ResolveAssemblyReference fails with error MSB4018 on Linux: "InvalidOperationException: PE image does not have metadata"

From @phil-harmoniq on March 1, 2018 6:2
Steps to reproduce the issue
(e.g. copy your Dockerfile or docker-compose.yml file here)

The repo in question: https://github.com/phil-harmoniq/vue-template
Successfully builds in my CI pipeline and on my Linux desktop: https://travis-ci.org/phil-harmoniq/vue-template
Try to build this on a MacBook

Expected behavior
Building my Docker image.
Actual behavior
Running dotnet publish -c Release in my Dockerfile results in the following during the restore step:
Restoring packages for /vue-template/vue-template.csproj...
  Restore completed in 45.13 ms for /vue-template/vue-template.csproj.
  Generating MSBuild file /vue-template/obj/vue-template.csproj.nuget.g.props.
  Generating MSBuild file /vue-template/obj/vue-template.csproj.nuget.g.targets.
  Restore completed in 569.53 ms for /vue-template/vue-template.csproj.
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018: The "ResolveAssemblyReference" task failed unexpectedly. [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018: System.InvalidOperationException: PE image does not have metadata. [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at System.Reflection.PortableExecutable.PEReader.GetMetadataBlock() [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at System.Reflection.Metadata.PEReaderExtensions.GetMetadataReader(PEReader peReader, MetadataReaderOptions options, MetadataStringDecoder utf8Decoder) [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at System.Reflection.Metadata.PEReaderExtensions.GetMetadataReader(PEReader peReader) [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at Microsoft.Build.Shared.AssemblyNameExtension.GetAssemblyNameEx(String path) in E:\A\_work\17\s\src\Shared\AssemblyNameExtension.cs:line 153 [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at Microsoft.Build.Tasks.ReferenceTable.SetPrimaryAssemblyReferenceItem(ITaskItem referenceAssemblyName) in E:\A\_work\17\s\src\Tasks\AssemblyDependency\ReferenceTable.cs:line 624 [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at Microsoft.Build.Tasks.ReferenceTable.SetPrimaryItems(ITaskItem[] referenceAssemblyFiles, ITaskItem[] referenceAssemblyNames, ArrayList exceptions) in E:\A\_work\17\s\src\Tasks\AssemblyDependency\ReferenceTable.cs:line 502 [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at Microsoft.Build.Tasks.ReferenceTable.ComputeClosure(DependentAssembly[] remappedAssembliesValue, ITaskItem[] referenceAssemblyFiles, ITaskItem[] referenceAssemblyNames, ArrayList exceptions) in E:\A\_work\17\s\src\Tasks\AssemblyDependency\ReferenceTable.cs:line 1634 [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at Microsoft.Build.Tasks.ResolveAssemblyReference.Execute(FileExists fileExists, DirectoryExists directoryExists, GetDirectories getDirectories, GetAssemblyName getAssemblyName, GetAssemblyMetadata getAssemblyMetadata, GetLastWriteTime getLastWriteTime, GetAssemblyRuntimeVersion getRuntimeVersion, GetAssemblyPathInGac getAssemblyPathInGac, IsWinMDFile isWinMDFile, ReadMachineTypeFromPEHeader readMachineTypeFromPEHeader) in E:\A\_work\17\s\src\Tasks\AssemblyDependency\ResolveAssemblyReference.cs:line 2160 [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at Microsoft.Build.Tasks.ResolveAssemblyReference.Execute() in E:\A\_work\17\s\src\Tasks\AssemblyDependency\ResolveAssemblyReference.cs:line 2939 [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at Microsoft.Build.BackEnd.TaskExecutionHost.Microsoft.Build.BackEnd.ITaskExecutionHost.Execute() in E:\A\_work\17\s\src\Build\BackEnd\TaskExecutionHost\TaskExecutionHost.cs:line 631 [/vue-template/vue-template.csproj]
/usr/share/dotnet/sdk/2.1.4/Microsoft.Common.CurrentVersion.targets(2041,5): error MSB4018:    at Microsoft.Build.BackEnd.TaskBuilder.<ExecuteInstantiatedTask>d__25.MoveNext() in E:\A\_work\17\s\src\Build\BackEnd\Components\RequestBuilder\TaskBuilder.cs:line 787 [/vue-template/vue-template.csproj]
The command '/bin/sh -c dotnet publish -c Release -o out' returned a non-zero code: 1
The terminal process terminated with exit code: 1

Additional information (e.g. issue happens only occasionally)
I don't know whether this is an issue with the aspnetcore-build image or the Mac Docker client itself. If you know of a better repo to post this in, please let me know. For the record, the dotnet publish command works fine when run natively (not in Docker).
Output of dotnet --info
.NET Command Line Tools (2.1.4)

Product Information:
 Version:            2.1.4
 Commit SHA-1 hash:  5e8add2190

Runtime Environment:
 OS Name:     Mac OS X
 OS Version:  10.13
 OS Platform: Darwin
 RID:         osx.10.12-x64
 Base Path:   /usr/local/share/dotnet/sdk/2.1.4/

Microsoft .NET Core Shared Framework Host

  Version  : 2.0.5
  Build    : 17373eb129b3b05aa18ece963f8795d65ef8ea54

Output of docker info
Containers: 22
 Running: 0
 Paused: 0
 Stopped: 22
Images: 70
Server Version: 17.12.0-ce
Storage Driver: overlay2
 Backing Filesystem: extfs
 Supports d_type: true
 Native Overlay Diff: true
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
 Volume: local
 Network: bridge host ipvlan macvlan null overlay
 Log: awslogs fluentd gcplogs gelf journald json-file logentries splunk syslog
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Init Binary: docker-init
containerd version: 89623f28b87a6004d4b785663257362d1658a729
runc version: b2567b37d7b75eb4cf325b77297b140ea686ce8f
init version: 949e6fa
Security Options:
 seccomp
  Profile: default
Kernel Version: 4.9.60-linuxkit-aufs
Operating System: Docker for Mac
OSType: linux
Architecture: x86_64
CPUs: 4
Total Memory: 1.952GiB
Name: linuxkit-025000000001
ID: QUJ6:7J7I:YD4Y:7HJ4:WXPA:CHYB:QQFR:UB6Y:N6PG:ARLH:FZKD:4M3O
Docker Root Dir: /var/lib/docker
Debug Mode (client): false
Debug Mode (server): true
 File Descriptors: 21
 Goroutines: 40
 System Time: 2018-03-01T06:02:02.970892468Z
 EventsListeners: 2
HTTP Proxy: docker.for.mac.http.internal:3128
HTTPS Proxy: docker.for.mac.http.internal:3129
Registry: https://index.docker.io/v1/
Labels:
Experimental: true
Insecure Registries:
 <IP_ADDRESS>/8
Live Restore Enabled: false

Copied from original issue: aspnet/aspnet-docker#382

I couldn't reproduce this using the steps you gave. Building the image passed just fine on my macBook. The error message seems to indicate there was a problem reading a .dll file. Are you volume mounting your local folder into the docker container?

From @Stealthfox on March 13, 2018 17:19
I had the same issue with a similar setup. Docker version 17.12.0-ce, Mac OS X 10.13 using dotnet SDK 2.1.4.
I resolved my issue by using aspnetcore-build:2.0-jessie rather than aspnetcore-build:2.0

I can confirm what @Stealthfox found. Using Jessie allows me to build my images.

Previously similar issue was reported https://github.com/dotnet/cli/issues/2660, with Microsoft.DotNet.Cli.Compiler.Common.BindingRedirectGenerator.GetAssemblyInfo in stacktrace, now it seems to be coming from MSBuild.

I don't know if it's still relevant but I had the same issue with a bit different packages. But I also have
dotnet Core SDK 2.1.4
This command solved it for me:
dotnet nuget locals --clear all
After that I ran dotnet restore, got the nuget packages installed and could run dotnet run without any errors.

This looks like corrupt .dll files are making it onto disk somehow. I think MSBuild is just the first thing to notice them.
I'm going to close this in the hopes that the Docker images now available with point updates since the original report are valid, and any remaining issues are resolvable via @Teo-ti's NuGet cache clearing mechanism.
If you see a consistent repro of this, please comment here. If something is corrupting files somehow it'd be great to track it down.


fix: Select All on 2nd filter in table not showing checked checkboxes #2386

Closes #2386
The PR fulfills these requirements: (check all the apply)

[x] It's submitted to the main branch.
[x] When resolving a specific issue, it's referenced in the PR's title (e.g. feat: Add a button #xxx, where "xxx" is the issue number).
[x] When resolving a specific issue, the PR description includes Closes #xxx, where "xxx" is the issue number.
[x] If changes were made to ui folder, unit tests (make test) still pass.
[ ] New/updated tests are included

I was able to find the root cause of this bug. The issue is in the definition of the ContextualMenu component that is used to display the column filtering options. The bug is in the isFilterChecked function in ContextualMenu:
  ContextualMenu = ({ onFilterChange, col, listProps, selectedFilters, setFiltersInBulk }: ContextualMenuProps) => {
    const
      isFilterChecked = (data: S, key: S) => !!selectedFilters && selectedFilters[data]?.includes(key),
      [menuFilters, setMenuFilters] = React.useState(col.cellType?.tag
        ? Array.from(listProps.items.reduce((_filters, { key, text, data }) => {
          key.split(',').forEach(key => _filters.set(key, { key, text, data, checked: isFilterChecked(data, key) }))
          return _filters
        }, new Map<S, Fluent.IContextualMenuItem>()).values())
        : listProps.items.map(i => ({ ...i, checked: isFilterChecked(i.data, i.key) }))
      ),

If the selectedFilters prop is not null, but does NOT contain an entry for the current column, then the isFilteredChecked function will return undefined. This eventually becomes the value of the checked prop where Fluent.Checkbox is defined. As a result, eventually changing that to true when checked, doesn't get recognized and therefore looks like nothing has changed.
The solution is to modify the isFilteredChecked function to explicitly return either true or false. Here's a code snipit for that fix:
      isFilterChecked = (data: S, key: S) => !!selectedFilters && selectedFilters[data]?.includes(key) ? true : false,

With this change, the checked prop is always set correctly, and the issue is resolved.
Here's a short video showing the fix:
https://github.com/user-attachments/assets/668b17e1-7000-4160-8267-1c60c01af30d
I re-ran all the existing unit tests and they still pass:

New unit test
I have been unable to create a new test for this issue. I've worked on this for several days and cannot find a solution. I suspect this might be an issue with @testing-library/react, but can't be sure. I did try upgrading the library to the latest version of 12.x, which is 12.1.5, but no luck. I'm unable to upgrade any higher since there is a dependency on React 18 in more recent versions.
Let me try to explain the problem I'm having: When the filter icon is clicked, the ContextualMenu component defined in table.tsx is rendered. On this component, there is a list of checkboxes based on the menuFilters state variable defined in the component. The problem is that from the unit test, when a filter icon is clicked for a different column, the ContextualMenu component is initialized with the menuFilters from the 1st column where the filter icon was clicked. I have verified this by debugging the code in table.tsx and in the unit test. I have also proven to myself that this problem never happens when you do the same thing in the browser, it only happens when I do this from the unit test.
And I'm fairly confident that my unit test doesn't have an issue, at least as far as I could figure out. I even tried adding an await thinking that it might be some timing issue waiting for the menuFilters state variable to be updated, but nothing works. I put a lot of debug statements in the test and in table.tsx and am confident that the code in there is all fine.
Here is a snipit of the test that I wrote to illustrate the problem:
    it('Filters correctly - multiple filters with select all', () => {
      tableProps = {
        ...tableProps,
        columns: [
          { name: 'colname1', label: 'col1', searchable: true },
          { name: 'colname2', label: 'col2', filterable: true },
          { name: 'colname3', label: 'col3', filterable: true },
        ],
        rows: [
          { name: 'rowname1', cells: [cell11, 'col2-val2', 'On'] },
          { name: 'rowname2', cells: [cell21, 'col2-val1', 'Off'] },
          { name: 'rowname3', cells: [cell31, 'col2-val3', 'On'] },
        ]
      }
      const { container, getByLabelText, getAllByRole, queryAllByTestId, queryAllByLabelText, getByText, getByTestId } = render(<XTable model={tableProps} />)

      expect(getAllByRole('row')).toHaveLength(tableProps.rows!.length + headerRow)

      //Make a selection on the filter in the 2nd column
      console.log("Unit test - about to select filter for 'col2'")
      fireEvent.click(container.querySelectorAll(filterSelectorName)[0]!)
      fireEvent.click(getByLabelText('col2-val3'))
      expect(getAllByRole('row')).toHaveLength(1 + headerRow)
      expect(queryAllByTestId('filter-count')[0]).toHaveTextContent('1')
      expect(getAllByRole('checkbox', {checked: true})).toHaveLength(1)

      //Now click somewhere so ContextualMenu is dismissed
      console.log("Unit test - about to click the search field, but don't actually search for anything - trying to force onDismiss() for context menu")
      fireEvent.click(getByTestId('search'))

      //Now select the filter on the 3rd column
      console.log("Unit test - about to select filter for 'col3'")
      fireEvent.click(container.querySelectorAll(filterSelectorName)[1]!)

      //But notice the menu filter options on the ContextualMenu component contain options from column 2, not column 3
      //This should give lenth of 1 since there should be a checkbox label of 'Off' - but it gives length of 0
      console.log("Unit test - number of 'Off' labels is ="+queryAllByLabelText('Off').length+"=, but should be 1 for col3")
      //This should give lenth of 0 since there should be NO checkbox label of 'col2-val1' - but it gives length of 1
      console.log("Unit test - number of 'col2-val1' labels is ="+queryAllByLabelText('col2-val1').length+"=, but should be 0 for col3")

      console.log("Unit test - about to click 'Select All'")
      fireEvent.click(getByText('Select All'))
      console.log("Unit test - number of 'Off' labels is ="+queryAllByLabelText('Off').length+"=, but should be 1 for col3")
      console.log("Unit test - number of 'col2-val1' labels is ="+queryAllByLabelText('col2-val1').length+"=, but should be 0 for col3")
    })

And here's a snipit from table.tsx where you can see that I've added console.log() to print out the listProps at the top and then menuFilters state variable after initialization.
  ContextualMenu = ({ onFilterChange, col, listProps, selectedFilters, setFiltersInBulk }: ContextualMenuProps) => {
    console.log("ContextualMenu - at top for col.name="+col.name+"=, listProps is:")
    console.log(listProps)

    const
      isFilterChecked = (data: S, key: S) => !!selectedFilters && selectedFilters[data]?.includes(key) ? true : false,
      [menuFilters, setMenuFilters] = React.useState(col.cellType?.tag
        ? Array.from(listProps.items.reduce((_filters, { key, text, data }) => {
          key.split(',').forEach(key => _filters.set(key, { key, text, data, checked: isFilterChecked(data, key) }))
          return _filters
        }, new Map<S, Fluent.IContextualMenuItem>()).values())
        : listProps.items.map(i => ({ ...i, checked: isFilterChecked(i.data, i.key) }))
      ),
      selectAll = () => {
        setMenuFilters(menuFilters.map(i => ({ ...i, checked: true })))
        setFiltersInBulk(col.key, menuFilters.map(f => f.key))
      },
      deselectAll = () => {
        setMenuFilters(menuFilters.map(i => ({ ...i, checked: false })))
        setFiltersInBulk(col.key, [])
      },
      getOnFilterChangeHandler = (data: S, key: S) => (_ev?: React.FormEvent<HTMLInputElement | HTMLElement>, checked?: B) => {
        setMenuFilters(filters => filters.map(f => f.key === key ? ({ ...f, checked }) : f))
        onFilterChange(data, key, checked)
      }
    console.log("ContextualMenu - after initialization for col.name="+col.name+"=, menuFilters is:")
    console.log(menuFilters)

    return (
      <div style={{ padding: 10 }}>
        <Fluent.Text variant='mediumPlus' styles={{ root: { paddingTop: 10, paddingBottom: 10, fontWeight: 'bold' } }} block>Show only</Fluent.Text>

And here is the output after running the test:
  console.log
    Unit test - about to select filter for 'col2'

      at Object.log (src/table.test.tsx:1035:15)

  console.log
    ContextualMenu - at top for col.name=col2=, listProps is:

      at log (src/table.tsx:296:13)

  console.log
    {
      ariaLabel: undefined,
      items: [
        { key: 'col2-val2', text: 'col2-val2', data: 'colname2' },
        { key: 'col2-val1', text: 'col2-val1', data: 'colname2' },
        { key: 'col2-val3', text: 'col2-val3', data: 'colname2' }
      ],
      totalItemCount: 3,
      hasCheckmarks: false,
      hasIcons: false,
      defaultMenuItemRenderer: [Function: defaultMenuItemRenderer],
      labelElementId: undefined
    }

      at log (src/table.tsx:297:13)

  console.log
    ContextualMenu - after initialization for col.name=col2=, menuFilters is:

      at log (src/table.tsx:320:13)

  console.log
    [
      {
        key: 'col2-val2',
        text: 'col2-val2',
        data: 'colname2',
        checked: false
      },
      {
        key: 'col2-val1',
        text: 'col2-val1',
        data: 'colname2',
        checked: false
      },
      {
        key: 'col2-val3',
        text: 'col2-val3',
        data: 'colname2',
        checked: false
      }
    ]

      at log (src/table.tsx:321:13)

  console.log
    ContextualMenu - at top for col.name=col2=, listProps is:

      at log (src/table.tsx:296:13)

  console.log
    {
      ariaLabel: undefined,
      items: [
        { key: 'col2-val2', text: 'col2-val2', data: 'colname2' },
        { key: 'col2-val1', text: 'col2-val1', data: 'colname2' },
        { key: 'col2-val3', text: 'col2-val3', data: 'colname2' }
      ],
      totalItemCount: 3,
      hasCheckmarks: false,
      hasIcons: false,
      defaultMenuItemRenderer: [Function: defaultMenuItemRenderer],
      labelElementId: undefined
    }

      at log (src/table.tsx:297:13)

  console.log
    ContextualMenu - after initialization for col.name=col2=, menuFilters is:

      at log (src/table.tsx:320:13)

  console.log
    [
      {
        key: 'col2-val2',
        text: 'col2-val2',
        data: 'colname2',
        checked: false
      },
      {
        key: 'col2-val1',
        text: 'col2-val1',
        data: 'colname2',
        checked: false
      },
      {
        key: 'col2-val3',
        text: 'col2-val3',
        data: 'colname2',
        checked: true
      }
    ]

      at log (src/table.tsx:321:13)

  console.log
    Unit test - about to click the search field, but don't actually search for anything - trying to force onDismiss() for context menu

      at Object.log (src/table.test.tsx:1043:15)

  console.log
    Unit test - about to select filter for 'col3'

      at Object.log (src/table.test.tsx:1047:15)

  console.log
    ContextualMenu - at top for col.name=col3=, listProps is:

      at log (src/table.tsx:296:13)

  console.log
    {
      ariaLabel: undefined,
      items: [
        { key: 'On', text: 'On', data: 'colname3' },
        { key: 'Off', text: 'Off', data: 'colname3' }
      ],
      totalItemCount: 2,
      hasCheckmarks: false,
      hasIcons: false,
      defaultMenuItemRenderer: [Function: defaultMenuItemRenderer],
      labelElementId: undefined
    }

      at log (src/table.tsx:297:13)

  console.log
    ContextualMenu - after initialization for col.name=col3=, menuFilters is:

      at log (src/table.tsx:320:13)

  console.log
    [
      {
        key: 'col2-val2',
        text: 'col2-val2',
        data: 'colname2',
        checked: false
      },
      {
        key: 'col2-val1',
        text: 'col2-val1',
        data: 'colname2',
        checked: false
      },
      {
        key: 'col2-val3',
        text: 'col2-val3',
        data: 'colname2',
        checked: true
      }
    ]

      at log (src/table.tsx:321:13)

  console.log
    Unit test - number of 'Off' labels is =0=, but should be 1 for col3

      at Object.log (src/table.test.tsx:1052:15)

  console.log
    Unit test - number of 'col2-val1' labels is =1=, but should be 0 for col3

      at Object.log (src/table.test.tsx:1054:15)

  console.log
    Unit test - about to click 'Select All'

      at Object.log (src/table.test.tsx:1056:15)

  console.log
    ContextualMenu - at top for col.name=col3=, listProps is:

      at log (src/table.tsx:296:13)

  console.log
    {
      ariaLabel: undefined,
      items: [
        { key: 'On', text: 'On', data: 'colname3' },
        { key: 'Off', text: 'Off', data: 'colname3' }
      ],
      totalItemCount: 2,
      hasCheckmarks: false,
      hasIcons: false,
      defaultMenuItemRenderer: [Function: defaultMenuItemRenderer],
      labelElementId: undefined
    }

      at log (src/table.tsx:297:13)

  console.log
    ContextualMenu - after initialization for col.name=col3=, menuFilters is:

      at log (src/table.tsx:320:13)

  console.log
    [
      {
        key: 'col2-val2',
        text: 'col2-val2',
        data: 'colname2',
        checked: true
      },
      {
        key: 'col2-val1',
        text: 'col2-val1',
        data: 'colname2',
        checked: true
      },
      {
        key: 'col2-val3',
        text: 'col2-val3',
        data: 'colname2',
        checked: true
      }
    ]

      at log (src/table.tsx:321:13)

  console.log
    Unit test - number of 'Off' labels is =0=, but should be 1 for col3

      at Object.log (src/table.test.tsx:1058:15)

  console.log
    Unit test - number of 'col2-val1' labels is =1=, but should be 0 for col3

      at Object.log (src/table.test.tsx:1059:15)

If you look at the debug statements carefully, you'll notice that when the 2nd filter icon is clicked for col3, it is getting passed the correct data in the listProps prop, but the menuFilters state variable is initialized for the col2 values.
Based on the debugging I've done, I think this is happening because the onDismiss() on the context menu is never called when running from the unit test. This gets called fine from the UI, but from the unit test onDismiss() isn't called, hence the context menu doesn't get initialized properly when it is opened for a different column. I even added a step in the test to click into the Search field, hoping that might trigger onDismiss() on the context menu, but that didn't help.
Also, I confirmed that clicking the Select All button anyway doesn't work as expected since it ends up selecting menu filter values which don't actually exist.
I hope this all makes sense. And if I'm overlooking something in the unit test or if you see an issue with the fix, please let me know. Thanks!

@mturoci I actually spent several days trying to create a meaningful unit test for this issue. I left a comment about this in the original PR yesterday, along with snipits from the test code and snipits from table.tsx where I added console.log() debug statements. You'll find this at the bottom of the original PR comment.
Based on the debugging I've done, I'm pretty sure the test isn't working because onDismiss() for the context menu doesn't get called when running from a unit test. As a result, I think this is leaving state values from previous instances of the ContextualMenu component. So this means in the unit test, the filter selection list on the popup is actually values from the first column that was selected.
I did go ahead and add a new test anyway, which just makes sure that all the checkboxes are selected after clicking Select All, but I'm not sure the test adds much value since these are selections for the wrong column. As a result, the row count will always be 0 + 1 for the header.
Let me know if you think the test should be removed or if I'm overlooking something in the post from yesterday about the issues with the unit test. Thanks!

@mturoci That's awesome that you found a way to get past this from the test! I tried just about everything, but didn't think about simulating the Esc key.
I know the PR is merged now, but I'm still curious to get to root cause of the problem with the menu not going away. I think I found the issue for this in FluentUI and it was resolved late last year. Tomorrow I'm going to replicate the problem locally without Wave and then upgrade to the latest FluentUI to see if this fix resolved it. I'll let you know how that goes. Like I said, I know this isn't necessary, I'm just curious.

I know this isn't necessary, I'm just curious.

Love the passion :) Feel free to make a PR to update the test in case you find the root cause.

@mturoci So it looks like the solution I had in mind is only available in Fluent v9, so not applicable to Wave. I've probably spent enough time in this rabbit hole, so I'm going to leave it there. On to something else now!


@gql directives: alias not working as expected

input: ```
{
hotels {
a: address
}
}
Getting error: "Cannot return null for non-nullable field Hotel.address"

Should work now with apollo-based version


event-dispatcher version conflict with Laravel

symfony/event-dispatcher version used in your package is incompatible with the latest Laravel version.

@speix  have you solved it?

@gelinger777 I am not using the SDK at the moment.

Thank you for raising this issue. Sorry for the very late response. We will investigate this conflict and how to resolve by upgrading the dependencies.
Feel free to submit proposed changes if you wish and we will review.

yes, please make sure the package is fully compatible with Laravel's latest editions...

Hello, any news on this?

Ive just created a PR (#115) for this


Subarray with Palindromic Concatenation

Is your feature request related to a problem? Please describe.
Problem statement: Subarray with Palindromic Concatenation
Describe the solution you'd like
For a given array and an integer K, we need to check if any subarray of size K exists in the array such that concatenation of elements form a palindrome.
Do you want to work on it
I will solve this problem using C++.

Please assign it to me . @nakul-19 @raksha009 @rish-singhal @yasharth291

Please assign this to me in Python

plz assign me this in java @nakul-19 @aaadddiii

Please assign this to me in C++.I am a GSSOC'21 participant


Anonymous record support for expressions in FCS

Testing to follow

Tests added, this is now ready.  It wasn't  hard change

I've enabled ExprTests.fs in VisualFSharp.Unittests.dll - that was disabled for some reason - we should find out why from test failures

FCS docs also updated

Linking #6189

OK this is ready

@alfonsogarciacaro Does this look good enough? I imagine so, since Fable code just works off of the types that have been adjusted.

Once this gets merged I can do a merge+release of FCS to support Fable.

@cartermp I think it's all the info we're able to give :-)

Fable REPL (Try a hard reload to clear the browser cache if it doesn't work) 😸


MRG: Azure

Let's see if it works.

Okay it appears to work, ready for review/merge from my end

Thx @larsoner


should do verify when component init

I specified a rule, if the sample field is '', it will produce error, but this rule not works when the component init. Sample
I must manually invoke the verify function now. Sample

This is a feature, not a bug.
The form component usually indicates what went wrong only after the user has entered something, rather than displaying the form screen and popping up a bunch of errors like "required field not filled" immediately afterwards because the form has no input. So by default, slimeform needs to check for valid input only after the content has changed, but you can do this manually at any time.


The google provider could better by default enforce the antiforgery state token.

As a extra security measurement, often in oauth/openidconnect, a kind of (session) state value is sent when requesting the authorization code, the STS simply return the same value. This is to verify that the user is making the request and not a malicious attacker.
Satellizer has already everything in place to save this state value, and to verify it. The only thing that is missing is a function to generate the state value, and an indication that the state should be encoded in the query string (e.g. via the optionalUrlParams array in the provider config).
So, adding following code in the google provider (in the satellizer config module) is doing the above:
optionalUrlParams: ['display', 'state'],
state: function(){
               var val = ((Date.now() + Math.random()) * Math.random()).toString().replace(".", "");
               return encodeURIComponent(val);
           }

More background here:
https://developers.google.com/identity/protocols/OpenIDConnect (see 1. Create an anti forgery state token)
If this make sense for you, I would be happy to submit a PR for this.
Cheers.

@paulvanbladel That sounds good to me. This may be a better pseudo-random generator though.
> Math.random().toString(36).substr(2);
Output: "tel1ede5l6h9qkt9"

Any update on this?

Ah OK,  you want me to make the PR.
No problem. Expect it tomorrow.

@paulvanbladel Any news on this?

Did pr.
#745

OK, thanks. @sahat, could we close this issue?

Yes forgot to close this issue.


Centos Base recommended?

Hi, was hoping to run some nix packaged code on Expanse. Would you recommend I use a Centos based container? I was planning on just using a nix based one.
Thanks!

Apologies for the delayed reply, this project is no longer maintained now that XSEDE has ended.
Clarification: These images do use CentOS as a base OS, and only include the Nix package manager, not all of NixOS.
However, please feel free to use these templates - though they are offered "as is" - if you feel they will be helpful to you.  You may also wish to contact Expanse help directly to see if they have any requirements for the containers run on their system.


bug while opening the https://practice.rs/why-exercise.html website

Are you still facing this issue?
Mostly it would be due to the loaded cache, try clearing them and re-load. It would work fine!


Filter edit icon component replaced with Font Awesome

CATEGORY
Choose one

[ ] Bug Fix
[ ] Enhancement (new features, refinement)
[x] Refactor
[ ] Add tests
[ ] Build / Development Environment
[ ] Documentation

SUMMARY
This is pretty minor, but just something I noticed while looking around. Since Superset uses FontAwesome, we can replace a custom component with custom SVG by using a simple FontAwesome image.
We should probably upgrade to FontAwesome 5 at some point... many more toys in that toybox!
BEFORE/AFTER SCREENSHOTS OR ANIMATED GIF
Before:

After:

REVIEWERS
@graceguo-supercat / @mistercrunch
Note: This doesn't change any functionality, but as far as I can tell, that button doesn't have functionality in the first place, or at least nothing happens when I click it. Is it for future use, or am I missing something?

Codecov Report

Merging #8600 into master will decrease coverage by 0.07%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #8600      +/-   ##
==========================================
- Coverage   71.69%   71.61%   -0.08%
==========================================
  Files         118      118
  Lines       12591    12591
==========================================
- Hits         9027     9017      -10
- Misses       3564     3574      +10

Impacted Files
Coverage Δ

superset/db_engine_specs/postgres.py
55.55% <0%> (-27.78%)
:arrow_down:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update f42aae8...4e560fe. Read the comment docs.

Oh, and for the record, if we do get FAB to upgrade to FontAwesome 5, we can change fa-pencil to fa-pen and make it look closer to the original icon ;)


Code maintenance

Hi,
I was trying to use SpecAugment (just run a simple augmentation for now).
I was able to install the package, but it seems to have many code issues like typos and other small bugs.
Is there a working instance of this project?
I saw other people get similar errors here.
For example the import problem caused by the capital letter package name import. (import Specaugment vs import specaugment).
Im trying to run SpecAugment on AWS SageMaker environment with pytorch.
It'll be great to get a new link or an easy fix.
Thanks
Yarden Karny

It seems that they are not maintaining this package any longer, if you have tensorflow with version 2.0 you can't use this.


Fix/7479 Add missing padding above the header image

Description
Add missing padding above the header image on RAT Profile info screen

As requested, add missing padding on test certificates screens as well

Link to Jira
https://jira-ibs.wbs.net.sap/browse/EXPOSUREAPP-7479
Screenshots

Actually, seems like there is a header space in iOS 12.5 and the bug assuming same in above iOS 12.5 too but let me check the figma designs with the colleagues.


export to HTML doesn't open easy in Excel anymore after update

System information:

Windows 10
DBeaver version: Latest

Describe the problem you're observing:
Because we have to distribute a large portion of data (200K rows but lots of columns) to our internal customers we export the data to HTML.
After that we copy it to Excel in a template as values so all values are shown correctly without any typical excel 'enhancements'.
Normally when we open the HTML -exportfile in Excel it takes a couple of minutes (the file is +300MB) and we get the data with the query in a topcell  spanning over all rows. the result is an 25MB Excelfile
But since yesterday after i update DBeaver to the latest version, opening the HTML export in Excel takes almost 2 hours.
At first it then looks like i'ts empty but the query is in white spread over  several rows ( = number of rows the query is long)
Underneath is the data we need intact.
how can this be fixed so Excel will open the HTML exports fast again an the query i shown as it was.
Not showing the query is also an option but i haven't found that functionallity yet

Have you tried exporting directly to excel? there is an office plugin available.

@p91paul where can i find that one?
Although we allways save als xlsb-files beacause of the mass load of data.

https://github.com/dbeaver/dbeaver/wiki/Optional-extensions


Bulk upload

ref: https://github.com/pandas-dev/pandas/issues/14670
R does this well, and it makes a material performance impact

I've got this working internally, by writing to a CSV and then uploading that.
I've used the google.cloud.bigquery library though, which this library doesn't seem to use. Is there an explicit reason for this? The credentials are handled a bit differently.

you could certainly add that as a dep. looks like that is a refactor of some older libs?

OK

yeah looks like these are the 'new' ones: https://cloud.google.com/bigquery/docs/reference/libraries#client-libraries-usage-python

Fixed by https://github.com/pydata/pandas-gbq/pull/25. I'll update the changelog to link to this.


Milestone 4 - Processing data in models

In this branch I implement:

I familiarize with 'rails c' command.
I implement All associations.
I create one user by running the following code:   first_user = User.create(name: 'Tom', photo: 'https://unsplash.com/photos/F_-0BxGuVvo', bio: 'Teacher from Mexico.')
   second_user = User.create(name: 'Lilly', photo: 'https://unsplash.com/photos/F_-0BxGuVvo', bio: 'Teacher from Poland.')

I create 4 posts written by one of the users I created by running the following code:   first_post = Post.create(author: first_user, title: 'Hello', text: 'This is my first post')

I create posts comments for one of the posts you created by running the following code:   Comment.create(post: first_post, author: second_user, text: 'Hi Tom!' )

I use other CRUD methods to find, update and delete entities.

HI dear CR this is my result of this milestone!


License?

Great work @wngh1187 !
Can you share under which license you publish the code?
Thank you

Thank you very much for your interest in my research.
Unfortunately, I didn't fully understand your question.
What exactly does license mean?
I referenced the DLA and DSP technique codes from the github address below.
https://github.com/allenai/elastic/tree/master/models

@wngh1187 I was asking under which license you publish your code, for example MIT. You can do this by adding a license.txt to your repo.
Currently it is not further specified, so it can’t be used by others.

@StefanOstwald Thank you so much for your valuable comments.
I created a MIT license file.
Please check this.


Symfony Yaml Library Inclusion

@cleentfaar: Resolves #11
Although there may be an issue with an included library not correctly declaring their own dependencies, friction can and should be reduced for users of the "cleentfaar/slack" package by masking them from this problem and taking the issue up separately with any maintainers of the underlying dependency libraries.
Wonderful library you have - thanks for considering the patch!

:+1: for this!
JMSSerializer only suggests the symfony/yaml, that's why it should be required here.
But I'm not sure about the correct version (comment on commit line).

Superseded by https://github.com/cleentfaar/slack/pull/18 due to minimal version being too high. Thanks for submitting @jimdelois and spotting @smatyas

np!  Sorry for the version confusion - my bad.  Thanks!


Added Section on SSL TLS Everywhere

Fixes #271

Hey there! Does this look good to merge in? Anything I need to change?

OMG yes!
But, I would suggest removing references to SSL since is is obsolete.
Title:
"HTTPS Everywhere"

Matches the name of the EFF plugin
HTTPS is what people see in the address bar

Remove:
or Secure Socket Layer (SSL)

Updated! Thanks @garster!


Card not getting loaded in Lovelace

Checklist:
[X] I updated to the latest version available
[X] I cleared the cache of my browser
Release with the issue:
v3.0.0
Last working release (if known):
N/A
Browser and Operating System:
Arch Linux, Google Chrome v101
Description of problem:
My HA is installed in a Docker container.  I also have HACS installed in the container.
I then installed the frigate-hass-card using HACS. Then I added the below in the configuration.yaml and restarted my container.
lovelace:
  resources:
    - url: /hacsfiles/frigate-hass-card/frigate-hass-card.js
      type: module

But the card is not getting loaded.
The message in Docker start console is:
homeassistant  | 2022-05-12 15:24:37 WARNING (MainThread) [homeassistant.components.lovelace] Lovelace is running in storage mode. Define resources via user interface
The message I get in HACS front page is:
Not loaded in Lovelace
You have 1 Lovelace elements that are not loaded properly in Lovelace.

If I add "mode: yaml" in the configuration, then it loads, but then I lose the capability to make updates to the dashboard using UI, so I can't add the card (and I dont want to add it using yaml coding).
Is this by design or is there a bug here? It's the first time I'm trying to install this card, so I may be doing a mistake or misunderstanding how it works.

Try this. In your dashboard:

Three dots menu on the top right
Edit Dashboard
Manage resources
Add resource

URL: /hacsfiles/frigate-hass-card/frigate-hass-card.js
Type: Javascript module

Hit create

No editing your configuration.yaml at all. Then try adding a Frigate card.
Does that work?

[If yes, I think this is actually a request to improve the documentation for those with frontend resources outside of YAML]

OK, I deleted the card from my previous setup, I removed the repository, restarted HACS.
I restarted HA and then added back the repository. Now when I tried to check the "Manage Resources", I saw this already there:
URL:  /hacsfiles/frigate-hass-card/frigate-hass-card.js?hacstag=394082552300
Type: Javascript Module

And then I tried to add the Card and it worked! So I think this is good.
Though the video type selection looked weird with 5 options, top one selected, but no text (does not show what is that option). This may be another bug though...
Live view provider for this camera
(o)  --> This one is already selected but no description visible
( ) Automatic
( ) Home Assistant (i.e. HLS, LL-HLS, WebRTC native)
( ) Frigate JSMpeg
( ) WebRTC Card (i.e. AlexxIT's WebRTC Card)

And then I tried to add the Card and it worked! So I think this is good.

Great! I updated the installation instructions, as they were really aimed at YAML users rather than (modern out of the box) Home Assistant users, and I think that may have made them more confusing for you in this case.

Though the video type selection looked weird with 5 options, top one selected, but no text (does not show what is that option). This may be another bug though...

I don't think that's a bug, at least if it looks like this:

You just don't have that parameter set in your config, so nothing is selected. Please re-open if I'm missing the point!

Just some feedback - Brand new frigate (and card) non-yaml user, but I also had to manually add the resource as per https://github.com/dermotduffy/frigate-hass-card/issues/583#issuecomment-1125624554, and I didn't see any instructions for that either. I do see the instructions for yaml users though. Should this resource have been made available automatically on installation or have I missed the instruction?

Just some feedback - Brand new frigate (and card) non-yaml user, but I also had to manually add the resource as per #583 (comment), and I didn't see any instructions for that either. I do see the instructions explicitly for yaml users though (which I don't think I am?). Should this resource have been made available automatically on installation or have I missed the instruction?

same here- was Confused on this and spent a decent amount of time trying to find this new frigate-hass-card.  Since I was on a brand new HA install I expected the card to be available after I had downloaded /installed the frigate-hass-card though HACS.
It's still not clear if there is any scenario in which a user can simply click download via HACS and then have access to the card (ie wo having to do add module ->
url: /hacsfiles/frigate-hass-card/frigate-hass-card.js
type: module

to be clear - i am brand new to Home assistant (but not IT/tech) , so prehaps this is more an issue on my end.
thanks!


Support Windows network shares as absolute paths

Windows shares start with \\. It would be nice if webpack could output a bundle directly to a folder on a Windows share.

What kind of change does this PR introduce?
Allows config.output.path to start with \\ which, on Windows systems, is a valid absolute path to a network share.

Did you add tests for your changes?
No - it is not clear to me how to "test" this.
Do I add a test that checks if a path that starts with \\ is now allowed?
Or a test that depends on a network share being available and actually writing to that output?

Does this PR introduce a breaking change?
No.

What needs to be documented once your changes are merged?
https://webpack.js.org/concepts/output/ should probably include an example of using a Windows share.

Do I add a test that checks if a path that starts with \\ is now allowed?

You can test this in test/Validation.test.js. Instead of testing that an absolute path is allowed for output.path, test that an absolute path (network share) is forbidden for i. e. output.filename
output: {
  filename: "//computer/share/path"
}

This should cause an validation error, because absolute paths are not allowed here.

test that an absolute path (network share) is forbidden for i. e. output.filename
output: {
  filename: "//computer/share/path"
}

This should cause an validation error, because absolute paths are not allowed here.

I'm not following. The point of this was to allow another form of absolute path for the output.path. I'm not seeing how output.filename relates. Could you please elaborate?

Could you please elaborate?

They use the same check for absolute paths, just inversed. This way you test that network share paths are disallowed for output.filename. That's easy to test compared to really using an network share in CI...

I think I see what you're saying. How would that differ from just testing that a path starting with \\ is allowed in output.path?

How would that differ from just testing that a path starting with \\ is allowed in output.path?

You can do this too.

I still intend to finish this but this has been kicked low on my priority list. If someone else wants to add the tests, please feel free. I might get inspired to push this over the finish line one night but I'd be happy if someone else took the lead.

/cc @sokra this PR we should move in schema-utils, right?


[ Bug] Back button from Home screen - Displays loading screen indefinitely

When you press the back button from Home screen - It displays the loading screen indefinitely. The only way to fix it is to close the app and reopen it. Can the loading screen be popped from the Navigation history?

duplicate of #460


Strange program output

Dear researchers (Or anyone looking this issue):
I got the strange output when running an example code which is slightly modified by myself, and I don't know why it was so.
This is my source code:
#include <librealsense2/rs.hpp> // Include RealSense Cross Platform API
#include              // for cout
#include <opencv/cv.hpp>
// Hello RealSense example demonstrates the basics of connecting to a RealSense device
// and taking advantage of depth data
int main(int argc, char * argv[]) try{
// Create a Pipeline - this serves as a top-level API for streaming and processing frames
rs2::pipeline p;
// Configure and start the pipeline
p.start();

while (true){
    // Block program until frames arrive
    rs2::frameset frames = p.wait_for_frames();

    // Try to get a frame of a depth image
    rs2::depth_frame depth = frames.get_depth_frame();
    rs2::video_frame color = frames.get_color_frame();

    auto w = color.get_width();
    auto h = color.get_height();
    cv::Mat image(cv::Size(w, h), CV_8UC3, (void*)color.get_data(), cv::Mat::AUTO_STEP);

    std::cout<<"color frame, width="<<w<<" ,height="<<h<<std::endl;
    std::cout<<std::endl<<std::endl;

    // Get the depth frame's dimensions
    auto width = depth.get_width();
    auto height = depth.get_height();

    // Query the distance from the camera to the object in the center of the image
    float dist_to_center = depth.get_distance(width / 2, height / 2);

    // Print the distance
    std::cout << "The camera is facing an object " << dist_to_center << " meters away \r";
}
return EXIT_SUCCESS;

}
catch (const rs2::error & e){
std::cerr << "RealSense error calling " << e.get_failed_function() << "(" << e.get_failed_args() << "):\n    " << e.what() << std::endl;
return EXIT_FAILURE;
}
catch (const std::exception& e){
std::cerr << e.what() << std::endl;
return EXIT_FAILURE;
}
The output of the program is:
`
color frame, width=1280 ,height=720

color frame, width=1280 ,height=720ters away

color frame, width=1280 ,height=720ters away

color frame, width=1280 ,height=720ters away

color frame, width=1280 ,height=720ters away

color frame, width=1280 ,height=720ters away

color frame, width=1280 ,height=720ters away

...

`
It is obviously that the output 'height=720ters away ' is wrong, but why it was so?
I am looking forward to your reply and thanks in advance.

Required Info

Camera Model
L515

Operating System & Version
Linux (Ubuntu 20.04)

Platform
PC

SDK Version
2

Language
C++

the second line in source code is:
#include <iostream>

Hi @Billccx  I see that your code is based on the rs-hello-realsense C++ example program that prints out the distance in real-world meters from the center depth pixel to an observed object / surface.
https://github.com/IntelRealSense/librealsense/blob/master/examples/hello-realsense/rs-hello-realsense.cpp
When you print the width and height of the color frame though, you are simply printing out the default color resolution of the L515 - 1280x720

Hi @Billccx I see that your code is based on the rs-hello-realsense C++ example program that prints out the distance in real-world meters from the center depth pixel to an observed object / surface.
https://github.com/IntelRealSense/librealsense/blob/master/examples/hello-realsense/rs-hello-realsense.cpp
When you print the width and height of the color frame though, you are simply printing out the default color resolution of the L515 - 1280x720

Thanks a lot for such a quick reply !
But actually, what confused me is that the output of the program is not "intact".
According to the source code, the right output should be:
color frame, width=1280 ,height=720
The camera is facing an object "xxx" meters away
color frame, width=1280 ,height=720
The camera is facing an object "xxx" meters away
...
however, it turned out to be:
color frame, width=1280 ,height=720ters away
color frame, width=1280 ,height=720ters away
color frame, width=1280 ,height=720ters away
...
which is very strange.
I just wonder why it was so.

I wonder if you are missing a quotation mark when printing the color.  The width 'w' has opening and closing quotation marks - " " - but height 'h' only has opening quotation marks but not a closing one.

I wonder if you are missing a quotation mark when printing the color. The width 'w' has opening and closing quotation marks - " " - but height 'h' only has opening quotation marks but not a closing one.

Got it. Thank you so much.

It's no trouble at all - I'm pleased that I could help. :)

Case closed due to solution achieved and no further comments received.


feature/ledger management

Introduce sqlstorage.DB interface and sqlstorage.Schema. sqlstorage.DB represents the entire set of ledgers. sqlstorage.Schema represents a specific ledger.
wip : add ledger list on driver
Remove storage.Factory.
Add storage list command.
Fix tests and remove rememeber_config storage.
Remove useless packages.
Simplify storage.
Add command to upgrade storages.
Add upgrade command.
Add storage delete.
Add postgresql migration.

Quick question on this: should we have the _info endpoint list ledgers according to ledgers found by scan or are we keeping this for another PR?


What should we access ?

if we  allow all resources for the access token. may have security risk. so ,
what is necessary and must select to run this app properly.

@Md-Asaduzzaman-Muhid I don't have an exact list right now. You can find all rest API endpoints which use access token in src/magento/lib/admin/index.js.
Then you can open Magento source and search for webapi.xml file somewhere in vendor/magento directory and find what resource it requires.
For example GET /V1/store/storeConfigs is defined in vendor/magento/module-store/etc/webapi.xml
<!-- Store Config -->
<route url="/V1/store/storeConfigs" method="GET">
    <service class="Magento\Store\Api\StoreConfigManagerInterface" method="getStoreConfigs"/>
    <resources>
        <resource ref="Magento_Backend::store"/>
    </resources>
</route>

So the required resource for this particular endpoint is Magento_Backend::store.
In case you are going to collect all the required resources please share it here then I'll add it to the docs.

Thank you so much for your quick response.


Added current model indicator with an * when --listmodels is called

What this Pull Request (PR) does
Trying to add a small and simple feature for my first contribution. Whenever 'fabric --listmodels' is called, the output will denote the currently used model with an asterisk after it. Hopefully this will give users a better idea of the current model they've set Fabric to utilize.
Related issues
closes #446
Screenshots

Just encountered the same thing and would love having it in. Would maybe write a model print helper function, to not have so many if repetitions and only one place to change the pattern of what is the current model and what not
maybe would also have instead of a * something like (current)

Hey @auryn31 , I implemented the changes you mentioned. What do you think?

This is great, but we're moving to Go. Please resubmit if this isn't fixed after the migration. Thank you!


nuclei: 2.7.3 -> 2.7.4

Description of changes
https://github.com/projectdiscovery/nuclei/releases/tag/v2.7.4

Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
22.11 Release Notes (or backporting 22.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module
[ ] (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes

[x] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 182232 run on x86_64-linux 1

1 package built:

nuclei


chore: upgrade to wing 0.50

adapt to https://github.com/winglang/wing/releases/tag/v0.50.0

I was working on updating this, but the build is failing during terraform plan with an cyclic resource dependency issue. I think it's the same issue as https://github.com/winglang/wing/issues/2740

The code won't deploy but let's merge it anyway for anyone viewing the code / trying it out locally.


Handle un-formatting nodes

Allow to un-format selected nodes

I'm actually surprised at how little code it took to write unformat_several_nodes by just removing the formatting node altogether and then re-creating it. I spent several days in this banging my head before giving up and this solution is so simple. Congrats!


implement class bmpl::frmt::BAHeadersList

This class inherits from bmpl::utils::ErrorStatus. It internally sets its error status while running through the BA headers contained in an OS/2 BAfile.

Completed. Compiles. Still to be tested.


Create trivial go routine for negative scrape interval.

Resolves #233
Description
Creates a trivial go routine that simply waits for stop when the scrape interval is negative. This prevents prom scraper from exiting immediately when only negative scrape intervals are configured.
Type of change

[X] Bug fix (non-breaking change which fixes an issue)

Testing performed?

[X] Unit tests

I sorta prefer blocking on <-p.stop at the end of the Run, or startScrapers, function instead. That way, it can be made more clear why we're blocking and what the reasoning is, and we're only leaving one goroutine open instead of N+1 where N is the number of prom scraper configs.

We should actually only be creating N go routines, since a config with a negative scrape interval is still a config (without this change, we were creating N-1 go routines). However, I'm happy for there to be a simple <-p.stop at the end of the Run, it is indeed clearer.

It sounds like this is closable?


Add ability to customize docker image using labels

Implemented option from comment to PR https://github.com/jenkinsci/mesos-plugin/pull/198

Thank you for this pull request! Please check this document for how the Jenkins project handles pull requests.

FWIW you can update the existing PR by pushing to the same branch, instead of creating a new PR

@Vlatombe, could you please review my PR

@Vlatombe, Thanks for quick response!
I've implemented the requested changes so could you please take a look then you have time.

I'm getting a NPE on the following assertion added to getMesosSlaveInfoForLabelTest
assertEquals(null, buildMesosSlaveInfo(null, false).getMesosSlaveInfoForLabel(null).getLabelString());

This matches a case where a slave configuration with a null (empty) labelString (cf. https://github.com/jenkinsci/mesos-plugin/pull/178 introducing this feature)

@Vlatombe, Thank you for noticed! I've added a few assertions and fix logic.

LGTM. Thank you for your contribution!


Don't show 'Incomplete Journeys' section if there aren't any

On reflection, prefer to keep it in place


Secure login to the desktop

How can one enable secure login to the desktop?
Like https://<IP_ADDRESS>:6080/vnc.html

Hi, I don't consider this will be one feature of this image. If you wanna add this, you may refer nginx as a reverse proxy before this service.

FYI I use ngrok to do so. It is easy and straight forward.

Close inactive thread


x/tools/go/ssa: BuilderMode methods do not handle BareInits option

The documentation for ssa.BuilderMode states:
const BuilderModeDoc = `Options controlling the SSA builder.
The value is a sequence of zero or more of these letters:
...
I	build bare [I]nit functions: no init guards or calls to dependent inits.
`

In fact, the I option is not handled by the String and Set methods on BuilderMode. In practice, this means that using the BareInits option is inaccessible through e.g. ssadump:
$ ssadump -build=I main.go
invalid value "I" for flag -build: unknown BuilderMode option: 'I'

CC @alandonovan
I accepted this fix, but probably should have confirmed that this was an accidental omission in https://golang.org/cl/5172. If not, please let me know and I'll revert.


[BUG]: Error in mkv videos "errorCode": "24001"

Version
6.5.0
What platforms are you having the problem on?
Android
System Version
14
On what device are you experiencing the issue?
Real device
Architecture
Old architecture
What happened?
Getting error in some mkv files
{"errorCode": "24001", "errorException": "androidx.media3.exoplayer.ExoPlaybackException: MediaCodecAudioRenderer error, index=1, format=Format(2, Hindi - NimitMak SilverRG, null, audio/mpeg-L2, null, -1, hi, [-1, -1, -1.0, null], [2, 48000]), format_supported=NO_UNSUPPORTED_TYPE", "errorStackTrace": "androidx.media3.exoplayer.ExoPlaybackException: MediaCodecAudioRenderer error, index=1, format=Format(2, Hindi - NimitMak SilverRG, null, audio/mpeg-L2, null, -1, hi, [-1, -1, -1.0, null], [2, 48000]), format_supported=NO_UNSUPPORTED_TYPE
        at androidx.media3.exoplayer.ExoPlayerImplInternal.handleMessage(ExoPlayerImplInternal.java:623)
        at android.os.Handler.dispatchMessage(Handler.java:102)
        at android.os.Looper.loopOnce(Looper.java:224)
        at android.os.Looper.loop(Looper.java:318)
        at android.os.HandlerThread.run(HandlerThread.java:67)
Caused by: androidx.media3.exoplayer.mediacodec.MediaCodecRenderer$DecoderInitializationException: Decoder init failed: [-49999], Format(2, Hindi - NimitMak SilverRG, null, audio/mpeg-L2, null, -1, hi, [-1, -1, -1.0, null], [2, 48000])
        at androidx.media3.exoplayer.mediacodec.MediaCodecRenderer.maybeInitCodecWithFallback(MediaCodecRenderer.java:1079)
        at androidx.media3.exoplayer.mediacodec.MediaCodecRenderer.maybeInitCodecOrBypass(MediaCodecRenderer.java:551)
        at androidx.media3.exoplayer.mediacodec.MediaCodecRenderer.onInputFormatChanged(MediaCodecRenderer.java:1560)
        at androidx.media3.exoplayer.audio.MediaCodecAudioRenderer.onInputFormatChanged(MediaCodecAudioRenderer.java:517)
        at androidx.media3.exoplayer.mediacodec.MediaCodecRenderer.readSourceOmittingSampleData(MediaCodecRenderer.java:994)
        at androidx.media3.exoplayer.mediacodec.MediaCodecRenderer.render(MediaCodecRenderer.java:814)
        at androidx.media3.exoplayer.ExoPlayerImplInternal.doSomeWork(ExoPlayerImplInternal.java:1112)
        at androidx.media3.exoplayer.ExoPlayerImplInternal.handleMessage(ExoPlayerImplInternal.java:544)
        ... 4 more
", "errorString": "ExoPlaybackException: ERROR_CODE_DECODER_INIT_FAILED"}

showing audio is unsupported but I tried in various other native players that use Exoplayer and the video is playing fine
Reproduction Link
No response
Reproduction
Try playing the sample URL and the player shows error
here is a sample video URL = https://pixeldra.in/api/file/bQb6RKk3?download,

@himanshu8443
I tested it with your URL, and everything works correctly. I didn't see any errors in logcat. Could you please give me some clues about it?

@himanshu8443 I tested it with your URL, but I didn't see any errors in logcat. Could you please give me some clues about it?

I don't know if it is a device-specific issue but I am also getting the same error in android emulator. Have you tried it in emulator?
Properties
avd.ini.displayname      Pixel_3a_API_34_extension_level_7_x86_64
avd.ini.encoding         UTF-8
AvdId                    Pixel_3a_API_34_extension_level_7_x86_64
disk.dataPartition.size<PHONE_NUMBER>
hw.accelerometer         yes
hw.arc                   false
hw.audioInput            yes
hw.battery               yes
hw.camera.back           emulated
hw.camera.front          emulated
hw.cpu.ncore             2
hw.device.hash2          MD5:0e6953ebf01bdc6b33a2f54746629c50
hw.device.manufacturer   Google
hw.device.name           pixel_3a
hw.dPad                  no
hw.gps                   yes
hw.gpu.enabled           yes
hw.gpu.mode              auto
hw.keyboard              yes
hw.lcd.density           440
hw.lcd.height            2220
hw.lcd.width             1080
hw.mainKeys              no
hw.ramSize               1536
hw.sdCard                yes
hw.sensors.orientation   yes
hw.sensors.proximity     yes
hw.trackBall             no
image.androidVersion.api 34
image.sysdir.1           system-images\android-34\google_apis\x86_64\
PlayStore.enabled        false
runtime.network.latency  none
runtime.network.speed    full
snapshot.present         no
tag.display              Google APIs
tag.id                   google_apis
vm.heapSize              256

I tested it on the emulator, and it works correctly.

The answer is here : https://github.com/google/ExoPlayer/issues/6525
The mime type is audio/mpeg-L2 which is not mandatory on android device integration. The solution should be to build with ffmpeg (I never try)

ok, I can confirm when I tried playing it without using onAudioTracks  property video played fine. The error only occurs on using onAudioTracks  property and changing the audio track.
for me even logging the value causing the issue
  onAudioTracks={e => {
          console.log('audioTracks', e.audioTracks);
        }}

I reproduce the issue on an exoplayer sample (without ffmpeg). In fact in the sample, the track is grey because it is not supported. Here user cannot identify the track as unsupported. I will add a new flag to be able to track unsupported tracks.
I really think the solution is to enable ffmpeg in exoplayer to be able to play this track...

I reproduce the issue on an exoplayer sample (without ffmpeg). In fact in the sample, the track is grey because it is not supported. Here user cannot identify the track as unsupported. I will add a new flag to be able to track unsupported tracks. I really think the solution is to enable ffmpeg in exoplayer to be able to play this track...

yes ffmpeg is really needed to provide support on various devices. this is the only blocker i am facing currently.

Let's follow up in: https://github.com/TheWidlarzGroup/react-native-video/issues/3106


Import CSV file

Hi team,
I went through all the documentation, but couldn't find a way to import a CSV via the better-sqlite3 library.
Is there a way to invoke the .import special sqlite3 command via the library?

"dot commands" such as .import are features of the sqlite command-line utility, not SQLite the library. So you'll have to parse and insert the CSV manually.

Closing due to inactivity


dataserver fail to start when one mount point does not exist - no message in error log

datanode.json
"disks": [
        "/mnt/btrfs/cha1:2474836480",
        "/doesnotexist:21474836480"
    ]

{1024 1048576}
Rlimit Final {1024000 1024000}
Fatal: failed to start the baud storage daemon -  bad config file

the error message could actually say what the problem is
there is no error message in the dataNode_error.log

#121 fixed


SeString payload exception causing full text search to fail.

I was wondering why full text search wasn't working on some sheets so I did some digging and apparently there's a couple of cells in the data sheets which are throwing exceptions when it tries to parse the SeString.
The problem cells in question are on CustomTalkDefineClient row 4, column 0, and QuestDefineClient row 136, column 0.
Here is the stack trace it spits out:
System.OverflowException: Arithmetic operation resulted in an overflow.
   at Lumina.Text.Payloads.BasePayload..ctor(Stream stream)
   at Lumina.Text.SeString.BuildPayloads()
   at System.Lazy`1.ViaFactory(LazyThreadSafetyMode mode)
   at System.Lazy`1.ExecutionAndPublication(LazyHelper executionAndPublication, Boolean useDefaultConstructor)
   at System.Lazy`1.CreateValue()
   at Alpha.Utils.UiUtils.XmlRepr(StringBuilder sb, SeString s) in ..\Alpha\Alpha\Utils\UiUtils.cs:line 68
   at Alpha.Utils.UiUtils.DisplaySeString(SeString s) in ..\Alpha\Alpha\Utils\UiUtils.cs:line 84
   at Alpha.Modules.Excel.ExcelModule.DisplayObject(Object obj) in ..\Alpha\Alpha\Modules\Excel\ExcelModule.cs:line 355
   at Alpha.Windows.ExcelWindow.<>c__DisplayClass31_1.<ResolveSidebarFilter>b__1() in ..\Alpha\Alpha\Windows\ExcelWindow.cs:line 605

I'm currently working on a full rewrite of Alpha at the moment, so it's unlikely I'll fix it soon, but I'll make sure this is accounted for there.


Add override scheduler option to Pods

Signed-off-by: Rohit-PX<EMAIL_ADDRESS>

Test job:  https://jenkins.portworx.co/job/Torpedo/job/tp-dev-test/322/


Add support for presigned URLs

Describe the solution you'd like
AWS allows sharing access to objects through presigned URLs:
https://docs.aws.amazon.com/AmazonS3/latest/userguide/using-presigned-url.html
Investigate what it would take to add similar support to the gateway

cli example:
aws --endpoint-url http://localhost:7070 s3 presign s3://my-bucket/my-object  --expires-in 604800


fix(clerk-js): Fix border inconsistencies

Description
This PR fixes border inconsistencies mostly for actions inside components & screens:

<OrganizatioSwitcher/>
<UserButton/>
<OrganizationList/>
Account switcher screen when multisession is enabled

Checklist

[ ] npm test runs as expected.
[ ] npm run build runs as expected.
[ ] (If applicable) JSDoc comments have been added or updated for any package exports
[ ] (If applicable) Documentation has been updated

Type of change

[ ] 🐛 Bug fix
[ ] 🌟 New feature
[ ] 🔨 Breaking change
[ ] 📖 Refactoring / dependency upgrade / documentation
[ ] other:

!preview

!preview


Remove unused Link component in Redux-example.md

Nothing related to next.js source code but a request to update the Redux-example.md wiki page:
The 4th import can be removed as it's not used in the rest of the example code:
import Link from 'next/link'
I guess this one's for @impronunciable. :-)

Done, thanks!


Mickle, Segurado, Hayashi

From pombelist:

I have a gff file (attached) that contains the ASM294v1.16 coordinates of both the Segurado/Antequera 2003 survey of A/T rich regions as well as the Hayashi/Masukata 2007 survey of PreRC sites.
It comes from data from Joel Huberman's 2007 paper (PMID 18093330), with the coordinates lifted over to the new assembly. The origins in this gff file overlap quite well with the origins identified by Dagaku/Carr via PuSeq, which were annotated with current coordinates, and the flanking genes coincide with Huberman's annotation, so I think the LiftOver went well.
Let me know if you have any questions.
Mikel Zaratiegui
On Aug 2, 2019, at 5:49 AM, Mukesh Pratap Yadav wrote:
Dear All
I am unable to find latest genomic coordinates for Hayashi et al. 2007 (Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast. Hayashi M, Katou Y, Itoh T, Tazumi A, Yamada Y, Takahashi T, Nakagawa T, Shirahige K, Masukata H, EMBO J. 2007 Mar 7; 26(5):1327-39), could you please help me to get the new coordinates. This would be great help.
With best wishes and best Regards
Attachments area

Note that it looks like this paper also contain their own data
oris_segurado_hayashi_ASM294.txt

I made 5 tracks using this mapping file, as attached.
I have added meta data for them.
They are GFFs, let me know if I should format them further before they can be loaded.
Replication origins with lower efficiency in replication checkpoint mutants - Mickle et al. (2007).txt
Replication origins with greater efficiency in replication checkpoint mutants - Mickle et al. (2007).txt
Replication origins with functional classification - Mickle et al. (2007).txt
Replication origins with greater efficiency in replication checkpoint mutant - Hayashi et al. (2007).txt

Pre-replicative complex localization, early and late firing origins - Hayashi et al. (2007).txt
A+T-rich islands - Segurado et al. (2003).txt

They are GFFs, let me know if I should format them further before they can be loaded.

From the JBrowse docs it looks like GFF is no problem for new tracks.  I've processed the GFF tracks as described here: http://jbrowse.org/docs/tutorial.html#loading-tabix-gff3
The files are now in the right place on the server and I've added the URLs to the metadata file.
So we should be able to try the new tracks when you're ready.

Awesome. Yes lets do it! I dont have my laptop with me to change to col to yes but can check when they are live.
On Fri, 23 Aug 2019 at 01:34, Kim Rutherford <notifications<EMAIL_ADDRESS>wrote:
They are GFFs, let me know if I should format them further before they can be loaded.
From the JBrowse docs it looks like GFF is no problem for new tracks. I've processed the GFF tracks as described here: http://jbrowse.org/docs/tutorial.html#loading-tabix-gff3https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fjbrowse.org%2Fdocs%2Ftutorial.html%23loading-tabix-gff3&data=02|01||9751ea08f6904cabd96708d727595624|1faf88fea9984c5b93c9210a11d9a5c2|0|0|637021136956402059&sdata=L9mxEXU0dojDfMz8kF4tLsFuu0S3qK0jdqhvdq%2B0fcM%3D&reserved=0
The files are now in the right place on the server and I've added the URLs to the metadata file.
So we should be able to try the new tracks when you're ready.
—
You are receiving this because you were assigned.
Reply to this email directly, view it on GitHubhttps://github.com/pombase/website/issues/1388?email_source=notifications&email_token=ADBDJURKCKHAEUYEUNRSXATQF4PB3A5CNFSM4IJSNSK2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD46WJ3I#issuecomment-524117229, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ADBDJUS3WHPN3DB7ONCMMHLQF4PB3ANCNFSM4IJSNSKQ.
--
Antonia Lock, PhD
PomBase Biocurator, http://www.pombase.org
Department of Genetics, Evolution and Environment,
The Darwin Building,
University College London
London WC1E 6BT, UK

Awesome. Yes lets do it!

That's the spirit!  :-)

I dont have my laptop with me to change to col to yes but can check when they are live.

I've turn on the tracks in the metadata file so they should be visible on Saturday morning if all goes well.  I'll check them too.

Those tracks are live now.
I think we might need to make the labels shorter:

Thanks! Yes if it can be moved elsewhere...can we add a column for "comment" or "misc"? I think it would be good for future reference to know the information at the end.

Yes if it can be moved elsewhere...can we add a column for "comment" or "misc"?

I think we could add another column.  I'll experiment with that.

I've added a "comment" column in the metadata file.  The comments show up in the "About track" dialog:

How's that?

Yes that's good - but I'd like to include the PMID for the paper in which the liftover was carried out PMID 18093330

does it make sense that when I click on a feature I don't see any of the track information? Where does the "source" come from? (this is from the mickle track)

ah, also, this is important, can we display a label for the features? I bunged the label into col 9 - e.g. for the Mickle track "ori 16 - medium"  "ori 14 - weak"

Where does the "source" come from? (this is from the mickle track)

That's the source column from the GFF file.  Should we change it?

Maybe PMID 18093330 would be better as a source? It's not a big deal I think

at leat I have a better idea for next file of how to do it. However you tweak the files now for display of label etc....just share a copy with me and I can use it as a template for subsequent files of this type (e.g. tweaks to display label)

ah, also, this is important, can we display a label for the features? I bunged the label into col 9 -
e.g. for the Mickle track "ori 16 - medium" "ori 14 - weak"

Done!  I added "Name=" at the start of column 9 so that JBrowse would use the label.
Here's an example:
https://www.pombase.org/external_datasets/Mickle_2007/Replication.origins.with.greater.efficiency.in.replication.checkpoint.mutants.-.Mickle.et.al.2007.gff.gz
The file looks like:
I       segurado_hayashi        replication_origin      9274    12158   .       .       .       Name=ori 1 - origin has greater activity in checkpoint mutant strains
I       segurado_hayashi        replication_origin      14555   18042   .       .       .       Name=ori 2 - origin has greater activity in checkpoint mutant strains
I       segurado_hayashi        replication_origin      293738  294902  .       .       .       Name=ori 24 - origin has greater activity in checkpoint mutant strains

whoopee, I have announced & made news item

I don't think we should put phenotype information into the "name" label. This is only for the name. FI it is required it should go int he comment even if this means that it does not get displayed.
The browser is only for features, associated data should go on feature pages.

Phenotypes for features should  be treated in the same way as features for genes.
This is a phenotype of the checkpoint mutant  assayed_using ori 1
(and could be displayed reciprocally on the feature pages when we have them).

For now, I would  i) remove ii) open a ticket for the rest. it isn't urgent to display this.

We also need to bear in mind that here we are creating features in the GFF file. These will require unique identifiers? How should we do this?
Where do the names "ori 1" "ori 2" and "ori 24" come from? (i.e which naming schema are we using for origins, I'm not aware that this has been decided.... but then again I don't know anything about this feature-type)

Note that in the contigs replication origins are annotated
FT   rep_origin      3320125..3321168
FT                   /note="5211 (-1) 1 1044 SPARS767 X07892 Yeast ARS element
FT                   (pARS767)"
(I thought they has SO IDs but they don't.....)

I don't understand the metadata, so maybe need to make this clearer.

cd2delta and rad3 delta
two single mutant strains
How do we get one track from 2 strains?

sorry Val, I don't follow...what phenotypes?
the weak/strong refers to the strength of the origin (I think it is the same as early/late, but wanted to reciprocate what is in the paper in case they differ....can always tidy up later if required/appropriate).
I've named the features what they are named in the paper. Should we settle on a consensus we can always make them synonyms

If the data label is
Replication origins with greater efficiency in replication checkpoint mutants - Mickle et al. (2007)
I don't see why you need the appendage to "name" at all...?

6 is an intersect...i can put that in a comment (there was nowhere easy to explain this before we had a comment column)

I don't see why you need the appendage to "name" at all...?

I don't understand this comment

7 continued.
because when you are looking at the track you can see that the "origin has greater activity in checkpoint mutant" from the track label?

Putting it in "name" will cause all sorts of problems....

6 is an intersect...i can put that in a comment (there was nowhere easy to explain this before we had a comment column)

I don't understand what an "intersect" is either in this context?

I see, strong medium weak refers to the strength of the WT origins. We need to move this to somewhere else, it can't go in "Name"
I was looking at  the labels "checkpoint has greater activity in checkpoint mutants". This is a phenotype. However, this is easy to deal with. It isn't required in the name label at all because the track description provides this information?

OK to use these names here.
As you say we can make them synonyms. Imooirtant point is that the name fiels only has "name" in it (never put data in a field that does not belong in there, if required  need to think of a better solution)

If we need to display the weak, strong, medium designation,  and only the name label  can  be displayed, we would need to split into separate tracks.

color coding?

yeah can split...presumably people want to know which ones are early and whihc ones are late or so many papers wouldnt look at it?

Ignore point 5...

Colour coding would be good if that is possible!

by "intersection"  do you mean that the data from both mutant arrays is pooled?

Maybe I am being overly twitch about the gff "name=" but this  seems to be the source we will use for these  origin names, so I think it is good to keep this clean.

Also great to get these data hosted.... these are only minor comments

no, it is data points common to both mutants

no, it is data points common to both mutants

ugg....that sounds highly selective.... but I guess it's old data.
We need to use text which makes this clearer...

I think I would say explicitly :
common data points from two single mutant strains

This dataset was nevefr announced, but I think there may be outstanding issues with the labelling.
Essentially the "label" which should be an ID also contain information that is not required, it is in the track label:
see

I just found a ticket that says this was announced
was it ?
https://github.com/pombase/website/issues/772

yes.

@Antonialock  what does the phrase "replication origins with functional classification" mean?
I don't like using 'functional classification in this context. What is the axis of classification here?
is that "experimentally described origins" or something else?

whether they are weak or strong ORIs

OK got it. I thought that was the other 2 tracks, but they are in mutants.

Would "DNA replication origin strength" be better? @mah11
Or is "functional classification" well used in this context.

I can see the value of having the strength visible in the label, but conflating the origin name and strength niggles me.
At least  the data should be available "typed" in the popup, and stored for display once we have other sequence features

label= ori123 weak
name=ori123
origin_strength=weak

I'm also not sure where this  origin naming system comes from. I think there is aa 'definitive' naming system developed by Conrad Nieduszynski  at oridb and we should use that.....maybe this is the oriDB system
I will check that.

Would "DNA replication origin strength" be better? @mah11
Or is "functional classification" well used in this context.

Neither; I'd go with "DNA replication origins (classified by usage frequency)", or put "initiation frequency" or "initiation efficiency" as the classified-by thing.

OK,   I thought that did not sound right. we will change to
DNA replication origins (classified by usage frequency)

I think there is only one thing to do here.
change the track labels on the mickle dataset to
DNA replication origins (classified by usage frequency)
@mah11 or @kimrutherford  could you do this. I need to have c-line Git editing before I dare edit this table (it's impossible in the webinterface)

change the track labels on the mickle dataset to
DNA replication origins (classified by usage frequency)

Just to be clear, do you want to change "Replication origins" to "DNA replication origins (classified by usage frequency)" in each label?

no it's the "track label"
Replication origins with greater efficiency in replication checkpoint mutants
to
DNA replication origins (classified by usage frequency)

no it's the "track label"
Replication origins with greater efficiency in replication checkpoint mutants
to
DNA replication origins (classified by usage frequency)

Sorry it's still not clear.  Only one label contains "Replication origins with greater efficiency in replication checkpoint mutants".
The track labels are:
Replication origins with functional classification - Mickle et al. (2007)
Replication origins with greater efficiency in replication checkpoint mutants - Mickle et al. (2007)
Replication origins with lower efficiency in replication checkpoint mutants - Mickle et al. (2007)
What should they be changed to?

Oh right I will need to check that.
I think the one I was most concerned about was
Replication origins with functional classification
I did not know what that meant.
Will find out more tomorrow...

I think
Replication origins with functional classification-> Replication origins (classified by usage frequency)
the other two can stay as they are.
Phew, I made a meal of that!
Anyway I think that all of the data in this ticket is hosted...which is the important thing.

I've made the config file change.  It should be visible in the morning.


Add note about LightmapGI only baking nodes under its parent

LightmapGI's documentation currently doesn't mention the fact it only bakes nodes under its parent.
This can make the user think there is something wrong with their scene setup or 3D models, as it refuses to bake when the user's models / world isn't under the same parent as the LightmapGI.
I personally encountered this issue because I tried adding a LightmapGI underneath a blank node called "Environment" under which a WorldEnvironment was also present, and the LightmapGI complained about having nothing to bake.
Made for the godotengine/godot-docs#9694 issue
Linked PR: godotengine/godot-docs#10247

Meshes or its the same for lights?

LGTM. Just merged the corresponding docs repo PR.

@jcostello Meshes or its the same for lights?

Sorry for the very late reply!
The LightmapGI node only looks at nodes underneath its parent, its the same for all types.
I believe this was done so you could have several separate lightmaps in the same scene (which is neat!)
For a more in-depth explanation:
The editor calls the bake function via _bake_select_file and provides either the LightmapGI or the LightmapGI's parent as the node to scan from. The bake function then calls _find_meshes_and_lights which is a recursive function that gets all the children of the node thats passed into it

Thanks! Congratulations on your first merged contribution! 🎉


[Bug]: MOE模型，2卡推理，报错AssertionError("Invalid device id")

Your current environment
PyTorch version: 2.1.2+cu121
Is debug build: False
CUDA used to build PyTorch: 12.1
ROCM used to build PyTorch: N/A
OS: Ubuntu 22.04.2 LTS (x86_64)
GCC version: (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Clang version: Could not collect
CMake version: version 3.29.5
Libc version: glibc-2.35
Python version: 3.10.13 (main, Sep 11 2023, 13:44:35) [GCC 11.2.0] (64-bit runtime)
Python platform: Linux-3.10.0-1160.el7.x86_64-x86_64-with-glibc2.35
Is CUDA available: True
CUDA runtime version: 12.1.105
CUDA_MODULE_LOADING set to: LAZY
GPU models and configuration:
GPU 0: NVIDIA A800-SXM4-80GB
GPU 1: NVIDIA A800-SXM4-80GB
GPU 2: NVIDIA A800-SXM4-80GB
GPU 3: NVIDIA A800-SXM4-80GB
Nvidia driver version: 470.199.02
cuDNN version: Probably one of the following:
/usr/lib/x86_64-linux-gnu/libcudnn.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_adv_infer.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_adv_train.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_cnn_infer.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_cnn_train.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_ops_infer.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_ops_train.so.8.9.0
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: True
CPU:
架构：                           x86_64
CPU 运行模式：                   32-bit, 64-bit
Address sizes:                   46 bits physical, 57 bits virtual
字节序：                         Little Endian
CPU:                             128
在线 CPU 列表：                  0-127
厂商 ID：                        GenuineIntel
型号名称：                       Intel(R) Xeon(R) Platinum 8369B CPU @ 2.90GHz
CPU 系列：                       6
型号：                           106
每个核的线程数：                 2
每个座的核数：                   32
座：                             2
步进：                           6
CPU 最大 MHz：                   3500.0000
CPU 最小 MHz：                   800.0000
BogoMIPS：                       5800.00
标记：                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 invpcid_single intel_pt ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req avx512vbmi umip pku ospke avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq md_clear pconfig spec_ctrl intel_stibp flush_l1d arch_capabilities
虚拟化：                         VT-x
L1d 缓存：                       3 MiB (64 instances)
L1i 缓存：                       2 MiB (64 instances)
L2 缓存：                        80 MiB (64 instances)
L3 缓存：                        96 MiB (2 instances)
NUMA 节点：                      2
NUMA 节点0 CPU：                 0-31,64-95
NUMA 节点1 CPU：                 32-63,96-127
Vulnerability Itlb multihit:     Not affected
Vulnerability L1tf:              Not affected
Vulnerability Mds:               Not affected
Vulnerability Meltdown:          Not affected
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
Vulnerability Spectre v1:        Mitigation; Load fences, usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:        Mitigation; Enhanced IBRS, IBPB
Vulnerability Srbds:             Not affected
Vulnerability Tsx async abort:   Not affected
🐛 Describe the bug
在对Qwen2-57B-A14B-Instruct进行两卡推理的时候，运行如下指令：
os.environ['CUDA_VISIBLE_DEVICES'] = '0,1'
model_dir = '/publicdata/huggingface.co/Qwen/Qwen2-57B-A14B-Instruct'
model_type = ModelType.qwen2_57b_a14b_instruct
template_type = get_default_template_type(model_type)
llm_engine = get_vllm_engine(model_type, model_id_or_path=model_dir, tensor_parallel_size=2)
tokenizer = llm_engine.hf_tokenizer
template = get_template(template_type, tokenizer)
报错如下：
(RayWorkerVllm pid=2689517) INFO 06-14 11:52:26 selector.py:16] Using FlashAttention backend.
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44] Error executing method init_device. This might cause deadlock in distributed execution.
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44] Traceback (most recent call last):
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]   File "/opt/conda/lib/python3.10/site-packages/vllm/engine/ray_utils.py", line 37, in execute_method
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]     return executor(*args, **kwargs)
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]   File "/opt/conda/lib/python3.10/site-packages/vllm/worker/worker.py", line 93, in init_device
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]     _check_if_gpu_supports_dtype(self.model_config.dtype)
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]   File "/opt/conda/lib/python3.10/site-packages/vllm/worker/worker.py", line 309, in _check_if_gpu_supports_dtype
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]     compute_capability = torch.cuda.get_device_capability()
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]   File "/opt/conda/lib/python3.10/site-packages/torch/cuda/init.py", line 435, in get_device_capability
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]     prop = get_device_properties(device)
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]   File "/opt/conda/lib/python3.10/site-packages/torch/cuda/init.py", line 452, in get_device_properties
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44]     raise AssertionError("Invalid device id")
(RayWorkerVllm pid=2689517) ERROR 06-14 11:52:26 ray_utils.py:44] AssertionError: Invalid device id

can you try https://github.com/vllm-project/vllm/pull/5473 ? it should fix your error i think.

can you try #5473 ? it should fix your error i think.

I had pull the latest vllm code and try to install it.

can you try #5473 ? it should fix your error i think.

I pulled the latest vllm code and tried to install it
but it encountered some problems during installation
if I use pip install -e . ,it will get stuck here:
Looking in indexes: https://mirrors.aliyun.com/pypi/simple
Obtaining file:///workspace/huj11%40xiaopeng.com/code/vllm
Installing build dependencies ... |
if I use pip install --editable ./ --no-build-isolation, it will get stuck here:
Looking in indexes: https://mirrors.aliyun.com/pypi/simple
Obtaining file:///workspace/huj11%40xiaopeng.com/code/vllm
Checking if build backend supports build_editable ... done
Preparing editable metadata (pyproject.toml) ... done
Requirement already satisfied: cmake>=3.21 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (3.29.5)
Requirement already satisfied: ninja in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (<IP_ADDRESS>)
Requirement already satisfied: psutil in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (5.9.7)
Requirement already satisfied: sentencepiece in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (0.1.99)
Requirement already satisfied: numpy in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (1.26.3)
Requirement already satisfied: requests in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (2.31.0)
Requirement already satisfied: py-cpuinfo in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (9.0.0)
Requirement already satisfied: transformers>=4.40.0 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (4.41.2)
Requirement already satisfied: tokenizers>=0.19.1 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (0.19.1)
Requirement already satisfied: fastapi in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (0.109.0)
Requirement already satisfied: openai in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (1.33.0)
Requirement already satisfied: uvicorn[standard] in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (0.27.0.post1)
Requirement already satisfied: pydantic>=2.0 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (2.5.3)
Requirement already satisfied: prometheus-client>=0.18.0 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (0.19.0)
Requirement already satisfied: prometheus-fastapi-instrumentator>=7.0.0 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (7.0.0)
Requirement already satisfied: tiktoken==0.6.0 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (0.6.0)
Requirement already satisfied: lm-format-enforcer==0.10.1 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (0.10.1)
Requirement already satisfied: outlines==0.0.34 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (0.0.34)
Requirement already satisfied: typing-extensions in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (4.9.0)
Requirement already satisfied: filelock>=3.10.4 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (3.13.1)
Requirement already satisfied: ray>=2.9 in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (2.9.1)
Requirement already satisfied: nvidia-ml-py in /opt/conda/lib/python3.10/site-packages (from vllm==0.4.2) (12.555.43)
Collecting vllm-nccl-cu12<2.19,>=2.18 (from vllm==0.4.2)
Downloading https://mirrors.aliyun.com/pypi/packages/41/07/c1be8f4ffdc257646dda26470b803487150c732aa5c9f532dd789f186a54/vllm_nccl_cu12-<IP_ADDRESS>.4.0.tar.gz (6.2 kB)


"brew update" on MacOS 13 fails with an error: error: https://github.com/Homebrew/homebrew-cask did not send all necessary objects

Description
MacOSX 13 builds fail (e.g. https://github.com/lsh123/xmlsec/actions/runs/5458349250):
Run brew update
error: Could not read ffac597fdb6ce8236b5e2da77ab6fbae3d9d9cb7
fatal: revision walk setup failed
error: https://github.com/Homebrew/homebrew-cask did not send all necessary objects

error: Could not read 623226b77a148708197a10c0d1eab3f8d6ca005b
fatal: revision walk setup failed
error: https://github.com/Homebrew/homebrew-core did not send all necessary objects

Error: Fetching /usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask failed!

Platforms affected

[ ] Azure DevOps
[x] GitHub Actions - Standard Runners
[ ] GitHub Actions - Larger Runners

Runner images affected

[ ] Ubuntu 20.04
[ ] Ubuntu 22.04
[ ] macOS 11
[ ] macOS 12
[X] macOS 13
[ ] Windows Server 2019
[ ] Windows Server 2022

Image version and build link
https://github.com/lsh123/xmlsec/actions/runs/5458349250
Current runner version: '2.305.0'
Operating System
Runner Image
Runner Image Provisioner
GITHUB_TOKEN Permissions
Secret source: Actions
Prepare workflow directory
Prepare all required actions
Getting action download info
Download action repository 'actions/checkout@v2' (SHA:ee0669bd1cc54295c223e0bb666b733df41de1c5)
Complete job name: check-osx

Is it regression?
It worked on same version last week (https://github.com/lsh123/xmlsec/actions/runs/5384482840/jobs/9772463248)
Expected behavior
Builds work
Actual behavior
Builds fail (see details above)
Repro steps
See https://github.com/lsh123/xmlsec/actions/runs/5458349250

Hello @lsh123,
The seems to be an issue when cloning homebrew-cask. You can track in https://github.com/Homebrew/homebrew-cask/issues/150323, which also provides workaround options. E.g. adding following action allowed brew update to complete:
    - name: Set up Homebrew
      id: set-up-homebrew
      uses: Homebrew/actions/setup-homebrew@master

I will close the issue for now. Feel free to reopen in case of any


'Connect' not working?

Thanks for making such a cool plugin!
I can't seem to get the Connections working (nothing happens) despite trying to replicate what the video and gif show.
Maybe I'm doing something wrong…
Sketch (Mac App Store) Version 3.0.3 (7891) on 10.9.3

Not working for me either :(!
Sketch: Version 3.2.2 (9983)
AEFlowchart: Version: 1.0

It's recently updated for version 3.3, so you should use some previous commit for 3.2.2.

After updating to Sketch 3.3.1 (12005), it started working. :+1:

Hi, I am having the same issue.
I am under version 3.4.1 (15681) and recreating the flow on the readme it doesn't connect the states, as shown in the gif below. Also, is there any constrains to have two elements connected, i.e. is there a need to have a start and end element, or a decision box to have two points connected?
Thanks in advance!

Hi, this is fixed now, thanks for reporting.

Thanks! :+1:


system tests: add pod, inspect testing

Followup to #6761: confirm that 'podman ps' shows the ports
on a running container in a pod created with -p (not to
be confused with the container itself running with -p,
tested in 500-networking.bats).
While we're at it, test that the port handling itself works,
by sending random text to the container and making sure the
container receives it.
Followup to #6752: 'podman inspect' should show multiple
security opts
Signed-off-by: Ed Santiago<EMAIL_ADDRESS>

Logging flakes for possible future analysis
in-podman fedora-31 fedora-31
2020-06-25T16:11:59  integration_test

Podman port [It] podman port multiple ports
[same]
[same]
Podman network [It] podman network rm
Podman run with --ip flag [It] Podman run two containers with the same IP
Podman create with --ip flag [It] Podman create two containers with the same IP
Podman run with --ip flag [It] Podman run two containers with the same IP

/approve

LGTM


Tmds.DBus.SourceGenerator namespace members should be internal

Describe the bug
In https://github.com/AvaloniaUI/Avalonia/pull/10051 it was noticed that after https://github.com/AvaloniaUI/Avalonia/pull/9810 we have lots of new public APIs available from Avalonia.FreeDesktop project.
Seems to be source generated files that are intended to be used internally in the FreeDesktop project, but instead are publicly available now.

cc @kekekeks @affederaffe

For reference https://github.com/AvaloniaUI/Avalonia/pull/10051/commits/4a5f1add0a775fb7838d1d4d7f53573ebc2e551a#diff-4c8d5b1cab7c9e337cc02457d4224dc501e8ec0e4e7c38e84aebfa3dc746fd0e