runtime: _cgoCheckPointer0 extreme overhead

What version of Go are you using (go version)?
go1.6rc2

What operating system and processor architecture are you using?
linux/amd64

What did you do?
Call C code with cgo.

What did you expect to see?
Almost the same performance with GODEBUG=cgocheck=1 and GODEBUG=cgocheck=0.

What did you see instead?
22 times more running time with GODEBUG=cgocheck=1 than with GODEBUG=cgocheck=0.

The overhead is 22x in practice and 36000 in this contrived example:
$ GODEBUG=cgocheck=1 go test -bench=. -run=-
testing: warning: no tests to run
PASS
BenchmarkCGO-4        50          28792524 ns/op
ok      github.com/tgulacsi/go/cgo22    1.855s
:gthomas@waterhouse: ~/src/github.com/tgulacsi/go/cgo22
$ GODEBUG=cgocheck=0 go test -bench=. -run=-
testing: warning: no tests to run
PASS
BenchmarkCGO-4   2000000               796 ns/op
ok      github.com/tgulacsi/go/cgo22    2.988s
:gthomas@waterhouse: ~/src/github.com/tgulacsi/go/cgo22
The code is at https://github.com/tgulacsi/go/tree/master/cgo22
cgo22.zip

Thanks for the test case.  I don't know how to do much better for this kind of example.  The pointer passing rules say that if you pass the address of an element of a slice, the C code is permitted to examine every element of the slice.  You are passing the address of a 1000000 slice of pointers, so each call needs to check 1000000 pointers to make sure that they are not Go pointers.

Thanks Ian for the clear description!
Now I think I understand another strange thing: with
s := struct { p C.ub4, q *GoObj }
C.f(&s.p)
does not work, but (!) with
s := struct{ p [1]C.ub4, q *GoObj },
C.f(&s.p[0])
does work - here we encapsulated the referent, so cgo does not check q.
Back to the original issue: this understanding allows a not-too-ugly workaround:
    i := i % int(n)
    carr := arr[i : i+1 : i+1]
    i = (i + 100) % int(n)
    darr := arr[i : i+1 : i+1]
    //C.call(&arr[i%int(n)], &arr[(i+100)%int(n)])
    C.call(&carr[0], &darr[0])

By calling with a one-element-length array (capped), it works:
:tgulacsi@tgulacsi-Aspire-V3-371: ~/src/github.com/tgulacsi/go/cgo22
! GODEBUG=cgocheck=0 go test  -run=X -bench=.
testing: warning: no tests to run
PASS
BenchmarkCGONaive-4      3000000               494 ns/op
BenchmarkCGOSliced-4     3000000               501 ns/op
BenchmarkCGOCapped-4     3000000               507 ns/op
ok      github.com/tgulacsi/go/cgo22    6.400s
:tgulacsi@tgulacsi-Aspire-V3-371: ~/src/github.com/tgulacsi/go/cgo22
$ GODEBUG=cgocheck=1 go test  -run=X -bench=.
testing: warning: no tests to run
PASS
BenchmarkCGONaive-4<PHONE_NUMBER>8 ns/op
BenchmarkCGOSliced-4<PHONE_NUMBER>6 ns/op
BenchmarkCGOCapped-4     3000000               568 ns/op
ok      github.com/tgulacsi/go/cgo22    6.305s
Here the "Naive" is the old version, the "Sliced" is the carr := arr[i:i+1] version, and the "Capped" is the above carr := arr[i:i+1:i+1] version.
(same repo has the new code).
I think at least we should document it more explicitly, that the cgo checker checks all reachable pointers in the struct/array/slice level.


Get error details on error event

[x] Issue does not already exist
[ ] Issue observed on https://plyr.io

Expected behaviour
Get the error details on the error event (for instance a HTTP error 401), by doing :
instance.on("error", function (event) {
	var error = event.detail.plyr.getContainer().error;
	console.error("plyr error", error);
});

Actual behaviour
Got undefined
Environment

Browser: Chromium
Version:  57
Operating System: Ubuntu
Version: 16.04

Players affected:

[ ] HTML5 Video
[x] HTML5 Audio
[ ] YouTube
[ ] Vimeo

Steps to reproduce

go to the page containing the audio player
remove website token from browser
try to play sound
401 in the console

Hello,
I'm looking for a way to get the details of an error using the error event. I tried to look for an error object in the container but didn't find anything...
Thank you for your work and for your help!

i can't figure this out either. the readme says "The element's error attribute contains more information," but 1) it's not very clear what "the element" is, and 2) i can't find an error attribute on anything that might be "the element" (the error object, the player, etc.).

See the other issue related to error handling for a more updated response. Sorry I’m on my phone so it’s hard to search.

Is it possible to link to the fix - i'm having a hell of time searching for the correct ticket. Sorry for being a bother.

any update on this? :D

still trying to figure this one out - not able to see the error details for debug or find which "element" is referred to in the README

error
Sent when an error occurs. The element's error attribute contains more information.

I believe that @sampotts was referring to issue #1231 also from Nov 2018, but it appears the solution is not finalized.

This is what I managed to find out:
plyr.on('error', event => {
        const plyr = event.detail.plyr;
        // original video is not documented in typescript
        // It's a reference to the <video> element which Plyr will override
        // A Plyr error won't happen in that element
        // const originalVideo = (plyr.elements as any).original;
        const container = event.detail.plyr.elements.container;
        const plyrVideoEl =
          container && container.getElementsByTagName('video')[0];
        const plyrVideoError: MediaError | null | undefined = plyrVideoEl?.error;

        // handle your error

      });

I think by element the README refers to the  HTML element which Plyr will add to the DOM


add imagePullPolicy configurable for istio-proxy

local test e2e, container istio-proxy always pull image even though go test with flag  istio.test.pullpolicy=IfNotPresent and local node has this image. So add imagePullPolicy configurable for istio-proxy, convenient for local testing.

[ ] Configuration Infrastructure
[ ] Docs
[ ] Installation
[ ] Networking
[ ] Performance and Scalability
[ ] Policies and Telemetry
[ ] Security
[x] Test and Release
[ ] User Experience
[ ] Developer Infrastructure

Please check any characteristics that apply to this pull request.

[ ] Does not have any user-facing changes. This may include CLI changes, API changes, behavior changes, performance improvements, etc.

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don't we pass it to the install? if it's not being set sounds like it might be a real bug

yes, there is no imagePullPolicy set in the test app deployment yaml and the default value Always is used.

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https://github.com/istio/istio/blob/16debb5891fd3fcc91bccd3837df7a93de500fc5/pkg/test/framework/components/istio/config.go#L312

Its because of ^. If we want to change it, we should change there

L312 No need to modify, this is correct, it only works for containers other than istio-proxy.
i use this command to test
export HUB="istio-test"
export TAG="v1"
go test -tags integ  -v ./tests/integration/pilot/  -istio.test.env kube -istio.test.hub=${HUB} -istio.test.tag=${TAG}  -istio.test.pullpolicy=IfNotPresent  -istio.test.kube.loadbalancer=false  -run TestXFFGateway

set istio.test.tag=v1 istio.test.pullpolicy=IfNotPresent , the tag is not latest

Container istio-proxy always pull image ,not valid for istio-proxy, but valid for other containers, such as app a-v1/b-v1 etc.
Application specific to testing TestXFFGateway, if imagPullPolicy is not set , will use default policy Always.

so, for container istio-proxy and application specific to testing TestXXX i add imagePullPolicy to use istio.test.pullpolicy. In this way, the imagePullPolicy of all containers can be configured through flag istio.test.pullpolicy.


[WIP] Remove Python 3.4 backports from utils

Utils contained a couple of backported items from Python 3.4 that are no longer necessary:

weakref.finalize
functools.total_ordering

This PR deletes the backports and replaces uses with the standard library versions. There were a couple of small related changes:

Whilst testing, I noticed that test_cuda_no_boundscheck can fail if you have a CUDA device, if it gets run by a child process - I've added a commit to make sure it has the SerialMixin to prevent this.
The mechanism for ensuring that shutting_down is set before finalizer exitfuncs run (added in PR #2024) is slightly modified, because this was implemented by modifying finalize, which is no longer applicable. I believe my logic for the change is sound, and I haven't noticed and problems (either in general running, or running things and hitting Ctrl-C to interrupt them an random times) but a second person's thoughts on the logic (https://github.com/numba/numba/compare/master...gmarkall:grm-remove-backports?expand=1#diff-e8ce4dc3f72e453a103a52be6032ff8bR293) would probably be good :-)

Removing [WIP] now that CI has passed.


Model interface defined?

By quickly reading the source code, I couldn't find a ML model interface like the one defined in ScikitLearnBase.jl. Could you please explain the interface implemented in MLJBase.jl? Is there an interface already?

There is a detailed description of the model interface in the MLJ docs. Happy to provide overview. The most effective start would be a face-to-face call. See my slack message.

Thank you @ablaom , couldn't find your slack message though. I will read the docs to see what is already there.


VS Code Speech cannot use macOS voices.

Does this issue occur when all extensions are disabled?: Yes

VS Code Version: 1.86.2
OS Version: macOS 14.3.1

I expect the extension to be able to read the text from the Copilot Chat Box. But I do not get any TTS anywhere in VS Code.
Steps to Reproduce:

Install voice extension on macOS https://marketplace.visualstudio.com/items?itemName=ms-vscode.vscode-speech&ssr=false#overview
Observe TTS is not working.
Grab system voices from terminal via say -v ?. For example use "Tessa" (confirming working via say -v Tessa "hello world"
Go to VS Code extension settings and observe that "liveshare.accessibility.voice" does not allow value Tessa. Only the Windows voices seem to be accepted in the settings.

This needs the label: workbench-voice

Text to speech is not supported yet by VS Code speech extension, only speech to text. We have https://github.com/microsoft/vscode/issues/196261 for that.


[Bug]: Node 20 --detect-leaks always triggers (transpiled import syntax)

Version
29.7.0
Steps to reproduce

Clone my repo: https://github.com/GabeAtWork/node-20-jest-leak-min-repro
Follow README instructions

Expected behavior
I expect to see no leaks detected
Actual behavior
I get the following error:
EXPERIMENTAL FEATURE!
    Your test suite is leaking memory. Please ensure all references are cleaned.

    There is a number of things that can leak memory:
      - Async operations that have not finished (e.g. fs.readFile).
      - Timers not properly mocked (e.g. setInterval, setTimeout).
      - Keeping references to the global scope.

Additional context
I suspect the transpilation of the import syntax to be related to the issue. I didn't find any way to make this repo work with ESM files, so I unfortunately can't confirm that's the problem.
When changing the syntax to CJS (require, ...), the issue does not happen.
Environment
System:
  OS: macOS 13.4
  CPU: (12) x64 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
 Binaries:
  Node: 18.18.2 - ~/.volta/tools/image/node/18.18.2/bin/node
  Yarn: 1.22.19 - ~/.volta/tools/image/yarn/1.22.19/bin/yarn
  npm: 9.8.1 - ~/.volta/tools/image/node/18.18.2/bin/npm
  pnpm: 8.6.9 - ~/Library/pnpm/pnpm
 npmPackages:
  jest: ^29.7.0 => 29.7.0

This is fixed in Jest 30 (jest@next) - I assume #14526 worked around whatever the issue is 🙂

@SimenB thanks for the reply, I've tried it out on the repro repository and it fixes the issue indeed (branch: jest_30).
Thanks for your support 🙏


my_map.launch file created by my_launch script does not complete properly

Hi,
I'm excited to test this software.
I'm following the Quick Start video on the Autoware GitHub landing page:
https://www.youtube.com/watch?v=Ursbp2qs1u0
I got the sample data OK, and got the my_launch script and ran it in ~/Autoware.
Following along with the video, everything is OK until the Map button is clicked.  When this happens, the "load files" portion finishes but it seems to stop on "start publish vector map".
Additionally, I see only an empty grid in RViz and the error message:
"No tf data.  Actual error: Fixed Frame [map] does not exist."
I had to create a symlink from ~/.autoware to ~/Autoware to allow me to get this far, otherwise I get a "No such file or directory"
I also loaded the .urdf file instead of the .dae file for the vehicle model as I received a COLLADA error.
Ubuntu 14.04 LTS
ASUS ROG Laptop w/ NVIDIA GTX970M, 32 GB

Hi friend,Have you soved this problem?,I met the same problem.

Hi,
Here is what I have found to work.  Note that there is still some instability with the simulation playback... for around the first 60 seconds, the LIDAR location does not appear to be synchronized with the GPS location.  Additionally, intermittently it seems as though the ROSBAG feed will 'desync' with RViz, and the playback within RViz will stop and then start up again.  I say intermittent because sometimes I can play the entire sensor recording without any issues, other times it desyncs.
A Quick Start PDF was released last week that really helped.
This procedure assumes you have followed the Quick Start PDF instructions (https://github.com/CPFL/Autoware/blob/master/docs/jp/autoware-quickstart.pdf) for installation and where to place files, and appropriate files are selected for Map, Localization and Simulation portions as per the same document.

Start Runtime manager (~/Autoware/ros/run)
Ensure appropriate files are selected as per the Quick Start PDF.
Simulation:
Start ROSBAG simulation playback, wait 3 seconds and then pause
Quick Start:
Start map, wait for "OK" to appear next to Ref button
Start localization, wait 10 seconds
Start RViz
Open ~/Autoware/ros/src/.config/rviz/default.rviz
Return to Runtime Manager
Simulation:
Unpause playback for 5 seconds, then pause again
Return to RViz, uncheck Vector Map and recheck Vector Map
In RViz, uncheck Points Raw and recheck Points Raw
On the right hand side, change Target Frame field to base_link and click the Zero button above
Return to Runtime Manager
Unpause the simulation
Return to RViz and observe playback


New option for Modis::Model - :enable_all_index

Allows to disable creating of my:core:key:all kind of keys if they are not needed.
Getting rid of these keys is important feature, because those keys consume a huge amount of memory.
For example, one single *:all key having 158m ids consumes about of 10GB of RAM.
Assuming some people don't use Model.all in their code,
it's important to disable that feature on demand

Considering this is out in the wild, I'm a bit skeptic to introduce this as an opt-in feature as developers that update the gem would have to add the code to maintain current functionality.
What do you think about making this an opt-out option instead so that we can safely release a new 2.x version instead and make a future release make this opt-in. That would give you the ability to opt-out as needed for now without breaking others codebase.
Also, any thoughts on the behavior of all when this is turned off? Should it log a warning or raise an exception rather than returning an empty array when this is turned off?

Considering this is out in the wild, I'm a bit skeptic to introduce this as an opt-in feature as developers that update the gem would have to add the code to maintain current functionality.

They don't have to. "all" index is still enabled by default, so default behavior did not change. So if no use_all_index option is present, everything will remain the same as before. So no breaking code stuff.
def all_index_enabled?
  @use_all_index == true || @use_all_index.nil?
end

Or, are you speaking more about semantic stuff like disable_all_index true is more clear than enable_all_index false?

Also, any thoughts on the behavior of all when this is turned off? Should it log a warning or raise an exception rather than returning an empty array when this is turned off?

I thought on this, but wasn't sure about the details. You're right. I've added another commit introducing error when user is trying to get :all records with that option disabled.

Sorry to get back at this so late, I've been pretty swamped with life 😄

Or, are you talking more about semantic stuff like disable_all_index true is more clear than enable_all_index false?

Yeah, I was talking about the name as it originally confused me. Though reading the code it makes sense the way you implemented it. If you don't mind making the name change that would be great, I'll merge this and release a new minor version update 👍

Actually, disregard...thinking about it, it makes sense to leave it as is if in the future we make this an opt-in feature the name will make better sense

Thank you! Are you going to release a minor version with this update soon? (I just want to use this fix in our production, so we prefer setting version instead of github's master branch)

Thank you! Are you going to release a minor version with this update soon? (I just want to use this fix in our production, so we prefer setting version instead of github's master branch)

Yeah, I'll do that today as I'm at GORUCO for the day and I tend to do a lot of OSS work when I'm at conferences 😄

@Nattfodd I've released version 2.1.0 of the gem which includes your change! Thank you for this! 🎉


Git: Please show git credential dialog on VSCode window center

When do git-push on left-pane, git credential dialog may be shown on top-center of the VSCode window and it's sometimes an issue if user uses large display. User's eyes are on left-page and they miss the dialog; they don't expect a dialog popup and therefore they don't move their eyes to center-top of the window.

Can you show me a screenshot of the git credential dialog?

When I do git pull/push, VSCode shows the following dialog:

Unfortunately since git is an extension, there is no other API than this to prompt the user for a username/password.
Are you using the automatic github authentication?
What version of VS Code are you one?

I see. I don't need quick fix for this. But I think VSCode should have some API to realize popup input dialog of other style.
Or, for such dialog that user does not expect (at least, I didn't expect the dialog), there should be some other magic to attract user attention.
My VSCode:
Version: 1.48.0-insider (user setup)
Commit: e7920dce7bfd0b707ebfc0a5379c6edd2233e475
Date: 2020-07-10T11:58:37.847Z
Electron: 8.3.3
Chrome: 80.0.3987.165
Node.js: 12.13.0
V8: 8.0.426.27-electron.0
OS: Windows_NT x64 10.0.20161


Mobile search filters

Who is this for?
People who want to use filters on smaller screens
What is it doing for them?
Giving them a better UI to do it.

TODO

[x] trap focus in filters modal

This creates quite a lot of code to maintain - where was the issue raised with the current mobile UI?

#4926
The current mobile UI barely scales to the two filter types (date and format) we have, and certainly won't handle a third. Unsightly horizontal scrollbars are already a thing on my small screen with the current setup.

What does this need to merge?

Not a massive fan of the fact that we now have multiple ways and methods of dealing with responsie layouts.
Could we keep the current method of wrapping things in containers that show and hide via CSS (and thus follow all other layout logic)?
e.g.
// from is inclusive, to is exclusive
<div className={display({ from: 's', to: `m`  })}>

<div className={display({ from: `m`, to: `xl` })}>

We've not made the decision anywhere to have the UI respond via JS, unless there is a piece of functionality that requires JS, which this doesn't.
It feels a shame to start fragmenting from a core understanding of responsive design.

I don't think this is 'degrading' to mobile, but rather a different, more appropriate, mobile layout.
Even if we show/hide the two layouts, rather than conditionally rendering them with JS, we'd still have to handle the fact the form elements are duplicated on the page, which creates bugs when submitting. We'd have to e.g. add/remove form element attributes – and at that point I don't know what's gained from using a CSS approach, because it would still be reliant on JS.
Having said that, I think I take the point about reflow.

I don't think this is 'degrading' to mobile, but rather a different, more appropriate, mobile layout.

Do we think mobile first is still appropriate? Thinking of writing up some dev processes, and wondering if this should be included?
I always thought the point of mobile first was to start with a simple design that is likely to scale as it works on the lowest, most frugal space and availability of functionality. What is feels like is that we have designed something that doesn't scale, made it the default, and are now pathing it for mobile. It is a process that stung us on the editorial content, so just trying to mitigate repating that.
Sorry, I didn miss the point on replicated form elements - that's a tricky one...

I think mobile first by default makes sense. What we started with (iterating from the two prototypes)  was mobile first in its strictest sense, with the mobile and desktop layouts using the same elements with just some CSS amends.
But after design review and iteration, the view was taken that we shouldn't have to be slaves to the strictest of responsive layouts where a more appropriate layout was available (so long as it wasn't at the expense of content availability/comprehension).
FWIW it feels like this overarching design decision has been open-eyed, rather than a post-rationalised shoe-horning. But I agree we should be eager to sweat the implementation specifics.

Just wanted to capture some of the thinking behind the two filter UIs for desktop and mobile - here you go: https://wellcome.slack.com/archives/C294K7D5M/p1578568546011400
I would like to get this deployed today and then we can revisit and refactor later on if necessary.


Error in log_warning() : could not find function "log_warning"

Hey Kai,
BigSur is not running for me because the log_warning function appears to be missing.  How can I correct this?
I tried with correlations = T and correlations = F, and the error is the same both ways.
Thanks!
epi_bigsur <- BigSur(epi, variable.feature=T, correlations=T)
[1] "Pipeline started execution."
Error in log_warning() : could not find function "log_warning"
[1] "Error in log_warning() : could not find function "log_warning"\n"
[1] "Traceback:"
[1] "10: doWithOneRestart(return(expr), restart)"
[2] "9: withOneRestart(expr, restarts[[1L]])"
[3] "8: withRestarts({"
[4] "       .Internal(.signalCondition(simpleWarning(msg, call), msg, "
[5] "           call))"
[6] "       .Internal(.dfltWarn(msg, call))"
[7] "   }, muffleWarning = function() NULL)"
[8] "7: .signalSimpleWarning("sparse->dense coercion: allocating vector of size 7.0 GiB", "
[9] "       base::quote(asMethod(object)))"
[10] "6: asMethod(object)"
[11] "5: as(x, "matrix")"
[12] "4: as.matrix.Matrix(GetAssayData(object = seuratob, slot = counts.slot))"
[13] "3: as.matrix(GetAssayData(object = seuratob, slot = counts.slot))"
[14] "2: get.residuals(seurat.obj, assay, counts.slot, c, depthlist)"
[15] "1: BigSur(epi, variable.feature = T, correlations = T)"
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.8 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /opt/apps/OpenBLAS/0.3.21/lib/libopenblas_zenp-r0.3.21.so
locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] BigSur_1.0.1       Seurat_5.0.3       SeuratObject_5.0.1 sp_2.1-3
loaded via a namespace (and not attached):
[1] Rtsne_0.17             colorspace_2.1-0       deldir_2.0-4
[4] ellipsis_0.3.2         ggridges_0.5.6         RcppHNSW_0.6.0
[7] spatstat.data_3.0-4    leiden_<IP_ADDRESS>         listenv_0.9.1
[10] ggrepel_0.9.5          RSpectra_0.16-1        fansi_1.0.6
[13] codetools_0.2-18       splines_4.2.2          rootSolve_<IP_ADDRESS>
[16] polyclip_1.10-6        spam_2.10-0            jsonlite_1.8.8
[19] common_1.1.2           ica_1.0-3              cluster_2.1.4
[22] png_0.1-8              uwot_0.1.16            shiny_1.8.0
[25] sctransform_0.4.1      spatstat.sparse_3.0-3  compiler_4.2.2
[28] httr_1.4.7             Matrix_1.6-5           fastmap_1.1.1
[31] lazyeval_0.2.2         cli_3.6.2              later_1.3.2
[34] htmltools_0.5.7        tools_4.2.2            igraph_2.0.3
[37] dotCall64_1.1-1        gtable_0.3.4           glue_1.7.0
[40] RANN_2.6.1             reshape2_1.4.4         dplyr_1.1.4
[43] Rcpp_1.0.12            scattermore_1.2        vctrs_0.6.5
[46] spatstat.explore_3.2-7 nlme_3.1-160           progressr_0.14.0
[49] lmtest_0.9-40          spatstat.random_3.2-3  stringr_1.5.1
[52] globals_0.16.3         mime_0.12              miniUI_<IP_ADDRESS>
[55] lifecycle_1.0.4        irlba_<IP_ADDRESS>          goftest_1.2-3
[58] future_1.33.1          MASS_7.3-58.1          zoo_1.8-12
[61] scales_1.3.0           promises_1.2.1         spatstat.utils_3.0-4
[64] parallel_4.2.2         RColorBrewer_1.1-3     reticulate_1.35.0
[67] pbapply_1.7-2          gridExtra_2.3          ggplot2_3.5.0
[70] stringi_1.8.3          fastDummies_1.7.3      logr_1.3.6
[73] rlang_1.1.3            pkgconfig_2.0.3        moments_0.14.1
[76] matrixStats_1.2.0      pracma_2.4.4           lattice_0.20-45
[79] ROCR_1.0-11            purrr_1.0.2            tensor_1.5
[82] patchwork_1.2.0        htmlwidgets_1.6.4      cowplot_1.1.3
[85] tidyselect_1.2.1       parallelly_1.37.1      RcppAnnoy_0.0.22
[88] plyr_1.8.9             magrittr_2.0.3         R6_2.5.1
[91] generics_0.1.3         withr_3.0.0            pillar_1.9.0
[94] fitdistrplus_1.1-11    survival_3.4-0         abind_1.4-5
[97] tibble_3.2.1           future.apply_1.11.1    KernSmooth_2.23-20
[100] utf8_1.2.4             spatstat.geom_3.2-9    plotly_4.10.4
[103] grid_4.2.2             data.table_1.15.2      digest_0.6.35
[106] xtable_1.8-4           tidyr_1.3.1            httpuv_1.6.14
[109] munsell_0.5.0          viridisLite_0.4.2

Wow I'm sorry Tatyana I didn't see this until now. I will check on this and get back to you.

Has this been corrected? I also have the same issue here.

adre.output <- BigSur(adre, variable.feature=T, correlations=F)
[1] "Pipeline started execution."
Error in log_warning() : could not find function "log_warning"
[1] "Error in log_warning() : could not find function "log_warning"\n"
[1] "Traceback:"
[1] "10: doWithOneRestart(return(expr), restart)"
[2] "9: withOneRestart(expr, restarts[[1L]])"
[3] "8: withRestarts({"
[4] "       .Internal(.signalCondition(simpleWarning(msg, call), msg, "
[5] "           call))"
[6] "       .Internal(.dfltWarn(msg, call))"
[7] "   }, muffleWarning = function() NULL)"
[8] "7: .signalSimpleWarning("sparse->dense coercion: allocating vector of size 13.9 GiB", "
[9] "       base::quote(asMethod(object)))"
[10] "6: asMethod(object)"
[11] "5: as(x, "matrix")"
[12] "4: as.matrix.Matrix(GetAssayData(object = seuratob, slot = counts.slot))"
[13] "3: as.matrix(GetAssayData(object = seuratob, slot = counts.slot))"
[14] "2: get.residuals(seurat.obj, assay, counts.slot, c, depthlist)"
[15] "1: BigSur(adre, variable.feature = T, correlations = F)"

When I try setting log.file = F as a parameter, then it starts computing but then R crashes (no message)and I have to start it again from scratch.

Hi Olivier. I fix for this will be out soon. For now, please continue performing your analyses with log.file = F. This parameter will not affect your results and is purely to track the progression of analysis.

The problem is that it leads to an R session abortion in that case (image attached)....

To me, that appears to be a separate issue. Often I've experienced R sessions aborting when the amount of RAM required to run a process greatly exceeds the amount available. I see in the console something mentioning sparse to dense matrix conversion, can you please send me the entire kernel output you get from that? Thanks for your patience while I sort this out.

Unfortunately, that issue could also be caused by things outside of my direct control -  the solution could be as simple as restarting your R session or re-downloading BigSur, or much more complicated, but I will do my best to look into it.

To me, that appears to be a separate issue. Often I've experienced R sessions aborting when the amount of RAM required to run a process greatly exceeds the amount available. I see in the console something mentioning sparse to dense matrix conversion, can you please send me the entire kernel output you get from that? Thanks for your patience while I sort this out.

Could that be due to the size of the matrix? (here I am trying to analyse a 5.5 GB seurat matrix).
Not sure where I can find the "kernel output"?
Thank's for your help!
PS: I tried to force BigSur re-installation but to no avail.

It's possible that it is due to the size of the matrix taking up too much RAM on your device. As a test, I recommend trying on a small subset of your data (i.e., 100 cells and 100 genes) to see if it completes on that small set. After that, we can discuss potential fixes to prune the data further without losing too much information. And sorry, I meant the output that you see in the "console" section of R studio after you run the code.

I tried 1000 genes and 1000 cells. After figuring ou how to remove null genes I obtained:

adre3
An object of class Seurat
941 features across 1000 samples within 1 assay
Active assay: RNA (941 features, 69 variable features)
3 layers present: counts, data, scale.data
2 dimensional reductions calculated: pca, umap

I now can run BigSur with no log.file error, nor R crashing, so this was indeed a size issue!
That a problem since I would like to make a feauture selection with my complete matrix.
But I also now have a new problem

adre.output <- BigSur(adre3, variable.feature=T, correlations=F)
[1] "Pipeline started execution."
[1] "Pre-computed depthlist was either not supplied or supplied as a non-numeric vector. Calculating depth scaling from scratch."
[1] "Modified corrected Pearson residuals calculated."
[1] "Modified corrected Fano factors calculated."
[1] "Beginning identification of significant mcFanos."
Error in (function (cl, name, valueClass)  :
‘meta.data’ is not a slot in class “Assay”
[1] "Error in (function (cl, name, valueClass)  : \n  ‘meta.data’ is not a slot in class “Assay”\n"
[1] "Traceback:"
[1] "3: stop(gettextf("%s is not a slot in class %s", sQuote(name), dQuote(cl)), "
[2] "       domain = NA)"
[3] "2: (function (cl, name, valueClass) "
[4] "   {"
[5] "       ClassDef <- getClass(cl)"
[6] "       slotClass <- ClassDef@slots[[name]]"
[7] "       if (is.null(slotClass)) "
[8] "           stop(gettextf("%s is not a slot in class %s", sQuote(name), "
[9] "               dQuote(cl)), domain = NA)"
[10] "       if (.identC(slotClass, valueClass)) "
[11] "           return(TRUE)"
[12] "       ok <- possibleExtends(valueClass, slotClass, ClassDef2 = getClassDef(slotClass, "
[13] "           where = .classEnv(ClassDef)))"
[14] "       if (isFALSE(ok)) "
[15] "           stop(gettextf("assignment of an object of class %s is not valid for @%s in an object of class %s; is(value, \"%s\") is not TRUE", "
[16] "               dQuote(valueClass), sQuote(name), dQuote(cl), slotClass), "
[17] "               domain = NA)"
[18] "       TRUE"
[19] "   })("Assay", "meta.data", "data.frame")"
[20] "1: BigSur(adre3, variable.feature = T, correlations = F)"

If I run:

slotNames(adre@assays$RNA)
[1] "counts"        "data"          "scale.data"    "assay.orig"    "var.features"  "meta.features"
[7] "misc"          "key"

There indeed seems not to be a meta.data class here...
Thank's a lot for your patience.

It appears like you might have an outdated version of Seurat. The "meta.features" slot has been changed to "meta.data" in versions 5 and up. I recommend checking to see that you have the most updated version, though I should plan to add some backwards compatibility with the older versions.
I have removed the dependency of BigSur on the logr package, so the original errors should no longer occur. I will be closing this issue. Olivier, I would be happy to continue helping you to troubleshoot the package - and, if you were looking to run the program on some larger data, I would be happy to run it for you on my device. Feel free to reach out to me at<EMAIL_ADDRESS>and we can continue this conversation!


Create hacktoberfest-accepted

📝 Description
Add a brief description.
💣 Is this a breaking change (Yes/No):

[ ] Yes
[x] No

🚧 How to migrate?
Don't need.
📝 Additional Information
lol

good

@Antiinflamatory1
Hey There:
We will not be able to merge this PR because we don't understand the meaning of this AI Agent and it doesn't seem to work.
You can check out Weekly PR Review Party @ILLA Cloud on Youtube to understand our Criteria and instructions for contributing AI agents. You can also join our Discord community for help.
If you can revise this AI Agent to better quality we would love to get it merged.


CI: temporary asv pin

temporarily pin the version of asv used by
Azure CI until gh-15535 can be investigated in
more detail

asv 0.5.1 has been released with a fix already, so closing


❓👂 Question/Feedback - add existing instance to the LB

Question/Feedback
how to add existing vms to the load balancer through bicep? am able to add new vm while creating load balancers. not sure how to add existing nic card or ip address to the load balancer. any idea on this?
Possible Answers/Solutions?
Just want us to confirm your thinking, let us know any possible answers you've considered and we can confirm 👍

Hi Arthi,
If you are keeping your Infrastructure-as-Code up to date in source control, any configuration for Azure resource code will be current with what is deploye
To add your VMs to your load balancers, I will point you in the direction of the sample code we have in our documentation:
https://learn.microsoft.com/azure/load-balancer/quickstart-load-balancer-standard-internal-bicep?tabs=CLI#review-the-bicep-file
The two sections which are important in this sample code is the ipConfigurations section in resource networkInterface as well as the loadBalancingRules properties under resource loadBalancer
Also do not forget your dependencies in there, you need the load balancer before the NIC or it will not be able to form as part of your backend pool.
Hope this helps!

this is the code guide me to add 2 existing vms to the LB. but not sure how to add the existing 2 vms(existing 2nic card) to the LB.
param loadbalancerName string = 'loadbalancer213'
param location string = 'australiaeast'
var lbSkuName = 'Standard'
var lbFrontEndName = 'frontend-ip'
var subnetid = resourceId('Microsoft.Network/virtualNetworks/subnets', virtualNetworkName, subnetName)
var virtualNetworkName = 'lb-vnet'
var subnetName = 'lb-subnet'
var BackendPoolName = 'BackendPool1'
var lbprobe = 'ProbeA'
resource internalloadbalancer 'Microsoft.Network/loadBalancers@2022-07-01' = {
name: loadbalancerName
location: location
sku: {
name: lbSkuName
}
properties: {
frontendIPConfigurations: [
{
name: lbFrontEndName
properties: {
subnet: {
id: subnetid
}
privateIPAddress: '<IP_ADDRESS>'
privateIPAllocationMethod: 'Static'
}
}
]
backendAddressPools: [
{
name: BackendPoolName
}
]
loadBalancingRules: [
{
name: 'HTTPRule'
properties: {
frontendIPConfiguration: {
id: resourceId('Microsoft.Network/loadBalancers/frontendIPConfigurations', loadbalancerName, lbFrontEndName)
}
backendAddressPool: {
id: resourceId('Microsoft.Network/loadBalancers/backendAddressPools', loadbalancerName, BackendPoolName)
}
frontendPort: 80
backendPort: 80
enableFloatingIP: false
idleTimeoutInMinutes: 4
protocol: 'Tcp'
enableTcpReset: false
loadDistribution: 'Default'
probe: {
id: resourceId('Microsoft.Network/loadBalancers/probes', loadbalancerName, lbprobe)
}
}
}
]
probes: [
{
name: lbprobe
properties: {
intervalInSeconds: 5
numberOfProbes: 2
port: 80
probeThreshold: 2
protocol: 'TCP'
}
}
]
}
}

As this is more focused around Azure Bicep itself rather than ALZ Bicep, I would advise you to raise an issue on the main repository itself rather than on this one:
https://github.com/azure/bicep


Fix information overlay issues.

There is a particular case in which when a user clicks on a tab, then
uses the goto method to go to another, and then clicks on the original
tab again, it will not load the original tab. This is due to the fact
that the goto function that is used to navigate to a tab without
clicking does not set the last_value, therefore leaving a state that is
incorrect and denying a view update in the case that a user performs
the following:
Click B -> Goto A -> Click B
In this case, it saves the last_value as “B” and so when a user clicks
back on “B” it does not trigger any change as it thinks the user is
going from “B” to “B”.

Automated message from Dropbox CLA bot
@brockwhittaker, it looks like you've already signed the Dropbox CLA. Thanks!

Merged, thanks @brockwhittaker!  I tweaked this as below to remove my scrollbar hack:
diff --git a/static/styles/informational-overlays.css b/static/styles/informational-overlays.css
index 2c50032..0a08ded 100644
--- a/static/styles/informational-overlays.css
+++ b/static/styles/informational-overlays.css
@@ -55,6 +55,7 @@

 .informational-overlays .overlay-modal .modal-body {
     height: 70vh;
+    text-align: center;
 }

 .informational-overlays .overlay-modal .modal-header h3 {
@@ -68,9 +69,3 @@
 .informational-overlays td.operator {
     font-size: 0.9em;
 }
-
-/* Hack to fix scrollbars on Linux */
-.informational-overlays #keyboard-shortcuts .modal-body {
-    overflow-y: hidden;
-    text-align: center;
-}


Povme3 refactor

Improved ConfigFile parser runtime
Moved some config file processing code from runit() to ConfigFile()
Added global variables as substitutes for parameter string names.   (Some string comparisons to parameter dictionary values may not be working yet, but don't seem to have an effect so far)
-various additional comments

I just realized that the integration testing service hasn't been working for a while. I'll fix that on this branch, just to be maximally confusing.


Create Posts “it技術動向”

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[Macros on Darwin] Use device platform paths when building for the simulator

To avoid having duplicated macro implementations in both the device and simulator platforms, when building for a simulator platform, pass -external-plugin-path that points into the device platform. There is no need to have macro implementations in the simulator platforms.
Implements rdar://112563655.

@swift-ci please test

Windows failure looks spurious, trying again.

@swift-ci please test Windows

@swift-ci please test


Corrected Dutch translations were not updated in NPSP 3.120

NPSP 3.120 contained a refresh of corrected Dutch translations, however it appears that prior incorrect values were not replaced as expected.

**lurch: add

Tracking W-023394

Included in beta release 3.134 (Beta 3)

Included in production release 3.134


Proxied page items not showing

This might be related to this incident. I only pulled a partial version of one of the suggested fixes so it may be hard to communicate what my current setup looks like.
But I wanted to open this ticket to see if anyone else is currently seeing any new issues with this library.
Non working proxied site:

Working site directly:

non working embedded site:

same site from the directly published link:

It looks like adding a version ie) ?v=fb79c36fff3c4428827fe9eed59922b5 could be helping.
if (slugs.indexOf(url.pathname.slice(1)) > -1) {
  const pageId = SLUG_TO_PAGE[url.pathname.slice(1)];
  return Response.redirect("https://" + MY_DOMAIN + "/" + pageId + "?v=fb79c36fff3c4428827fe9eed59922b5", 301);
}

yes, this fixed my issue. my code is somewhat deviated from the core code. I don't use the "MetaWriter" and I don't re-write URL's quite as hard as the default code wants. But, I'll leave this here in case this is a general change that affects more people. Thanks!

after trying a lot of things in #241 this was what finally worked for me. Thank you for the fix!


New version: BenBoyter.scc version 3.4.0

Created in https://github.com/stevenlele/winget-update/actions/runs/11096740953
Microsoft Reviewers: Open in CodeFlow

Automatic Validation ended with:

Installation failed with exit code -1978335187
2024-09-29 23:29:37.682 [FAIL] Installer failed security check. Url: https://github.com/boyter/scc/releases/download/v3.4.0/scc_Windows_i386.zip Result: 0x80004005

Automated error analysis suggests -1978335187 may mean Installer failed security check. Another script should retry this every 18 hours.
Automated error analysis suggests 80004005 may mean Resource missing
(Automated response - build 896.)

Automatic Validation ended with:

Installation failed with exit code -1978335187
2024-10-03 08:55:22.925 [FAIL] Installer failed security check. Url: https://github.com/boyter/scc/releases/download/v3.4.0/scc_Windows_i386.zip Result: 0x80004005

Automated error analysis suggests -1978335187 may mean Installer failed security check. Another script should retry this every 18 hours.
Automated error analysis suggests 80004005 may mean Resource missing
(Automated response - build 896.)


fix tickbox behaviour if page gets loaded with a box ticked

This happens when the page gets loaded from going back from a replay page, or when reloading

This doesn't fix the issue for me.
I am testing on edge btw, it seems to have the bug most consistently.

I tested in Firefox, I'll look into it. Maybe the load event isn't being triggered?

In Chromium, reloading doesn't leave the box ticked, and going back uses a cached version of the page that has the table fully intact

turns out Edge handles things a bit differently from Chromium sometimes. The correct event to use was pageshow

@32th-System could you please rebase/merge and re-run the tests? I've removed them for being flaky


The process cannot access the file because it is being used by another process, Unison not running in VM

For both:
vagrant unison-sync-once
vagrant unison-sync-polling
Getting:
The process cannot access the file because it is being used by another process.
Unison not running in VM

Is this on windows? Googling it I see this in unrelated circumstances on windows. It sounds like more of a unison or filesystem issue though.
This plugin prints the exact unison command it runs with all the args, so I would try explicitly running that in your VM and seeing what happens/ maybe googing resulting errors or asking about them in a unison forum or something.


chore(deps): upgrade configuration

Upgrades project dependencies. See details in workflow run.

Automatically created by projen via the "upgrade-configuration-1.x" workflow

⚪ Backport skipped
The pull request was not backported as there were no branches to backport to. If this is a mistake, please apply the desired version labels or run the backport tool manually.
Manual backport
To create the backport manually run:
backport --pr 1043

Questions ?
Please refer to the Backport tool documentation


jenkinsx-quickstart-nuxeo-poc to 1.0.8

Promote jenkinsx-quickstart-nuxeo-poc to version 1.0.8

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.jenkins-x-bot seems not to be a GitHub user. You need a GitHub account to be able to sign the CLA. If you have already a GitHub account, please add the email address used for this commit to your account.You have signed the CLA already but the status is still pending? Let us recheck it.


Unable to build the WindowsService

Since I don't have .Net 4.7x on my machine, it causes the project to fail.
Not quite sure how you would handle this, but there it is.

Not sure what you mean by that. This works with Dot net core SDK. There's fallback to 4.7.1 but this is intended for Dot net core SDK

It can't fall back to something that doesn't exist, and it looks for it on startup in VS.
Try to compile on a machine without the full framework on it and it won't succeed.
I made it work by manually editing the csproj to exclude 4.7.1.

Hmm so you say you have dot net core installed but it complains just because you don't have full framework? Ok I might need to take another look at it then.

You may want to weigh the "best use of your time" on this one.
It was trivial for me to remove it in the csproj, and I may be an outlier in not having the full framework on my laptop.

Cool, fair enough tbh, I'll keep it in the back of my mind. Thanks

No problem...


Volto Mail Control Panel has no "send test email and save configuration" button/option

Describe the bug
The Plone Classic Mail Control Panel has a "send test email and save configuration" button that the Volto control panel currently lacks.
To Reproduce
Steps to reproduce the behavior:

As admin
Go to http://localhost:3000/controlpanel/mail
There is no button to test the email settings

@tisto Duplicate of #3791 ?

@tiberiuichim yes. sorry for the noise. closing this ticket.


PVC of type RWM with CephFS fail

What happened:
PVC is all the time with status=Pending

What you expected to happen:
PVC from type RWM to be created successfully
How to reproduce it (as minimally and precisely as possible):

apply pvc.yml

Anything else we need to know?:

Storage class with name: kontena-storage-fs search to connect to service with name (yml snippet):  monitors: 'rook-ceph-mon0:6790,rook-ceph-mon1:6790,rook-ceph-mon2:6790' but in real life (after successfully Kontena Pharos install) there are only services with names: rook-ceph-mon-a, rook-ceph-mon-b, rook-ceph-mon-c this breaks connection problem.
One workaround that i apply manual is to create: rook-ceph-mon0, rook-ceph-mon1, rook-ceph-mon3 services that are the same as existing one just name is changed to match searched one from kontena-storage-fs (to this point all good)

Error logs:
cephfs-provisioner-xxx*
2019-09-27T12:56:43.666635467Z I0927 12:56:43.666128       1 controller.go:987] provision "default/test" class "kontena-storage-fs": started
2019-09-27T12:56:43.682068599Z I0927 12:56:43.681188       1 event.go:221] Event(v1.ObjectReference{Kind:"PersistentVolumeClaim", Namespace:"default", Name:"test", UID:"418d44e9-e126-11e9-ba6f-9600002dca37", APIVersion:"v1", ResourceVersion:"9485991", FieldPath:""}): type: 'Normal' reason: 'Provisioning' External provisioner is provisioning volume for claim "default/test"
2019-09-27T12:56:44.513557685Z E0927 12:56:44.513135       1 cephfs-provisioner.go:158] failed to provision share "kubernetes-dynamic-pvc-41978954-e126-11e9-a6cd-dea801ed06fc" for "kubernetes-dynamic-user-419789cd-e126-11e9-a6cd-dea801ed06fc", err: exit status 1, output: Traceback (most recent call last):
2019-09-27T12:56:44.513621714Z   File "/usr/local/bin/cephfs_provisioner", line 364, in <module>
2019-09-27T12:56:44.513639973Z     main()
2019-09-27T12:56:44.513653394Z   File "/usr/local/bin/cephfs_provisioner", line 358, in main
2019-09-27T12:56:44.513667432Z     print cephfs.create_share(share, user, size=size)
2019-09-27T12:56:44.513680841Z   File "/usr/local/bin/cephfs_provisioner", line 228, in create_share
2019-09-27T12:56:44.513694922Z     volume = self.volume_client.create_volume(volume_path, size=size, namespace_isolated=not self.ceph_namespace_isolation_disabled)
2019-09-27T12:56:44.513707874Z   File "/usr/local/bin/cephfs_provisioner", line 112, in volume_client
2019-09-27T12:56:44.513720993Z     self._volume_client.connect(None)
2019-09-27T12:56:44.513733894Z   File "/lib/python2.7/site-packages/ceph_volume_client.py", line 458, in connect
2019-09-27T12:56:44.51374801Z     self.rados.connect()
2019-09-27T12:56:44.51376213Z   File "rados.pyx", line 895, in rados.Rados.connect (/home/jenkins-build/build/workspace/ceph-build/ARCH/x86_64/AVAILABLE_ARCH/x86_64/AVAILABLE_DIST/centos7/DIST/centos7/MACHINE_SIZE/huge/release/13.2.1/rpm/el7/BUILD/ceph-13.2.1/build/src/pybind/rados/pyrex/rados.c:9815)
2019-09-27T12:56:44.513805902Z rados.IOError: [errno 5] error connecting to the cluster
2019-09-27T12:56:44.5138572Z W0927 12:56:44.513719       1 controller.go:746] Retrying syncing claim "default/test" because failures 0 < threshold 15
2019-09-27T12:56:44.514265319Z I0927 12:56:44.514018       1 event.go:221] Event(v1.ObjectReference{Kind:"PersistentVolumeClaim", Namespace:"default", Name:"test", UID:"418d44e9-e126-11e9-ba6f-9600002dca37", APIVersion:"v1", ResourceVersion:"9485991", FieldPath:""}): type: 'Warning' reason: 'ProvisioningFailed' failed to provision volume with StorageClass "kontena-storage-fs": exit status 1
2019-09-27T12:56:44.514973422Z E0927 12:56:44.514779       1 controller.go:761] error syncing claim "default/test": failed to provision volume with StorageClass "kontena-storage-fs": exit status 1
2019-09-27T12:56:44.515395802Z I0927 12:56:44.515239       1 controller.go:987] provision "default/test" class "kontena-storage-fs": started
2019-09-27T12:56:44.52517338Z I0927 12:56:44.524779       1 event.go:221] Event(v1.ObjectReference{Kind:"PersistentVolumeClaim", Namespace:"default", Name:"test", UID:"418d44e9-e126-11e9-ba6f-9600002dca37", APIVersion:"v1", ResourceVersion:"9485993", FieldPath:""}): type: 'Normal' reason: 'Provisioning' External provisioner is provisioning volume for claim "default/test"

rook-ceph-mon-a--xxx*

rook-ceph-mon-b--xxx*

rook-ceph-mon-c--xxx*
2019-09-27T12:56:40.75990484Z 2019-09-27 12:56:40.755 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:40.760567083Z 2019-09-27 12:56:40.755 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:41.773125806Z 2019-09-27 12:56:41.767 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:41.773183281Z 2019-09-27 12:56:41.767 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:42.766094155Z 2019-09-27 12:56:42.763 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:42.766153348Z 2019-09-27 12:56:42.763 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:43.765642589Z 2019-09-27 12:56:43.763 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:43.765675942Z 2019-09-27 12:56:43.763 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:44.765827781Z 2019-09-27 12:56:44.763 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:44.765913505Z 2019-09-27 12:56:44.763 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:45.77103638Z 2019-09-27 12:56:45.767 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:45.771097405Z 2019-09-27 12:56:45.767 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:46.771487355Z 2019-09-27 12:56:46.767 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:46.771535997Z 2019-09-27 12:56:46.767 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:47.772928775Z 2019-09-27 12:56:47.767 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:47.773223961Z 2019-09-27 12:56:47.767 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:48.774238557Z 2019-09-27 12:56:48.771 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:48.774292165Z 2019-09-27 12:56:48.771 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:49.773395851Z 2019-09-27 12:56:49.767 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:49.773462902Z 2019-09-27 12:56:49.767 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch
2019-09-27T12:56:50.772925256Z 2019-09-27 12:56:50.767 7f2e55e4a700  0 mon.d@2(peon) e3 handle_command mon_command({"prefix": "mds metadata", "who": "replicafs-a"} v 0) v1
2019-09-27T12:56:50.772965055Z 2019-09-27 12:56:50.767 7f2e55e4a700  0 log_channel(audit) log [DBG] : from='mgr.1205794 <IP_ADDRESS>:0/1' entity='mgr.a' cmd=[{"prefix": "mds metadata", "who": "replicafs-a"}]: dispatch

After applying pvc.yml 2 files are created inside provision pod:
/etc/ceph/ceph.conf"
[global]
mon_host = rook-ceph-mon0:6790,rook-ceph-mon1:6790,rook-ceph-mon2:6790
auth_client_required = cephx,none

/etc/ceph/ceph.client.admin.keyring"
[client.admin]
key = **************************************** {This is hidden from me for issue only}
caps mds = "allow *"
caps mon = "allow *"
caps osd = "allow *"

Created PVC is with status = Pending forever and events list show:
failed to provision volume with StorageClass "kontena-storage-fs": exit status 1

waiting for a volume to be created, either by external provisioner "ceph.com/cephfs" or manually created by system administrator

External provisioner is provisioning volume for claim "default/test"

PV element is missing of course.
Environment:

Pharos version (use pharos --version): 2.4.6
Cloud provider or hardware configuration: Cloud VPS provider, 3 master/ 3 worker nodes, 40GB SSD each node
OS (e.g. from /etc/os-release; both for the client and for the used nodes):
4.15.0-54-generic #58-Ubuntu SMP Mon Jun 24 10:55:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Others:

pvc.yml:
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: test
  labels:
    app:  test
    chart: "test-0.0.0"
    release: "test"
    heritage: "Tiller"
spec:
  accessModes:
    - "ReadWriteMany"
  resources:
    requests:
      storage: "1Gi"
  storageClassName: "kontena-storage-fs"

cluster.yml
  kontena-storage:
    enabled: true
    data_dir: /home/kontena-storage
    storage:
      use_all_nodes: true
      # It's highly recommended to set directories and/or device_filter,
      # otherwise expanding storage does not work properly (see https://github.com/rook/rook/issues/1957)
      directories:
      - path: /home/ceph
    pool:
      replicated:
        size: 3
    dashboard:
      enabled: true
    filesystem:  # Shared filesystem - ReadWriteMany persistent volumes
      enabled: true
      pool:
        replicated:
          size: 3

I do a test of PR and still not working for me.

Hi.
I made test on clear cluster (the same OS and kernel) and after apply manual the PR PVC are created and attached correctly/successfully  to pods. BUT something new popup. When i try to create file (evan with simple command) i receive this:
bash-4.4# echo "test" > text.txt
bash: echo: write error: Filename too long
bash-4.4# ls -la
total 4
drwxr-xr-x    1 root     root             1 Oct 10 08:52 .
drwxr-xr-x    1 root     root          4096 Oct 10 08:16 ..
-rw-r--r--    1 root     root             0 Oct 10 08:52 text.txt

File is created but empty. File is replicated to all pods that use it.

Pod use node:10.16.3-alpine image.
Host nodes are with type ext4

I think that is related in some way to CephFS but for now not found the reason for this error.
Thanks