fc/bfbfc230509df228884409566d85e6/best_tax_merged_freq_tax.tsv", metadata="run_metadata.tsv", sample_file="samplefile.txt", dada2_qc="dada2_qc.tsv", reads_qc="all_samples_seqkit.readstats.tsv", summarised_reads_qc="seqkit.summarised_stats.group_by_samples.tsv", cutadapt_qc="all_samples_cutadapt_stats.tsv", vsearch_tax_tab_file="vsearch_merged_freq_tax.tsv", colorby="condition", bray_mat="bray_curtis_distance_matrix.tsv", unifrac_mat="unweighted_unifrac_distance_matrix.tsv", wunifrac_mat="weighted_unifrac_distance_matrix.tsv", post_trim_readstats="all_samples_seqkit.readstats.post_trim.tsv"), output_dir="./")'

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  cp: cannot stat '/opt/biotools/pb-16S-nf/scripts/visualize_biom.Rmd': No such file or directory

Work dir:
  /opt/biotools/pb-16S-nf/work/39/434c7fc89fccb5c012de7fa3ad1410

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

On advice from my colleague Kobe I added to the docker block of nextflow.config but this did not help
    BPATH = "/opt/biotools/pb-16S-nf"
    runOptions = "-v $BPATH/scripts:$BPATH/scripts"

I still get the same error after re-running
Mike to you :-)

Hi Stephane, you mentioned that the test run finished successfully? My suspicion of what you just saw might have something to do with how docker and Nextflow mount the directory and I'm working on reproducing this to confirm my suspicion, but I am just curious that the test run completed without any issue because they should be using the exact same command.

I've made some changes to how the container works in the develop branch. Can you try to pull the develop commit:
git checkout develop
git pull

And rerun the samples? You can use the -resume flag so that Nextflow won't rerun everything.
Thanks.

I did it as clean as I could:

cloned develop to a new folder pb-16S-nf_develop and did not edit the cache PATH in nextflow.config (I also tried with editing it and it also failed the same)
activated my previous conda env with mamba and nextflow in it
ran the first command below

nextflow run main.nf --download_db
N E X T F L O W  ~  version 22.10.0
Launching `main.nf` [magical_brattain] DSL2 - revision: 6c347af324
No input file given to --input!

  Parameters set for pb-16S-nf pipeline for PacBio HiFi 16S
  =========================================================
  Number of samples in samples TSV: 0
  Filter input reads above Q: 20
  Trim primers with cutadapt: Yes
  Forward primer: AGRGTTYGATYMTGGCTCAG
  Reverse primer: AAGTCGTAACAAGGTARCY
  Minimum amplicon length filtered in DADA2: 1000
  Maximum amplicon length filtered in DADA2: 1600
  maxEE parameter for DADA2 filterAndTrim: 2
  minQ parameter for DADA2 filterAndTrim: 0
  Pooling method for DADA2 denoise process: pseudo
  Minimum number of samples required to keep any ASV: 0
  Minimum number of reads required to keep any ASV: 0
  Taxonomy sequence database for VSEARCH: /opt/biotools/pb-16S-nf_develop/databases/GTDB_ssu_all_r207.qza
  Taxonomy annotation database for VSEARCH: /opt/biotools/pb-16S-nf_develop/databases/GTDB_ssu_all_r207.taxonomy.qza
  Skip Naive Bayes classification: false
  SILVA database for Naive Bayes classifier: /opt/biotools/pb-16S-nf_develop/databases/silva_nr99_v138.1_wSpecies_train_set.fa.gz
  GTDB database for Naive Bayes classifier: /opt/biotools/pb-16S-nf_develop/databases/GTDB_bac120_arc53_ssu_r207_fullTaxo.fa.gz
  RefSeq + RDP database for Naive Bayes classifier: /opt/biotools/pb-16S-nf_develop/databases/RefSeq_16S_6-11-20_RDPv16_fullTaxo.fa.gz
  VSEARCH maxreject: 100
  VSEARCH maxaccept: 100
  VSEARCH perc-identity: 0.97
  QIIME 2 rarefaction curve sampling depth: null
  Number of threads specified for cutadapt: 16
  Number of threads specified for DADA2: 8
  Number of threads specified for VSEARCH: 8
  Script location for HTML report generation: /opt/biotools/pb-16S-nf_develop/scripts/visualize_biom.Rmd
  Container enabled via docker/singularity: false
  Version of Nextflow pipeline: 0.4

[-        ] process > pb16S:download_db -
Creating env using mamba: /opt/biotools/pb-16S-nf_develop/env/qiime2-2022.2-py38-linux-conda.yml [cache /home/luna.kuleuven.be/u0002316/nf_conda/qiime2-2022.2-py38-linux-conda-0f9d5d3ab8a678e45d02e511ce6c0160]

Now, it hangs forever creating the env with a lock file .qiime2-2022.2-py38-linux-conda-0f9d5d3ab8a678e45d02e511ce6c0160.lock in $HOME/nf_conda instead of downloading the databases as requested
I always saw this each time I started over with installing your tool and I each time had to install the qiime env manually using the exact same command as run by the nextflow pipeline (I looked it up in ps aux and replicated it)
It does not seem to have to do with my home folder as the failure is the same with or without editing the nextflow.config as I did before.
Is there a way to install the 3 conda envs manually before doing anything else? Maybe with a separate command or script like for the 'download db'. That way we could make sure all 3 conda envs are done well before proceeding
S

Hi Stephane, please add "-profile docker" to the run. The docker config does not need to install any Conda environment.

OK, I see
maybe you should edit your doc which proposes to do this using conda (and your run commands end with a backslash that should be removed)
BTW, I now added mamba and nextflow to my conda base env to see if this is causing all these troubles and I get exactly the same problem.
It seems that the command that creates the qiime env works quite fast when run manually but hangs when run inside the pipeline (whatever this can mean)
/opt/miniconda3/bin/python /opt/miniconda3/bin/mamba env create --prefix /home/luna.kuleuven.be/u0002316/nf_conda/qiime2-2022.2-py38-linux-conda-0f9d5d3ab8a678e45d02e511ce6c0160 --file /opt/biotools/pb-16S-nf_develop/env/qiime2-2022.2-py38-linux-conda.yml

I've noticed that, too. It happens on some system and not the others and unfortunately I have not been able to figure out why. Setting useMamba=false will usually resolve that, but the time to build environment will be longer.
Sure, I will improve the documentation. Thanks for the suggestion.
FYI the databases are the same you don't have to keep rerunning the "--download_db" step. Just copy the folder "databases" from the other pipeline folder that you've already downloaded. Jump straight into running with your sample in docker mode, there should not be any need to fiddle with Conda besides installing Nextflow. In fact, if you install Nextflow without Conda you can run everything without touching Conda at all :) Docker runs everything in a container it will not be affected by your Conda environment.

GOOD!
this worked for me from clean start:

re-cloned the develop git
cd and run :

echo -e "sample-id\tabsolute-filepath\ntest_data\t$(readlink -f test_data/test_1000_reads.fastq.gz)" \
  > test_data/test_sample.tsv

followed by

nextflow run main.nf \
  --download_db \
  -profile docker

then

nextflow run main.nf \
  --input test_data/test_sample.tsv \
  --metadata test_data/test_metadata.tsv \
  --outdir test_results \
  -profile docker

the run completed after ~6min and all expected files are present in the test_results folder

Not good but different from before, maybe getting to it soon
nextflow run main.nf \
  --input /data/analyses/Zymo-SequelIIe-Hifi/run_samples.tsv \
  --metadata /data/analyses/Zymo-SequelIIe-Hifi/run_metadata.tsv \
  --outdir /data/analyses/Zymo-SequelIIe-Hifi/results \
  --dada2_cpu 80 \
  --vsearch_cpu 80 \
  --cutadapt_cpu 80 \
  -profile docker

BTW, I have 88 threads & 512GB RAM, can you advise ideal cpu values above?
resulting in the below stdout.
looks like the Rmarkdown convert command does not see the input files (missing path?)
(base) u0002316@gbw-s-pacbio01:/opt/biotools/pb-16S-nf_develop $ nextflow run main.nf \
  --input /data/analyses/Zymo-SequelIIe-Hifi/run_samples.tsv \
  --metadata /data/analyses/Zymo-SequelIIe-Hifi/run_metadata.tsv \
  --outdir /data/analyses/Zymo-SequelIIe-Hifi/results \
  --dada2_cpu 80 \
  --vsearch_cpu 80 \
  --cutadapt_cpu 80 \
  -profile docker
N E X T F L O W  ~  version 22.10.1
Launching `main.nf` [romantic_agnesi] DSL2 - revision: 6c347af324

  Parameters set for pb-16S-nf pipeline for PacBio HiFi 16S
  =========================================================
  Number of samples in samples TSV: 5
  Filter input reads above Q: 20
  Trim primers with cutadapt: Yes
  Forward primer: AGRGTTYGATYMTGGCTCAG
  Reverse primer: AAGTCGTAACAAGGTARCY
  Minimum amplicon length filtered in DADA2: 1000
  Maximum amplicon length filtered in DADA2: 1600
  maxEE parameter for DADA2 filterAndTrim: 2
  minQ parameter for DADA2 filterAndTrim: 0
  Pooling method for DADA2 denoise process: pseudo
  Minimum number of samples required to keep any ASV: 1
  Minimum number of reads required to keep any ASV: 5
  Taxonomy sequence database for VSEARCH: /opt/biotools/pb-16S-nf_develop/databases/GTDB_ssu_all_r207.qza
  Taxonomy annotation database for VSEARCH: /opt/biotools/pb-16S-nf_develop/databases/GTDB_ssu_all_r207.taxonomy.qza
  Skip Naive Bayes classification: false
  SILVA database for Naive Bayes classifier: /opt/biotools/pb-16S-nf_develop/databases/silva_nr99_v138.1_wSpecies_train_set.fa.gz
  GTDB database for Naive Bayes classifier: /opt/biotools/pb-16S-nf_develop/databases/GTDB_bac120_arc53_ssu_r207_fullTaxo.fa.gz
  RefSeq + RDP database for Naive Bayes classifier: /opt/biotools/pb-16S-nf_develop/databases/RefSeq_16S_6-11-20_RDPv16_fullTaxo.fa.gz
  VSEARCH maxreject: 100
  VSEARCH maxaccept: 100
  VSEARCH perc-identity: 0.97
  QIIME 2 rarefaction curve sampling depth: null
  Number of threads specified for cutadapt: 80
  Number of threads specified for DADA2: 80
  Number of threads specified for VSEARCH: 80
  Script location for HTML report generation: /opt/biotools/pb-16S-nf_develop/scripts/visualize_biom.Rmd
  Container enabled via docker/singularity: true
  Version of Nextflow pipeline: 0.4

executor >  Local (32)
[ed/e2e039] process > pb16S:write_log                      [100%] 1 of 1 ✔
[29/9f8dbc] process > pb16S:QC_fastq (3)                   [100%] 5 of 5 ✔
[87/2acfb2] process > pb16S:cutadapt (5)                   [100%] 5 of 5 ✔
[50/4240c9] process > pb16S:QC_fastq_post_trim (5)         [100%] 5 of 5 ✔
[30/729570] process > pb16S:collect_QC                     [100%] 1 of 1 ✔
executor >  Local (32)
[ed/e2e039] process > pb16S:write_log                      [100%] 1 of 1 ✔
[29/9f8dbc] process > pb16S:QC_fastq (3)                   [100%] 5 of 5 ✔
[87/2acfb2] process > pb16S:cutadapt (5)                   [100%] 5 of 5 ✔
[50/4240c9] process > pb16S:QC_fastq_post_trim (5)         [100%] 5 of 5 ✔
[30/729570] process > pb16S:collect_QC                     [100%] 1 of 1 ✔
[93/14eed9] process > pb16S:prepare_qiime2_manifest        [100%] 1 of 1 ✔
[ce/c2b9b5] process > pb16S:import_qiime2                  [100%] 1 of 1 ✔
[ef/6b663f] process > pb16S:demux_summarize                [100%] 1 of 1 ✔
[50/44172d] process > pb16S:dada2_denoise                  [100%] 1 of 1 ✔
[24/1cd2c0] process > pb16S:filter_dada2                   [100%] 1 of 1 ✔
[32/ce8bc1] process > pb16S:dada2_qc (1)                   [100%] 1 of 1 ✔
[7d/2e2397] process > pb16S:qiime2_phylogeny_diversity (1) [100%] 1 of 1 ✔
[a5/2972ed] process > pb16S:dada2_rarefaction (1)          [100%] 1 of 1 ✔
[91/8e82f5] process > pb16S:class_tax                      [100%] 1 of 1 ✔
[38/d1e917] process > pb16S:dada2_assignTax                [100%] 1 of 1 ✔
[-        ] process > pb16S:export_biom                    -
[41/4ac036] process > pb16S:barplot_nb (1)                 [100%] 1 of 1 ✔
[-        ] process > pb16S:barplot (1)                    -
[ad/de7db7] process > pb16S:html_rep (1)                   [100%] 1 of 1, failed: 1 ✘
[-        ] process > pb16S:krona_plot                     -
Error executing process > 'pb16S:html_rep (1)'

Caused by:
  Process `pb16S:html_rep (1)` terminated with an error exit status (1)

Command executed:

  export R_LIBS_USER="/opt/conda/envs/pb-16S-vis/lib/R/library"
  cp /opt/biotools/pb-16S-nf_develop/scripts/visualize_biom.Rmd visualize_biom.Rmd
  cp /opt/biotools/pb-16S-nf_develop/scripts/import_biom.R import_biom.R
  Rscript -e 'rmarkdown::render("visualize_biom.Rmd", params=list(merged_tax_tab_file="/opt/biotools/pb-16S-nf_develop/work/38/d1e917ae6103a78cb57f1deea8eb8a/best_tax_merged_freq_tax.tsv", metadata="run_metadata.tsv", sample_file="samplefile.txt", dada2_qc="dada2_qc.tsv", reads_qc="all_samples_seqkit.readstats.tsv", summarised_reads_qc="seqkit.summarised_stats.group_by_samples.tsv", cutadapt_qc="all_samples_cutadapt_stats.tsv", vsearch_tax_tab_file="vsearch_merged_freq_tax.tsv", colorby="condition", bray_mat="bray_curtis_distance_matrix.tsv", unifrac_mat="unweighted_unifrac_distance_matrix.tsv", wunifrac_mat="weighted_unifrac_distance_matrix.tsv", post_trim_readstats="all_samples_seqkit.readstats.post_trim.tsv"), output_dir="./")'

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  cp: cannot stat '/opt/biotools/pb-16S-nf_develop/scripts/visualize_biom.Rmd': No such file or directory

Work dir:
  /opt/biotools/pb-16S-nf_develop/work/ad/de7db7e35fb422dafba170919b01d0

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Thanks!

  cp /opt/biotools/pb-16S-nf_develop/scripts/visualize_biom.Rmd visualize_biom.Rmd
  cp /opt/biotools/pb-16S-nf_develop/scripts/import_biom.R import_biom.R

These should not exist anymore in the develop branch (You can check in the repo here directly in main.nf under the html_rep process). Can you check main.nf in your workflow folder (pb_16s_develop) and make sure it's using the correct branch? You should not see the cp command in the html_rep process.

my very bad,
I probably cloned the main and named it develop
I start over

YES! It ran!
Very sorry about overlooking the cloning process, I forgot to add -p develop as I thought that the copied url would point to the develop build automatically.
Note that I also meanwhile installed nextflow system-wide and stopped using conda altogether in the process (full docker + system NF)
Thanks you very much for your continuous help and correcting my flows, this took quite some time but my 5 repeats of the Zymo sample give very similar results which are kind-of agreeing with the Zymo info besides strong bias for the abundance for some.
BTW: It also worked with data IO on the distant share
I will now hopefully deepen my knowledge of Q2 and get to know the other data produced by your nice (and fast) pipeline.
Cheers from Belgium!

Hi Stephanie, happy to hear that it worked for you. Sorry for all the troubles too. I'll reflect on your experience and see how I can make it more robust. I'm still puzzled by why Conda did not work for you but I'm glad Docker is working well.
In general I use only 32 CPUs for the cpu parameters and found it to be adequate. It can become very slow at high read depth because DADA2 pools all the reads for denoising. I can probably make it faster by letting it denoise samples individually but that can drop the very low abundance bacteria. In a future version I'll make that an option, thou.
You mentioned that you did Zymo. May I know which community did you sequence? I'm curious about the abundance bias. I've generally observed high correlation of abundance in all of the communities we've sequenced. Zymo D6323 in particular even showed high concordance with shotgun metagenomics.

Thanks Khi Pin,
We add the old Zymo microbial community (D6305) in each run as extra barcode to be able to spot technical issues with library prep. I used here the Zymo samples from 5 unrelated runs and get the following results

taxonomy_barplot_nb.qzv

taxonomy_barplot_vsearch.qzv

close but not identical to the expected equimolar representation.

I think we can be happy with the correlation and the database has very likely some effect on the findings.
Cheers,
Stephane

Hi Stephane, I assume that the abundance is whole microbe abundance. Some of the microbes have more copies of 16S so Zymo also provide the abundances after normalising for 16S copies. I. e. If you sequence 2 bacteria with metagenomics they may be 50:50, but if one bacteria has one 16S copy and the other has 2 16S copies, you actually have 25:75 in 16S abundance. I think if you normalise to that the abundance should be even more correlated :) For D6305 it's documented at page 1 of the protocol PDF here https://www.zymoresearch.com/collections/zymobiomics-microbial-community-standards/products/zymobiomics-microbial-community-dna-standard


Too many open files

Bug Information
Version Number of Plugin: 3.0.1
Device Tested On:  IPhone ai586
Simulator Tested On: n/a
Version of VS: 2017 community 15.5
Version of Xamarin: 4.8.0
Versions of other things you are using:
Plugin.Permissions 2.1.0
Plugin.Connectivity 3.0.3
Plugin.DeviceInfo 3.0.2
Plugin.Geolocator 4.1.3
Plugin.Settings 3.1.1
Steps to reproduce the Behavior
Invoke CrossMedia.Current.TakePhotoAsync() several (3 or more) times
detailed here: https://stackoverflow.com/questions/47757015/xam-plugin-media-too-many-open-files
Expected Behavior
get bytes from file, dispose file, be able to call again
Actual Behavior
receive exception 'too many open files'
error occurs here:
using (System.IO.Stream stream = file.GetStream())
Code snippet
https://stackoverflow.com/questions/47757015/xam-plugin-media-too-many-open-files
Screenshots

Unable to reproduce with my sample app.
Took about 25 photos with no issues. It must just be something with your logic of streams and maybe not cleaning something up.


REINFORCE and VPG

I think it will be better if REINFORCE and VPG are added!

any contribution is warmly welcomed


[Service Bus] Retry Guidance for Transactions Sample

Due to the way that transactions work with Service Bus, retries for service operations cannot be performed when there is an active ambient transaction. We should add a section to the transactions sample that highlights this.

Prerequisite:  #27931

Closing as this has been added to the troubleshooting guide - https://github.com/Azure/azure-sdk-for-net/blob/main/sdk/servicebus/Azure.Messaging.ServiceBus/TROUBLESHOOTING.md#operations-in-a-transaction-are-not-retried


Push releases to rubygems

Has not been updated in a while, would be great if it could be sync'd with Github :pray:
Thanks in advance :innocent:

I just hit this issue too. Updating rubygems would be good.

/cc @thommay I'm not sure what's going on with releases. Is there a wonky CI config somewhere?

I also ran into this. There is a major bug that has been fixed in the pre-release. #41

RubyGems updated with release v1.0.0