undefined symbol: gdcmjpeg8_jpeg_resync_to_restart

Hi,
We changed our R installation to 3.4.1 on Centos 7.  I am having difficulty rebuilding ANTsR. I use the git clone and R CMD INSTALL route with fresh clones. ITKR installs fine, so does ANTsRCore. I don't see a compilation error in ANTsR, but in the end I receive this message.
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘ANTsR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/lib64/R/library/ANTsR/libs/ANTsR.so':
/usr/lib64/R/library/ANTsR/libs/ANTsR.so: undefined symbol: gdcmjpeg8_jpeg_resync_to_restart
Error: loading failed
Execution halted
ERROR: loading failed
At the same time we also upgraded our cmake from 3.7 to 3.9.1
Apart from that, tool chains are the same. What might be the issue?
ps.
install_github("stnava/ANTsR") route also fails with the same reason.

Can you revert cmake build?  I had some issues with 3.9
On Thu, Aug 17, 2017 at 1:35 AM muratmaga<EMAIL_ADDRESS>wrote:

Hi,
We changed our R installation to 3.4.1 on Centos 7. I am having difficulty
rebuilding ANTsR. I use the git clone and R CMD INSTALL route with fresh
clones. ITKR installs fine, so does ANTsRCore. I don't see a compilation
error in ANTsR, but in the end I receive this message.
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘ANTsR’ in dyn.load(file,
DLLpath = DLLpath, ...):
unable to load shared object '/usr/lib64/R/library/ANTsR/libs/ANTsR.so':
/usr/lib64/R/library/ANTsR/libs/ANTsR.so: undefined symbol:
gdcmjpeg8_jpeg_resync_to_restart
Error: loading failed
Execution halted
ERROR: loading failed
At the same time we also upgraded our cmake from 3.7 to 3.9.1
Apart from that, tool chains are the same. What might be the issue?
ps.
install_github("stnava/ANTsR") route also fails with the same reason.
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--
John

I went back to Cmake 3.7.1. It is the same ITKR, ANTsRCore compiles, ANTsR fails with the same error.
My understand this is due to an incompatibility with some libraries. How can I see what the root cause of the problem?

these types of errors are usually either:

inconsistent compilation for ITKR / ANTsRCore/ ANTsR

failure to resolve symbols due to https://stackoverflow.com/questions/4802624/linking-libraries-that-contain-circular-references-in-gcc

we've tried to reduce the number of repeated libraries - but i just pushed a commit https://github.com/stnava/ANTsR/commit/9b4173396886b06b395ddd97d644beb2db1af002 that increases it.  let me know if you do a pull and INSTALL and this helps.

I am seeing the same error message. I am on CentOS 7, with cmake version <IP_ADDRESS> from the system. I have R 3.4.1 freshly compiled from source. I ran
install.packages('Rcpp')
install.packages('tools')
install.packages('methods')
install.packages('magrittr')

Though both 'tools' and 'methods' complain they are unavailable and are part of 'base' now.
I also install devtools, and I am using Method 1, with devtools in R
> library(devtools)
> install_github('stnava/ANTsR')

All of the following appear to install and load successfully:
$ ls /sw/arcts/centos7/ANTsR/3.4
abind  ITKR  magic  magrittr  mnormt  psych  Rcpp  RcppEigen  rsvd
$ R --quiet
> library(abind)
> library(ITKR)
> library(magic)
> library(magrittr)
> library(mnormt)
> library(psych)
> library(Rcpp)
> library(RcppEigen)
> library(rsvd)
>

I have access to cmake 3.5.2 if the problem is that cmake is too old. I am installing these into the folder defined by the environment variable R_LIBS_SITE.
ANTsR compiles successfully, but it fails when preparing for lazy loading with the undefined symbol message. I found something on the web suggesting that symbol might be in GDCM, so I have /sw/arcts/centos7/GDCM-2.8.2-Linux-x86_64/lib in my LD_LIBRARY_PATH when I start R, but it was not there when I compiled R.
Those libraries are stripped, but I find
$ for lib in *.so ; do
     echo $lib;
     strings $lib | grep gdcmjpeg16_jpeg_resync_to_restart;
done
libgdcmcharls.so
libgdcmCommon.so
libgdcmDICT.so
libgdcmDSED.so
libgdcmexpat.so
libgdcmIOD.so
libgdcmjpeg12.so
libgdcmjpeg16.so
gdcmjpeg16_jpeg_resync_to_restart
libgdcmjpeg8.so
libgdcmmd5.so
libgdcmMEXD.so
libgdcmMSFF.so
gdcmjpeg16_jpeg_resync_to_restart
libgdcmopenjp2.so
libgdcmuuid.so
libgdcmzlib.so
libsocketxx.so

If you have any insight, I would appreciate it.
Thanks, -- bennet

As a follow-up, I followed the binary installation instructions under Method 3.  In addition to the 'Rcpp' and 'magrittr' libraries, I also needed to install
> install.packages('RcppEigen')
> install.packages('magic')
> install.packages('psych')
> install.packages('rsvd')

before library(ANTsR) would load.  This is the final library list from R_LIBS_SITE, in case that is helpful.
$ ls
abind  ANTsRCore  ITKR   magrittr  psych  RcppEigen
ANTsR  devtools   magic  mnormt    Rcpp   rsvd

I was able to successfully run

mnifilename<-getANTsRData("mni")
--2017-08-24 12:07:17--  https://ndownloader.figshare.com/files/3674667
Resolving ndownloader.figshare.com (ndownloader.figshare.com)... <IP_ADDRESS>, <IP_ADDRESS>
Connecting to ndownloader.figshare.com (ndownloader.figshare.com)|<IP_ADDRESS>|:443... connected.
. . . .
img<-antsImageRead(mnifilename)
antsImageWrite(img,mnifilename)
antsGetSpacing(img)
[1] 1 1 1
antsGetDirection(img)
[,1] [,2] [,3]
[1,]    1    0    0
[2,]    0   -1    0
[3,]    0    0    1
antsGetOrigin(img)
[1] -90 126 -72
print( img[50,60,44] )
, , 1

 [,1]

[1,] 6356

print(max(img))
[1] 8364

Still, I would like to know about how to fix the library reference.  Please let me know if there is anything you would like me to try.

Thanks,  -- bennet

here is my previous comment:
these types of errors are usually either:

inconsistent compilation for ITKR / ANTsRCore/ ANTsR

failure to resolve symbols due to https://stackoverflow.com/questions/4802624/linking-libraries-that-contain-circular-references-in-gcc

i've seen this type of error before and it is - in all previous instances - one of the two causes above.
for 1, issues could include:  different compilation flags, cmake issues, compilers or different ITK versions.  since you used devtools, it is probably only the first of those which would point to some configuration issue.
for 2, issue is shown in the commit and in the stack overflow link.
i would attack 2 first by repeating the libraries as indicated above to see if that resolves anything.  alternatively, mess with cmake versions or perhaps itk versions to see if some configuration changed.
as you can tell from travis (and my own centos version), this appears to be a relatively new issue.

Well I don’t know if it helps other people, but I was using libopenblas.so instead of the default libRblas.so.  In dependently of this  I messed up my R installation and will take a while to figure out whether that’s was the issue with the symbol error.
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From<EMAIL_ADDRESS>Sent: Thursday, August 24, 2017 10:36 AM
To<EMAIL_ADDRESS>Cc<EMAIL_ADDRESS><EMAIL_ADDRESS>Subject: Re: [stnava/ANTsR] undefined symbol: gdcmjpeg8_jpeg_resync_to_restart (#178)
here is my previous comment:
these types of errors are usually either:

inconsistent compilation for ITKR / ANTsRCore/ ANTsR
failure to resolve symbols due to https://stackoverflow.com/questions/4802624/linking-libraries-that-contain-circular-references-in-gcc

i've seen this type of error before and it is - in all previous instances - one of the two causes above.
for 1, issues could include: different compilation flags, cmake issues, compilers or different ITK versions. since you used devtools, it is probably only the first of those which would point to some configuration issue.
for 2, issue is shown in the commit and in the stack overflow link.
i would attack 2 first by repeating the libraries as indicated above to see if that resolves anything. alternatively, mess with cmake versions or perhaps itk versions to see if some configuration changed.
as you can tell from travis (and my own centos version), this appears to be a relatively new issue.
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Hi, Brian,
I think the issue is not actually here, but in ANTsRCore.  I applied essentially the same patch to the configure script there as you did here with commit 9b41733 to ANTsR, namely:
[bennet@flux-build ANTsRCore]$ git diff configure
diff --git a/configure b/configure
index aef066b..404d916 100755
--- a/configure
+++ b/configure
@@ -60,7 +60,7 @@ echo "libants=\`find \${myantslib} -name \"lib*.a\"\`" >> Makevars
 # echo "libitk=\`find \\\`\$(R_HOME)/bin/Rscript -e 'ITKR:::itkLibs()'\\\` -name \"lib*.a\"\` " >> Makevars
 echo "libitk=\`find ${ITKRLIB} -name \"lib*.a\"\`" >> Makevars

-echo "PKG_LIBS=${PKG_LIBS} \${libants} \${libitk} \${libants} \${libitk}" >> Makevars
+echo "PKG_LIBS=${PKG_LIBS} \${libants} \${libitk} \${libants} \${libitk} \${libants} \${libitk} \${libants} \${libitk}" >> Makevars

 echo ".PHONY: all libs" >> Makevars

@@ -113,4 +113,4 @@ ${cmaker} -DITK_DIR:PATH=${ITKDIR} \
     -DCMAKE_BUILD_TYPE:STRING="${CMAKE_BUILD_TYPE}"  ../ants
 cd ../
 # needed for warning
-rm -rf ants/.git
\ No newline at end of file
+rm -rf ants/.git

and it complete the preparation for lazy loading and seems now to be usable.  All the previously undefined gdcmjpeg16* functions are now appearing as defined symbols in ANTsRCore.so.
Sorry for the misdirection.  This should be an issue in the ANTsRCore repository.  I was misled by not reading closely enough when install_github('stnava/ANTsR') was telling where it was in the process.
Would you like me to open an issue for this in the proper repository?

can you make a pull request for antsrcore?  perhaps with some of the context / information added around it.
that would be most helpful ...

Will do.
On Fri, Aug 25, 2017 at 9:26 AM, stnava<EMAIL_ADDRESS>wrote:

can you make a pull request for antsrcore? perhaps with some of the
context / information added around it.
that would be most helpful ...
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PR submitted to ANTsRCore, I hope in suitable format and commenting.


Metadata

Add: neutron-metadata-agents
Change: split neutron-agents into separated deployments.

I'm not reviewing the whole thing once again, made two small comments, other than that, it looks great overall: LGTM!

@ss7pro
@Quentin-M
@PiotrProkop
@mateusz-blaszkowski

Please make sure neutron-metadata-agent and neutron-l3-agent are scheduled on the same node.

LGTM.


Support @Module(includes = ...)

Hi Fabio,
Would be nice if DaggerMock had @Module(includes = OtherModule) support.
For example:
@Singleton
@Component(
    modules = arrayOf(
        AndroidInjectionModule::class,
        AppModule::class,
    )
)
interface ApplicationComponent

@Module(includes = arrayOf(
    RepositoryModule::class /* I would like to mock this module */
))
class AppModule

In Version 0.7.1-beta1 didn't work :(

Hi, I tried to reproduce this case and it works (even if I have never tested it before!).
You must pass both modules in the DaggerMockRule constructor, you can find an example here: https://github.com/fabioCollini/DaggerMock/tree/master/daggermock/src/test/java/it/cosenonjaviste/daggermock/moduledependency
Let me know if it works in your example.


Fix broken materials in Unreal Engine 5.1

UE 5.1 introduced breaking changes in how we obtain the names of material layers. I updated the code to compile, but didn't realize that the "Layer Name" I was now accessing was actually the name of the material layer asset, not the name of the material layer itself. So, for example, for this layer:

we wanted to get Overlay0, but in UE 5.1 we were instead getting ML_CesiumRasterOverlay.
Because various material parameters are assigned based on these names, Cesium materials pretty much completely stopped working in UE 5.1. This was most obvious for tilesets with raster overlays, which would just appear white.
You might wonder how this went unnoticed. Well, as long as the material was last saved in a previous version of Unreal Engine, it worked fine even in UE 5.1. It was only if we created or saved the material in UE 5.1 that it would fail to work.
Exactly this symptom was reported on the forum here:
https://community.cesium.com/t/material-instance-error-too-many-texture-coordinate-sets-defined-on-gpuskin-vertex-input-max-4/21693
I initially thought it was a bug in UE 5.1, and reported it on UDN, and Epic in fact found and fixed a bug. But even after the fix, our materials were still not working. So today I dug deeper and noticed the problem with the layer names.

Thanks for the pull request @kring!

:grey_exclamation: There was an error checking the CLA! If this is your first contribution, please send in a Contributor License Agreement.

Maintainers, this was the error I ran into while attempting to process the CLA check. Please resolve it to continue CLA checking.
You'll need to manually check for a submitted CLA

Error: The service is currently unavailable.

Reviewers, don't forget to make sure that:

[ ] Cesium for Unreal Samples works.

👍

Our CI builds were really broken, so this PR expanded to fix that, too. Here are the problems and solutions:

GitHub Actions switched macos-latest to start referring to macOS 12 instead of 11, and that broke our UE 5.0 macOS and iOS builds. Solution: use macos-11 instead of macos-latest. UE 5.1 works fine in macOS 12, fwiw.
Microsoft deprecated .NET Core 3.1, which our UE 5.0 builds use. See here for more details and solution.
While I was making other changes to build images, I also configured them to use Powershell 7 (instead of 5). But that broke the Powershell script used in the UE 5.1 Android build to work around its broken paths. Solution: use absolute paths, because PS 7 resolves relative paths relative to some odd place.


Release 1.4.7

Codecov Report

Merging #154 (48bda3f) into main (097277b) will decrease coverage by 0.00%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #154      +/-   ##
==========================================
- Coverage   99.22%   99.22%   -0.01%
==========================================
  Files          23       23
  Lines        1289     1288       -1
==========================================
- Hits         1279     1278       -1
  Misses         10       10

Impacted Files
Coverage Δ

src/axolpy/cryptography/__init__.py
100.00% <100.00%> (ø)

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.


<EMAIL_ADDRESS>invalid pseudo-version: does not match version-control timestamp (expected<PHONE_NUMBER>1619)

with the latest in go.mod:
require (
	gopkg.in/tomb.v2 v2.0.0-20141024135613-d5d1b5820637
)

I get this message trying to run anything in the project:
<EMAIL_ADDRESS>invalid pseudo-version: does not match version-control timestamp (expected<PHONE_NUMBER>5613)

closed this is a relic from a local environment issue


Plenticore G 3 ?

Hi,
I will get in a few weeks the new Plenticore G 3 L, will this iobroker plugin work with the new one?
I want to use SG Ready together with my Heatpump as well, would this be possible with this adapter?
Cheers
Olaf

Some updates in Plenticore G3
adapter shows no values, e.g. network , ModbusEnable , time, ExtModuleControl, DynamicSoc, MinHomeConsumption, MinSoc Dummy, EportEnable, LastExport, LastExportOK.
Will this still work?
Greetings
Olaf


Indentation should not change when typing

The language mode is TypeScript.
Why is it necessary to evaluate indentation rules on every keystroke?

The idea is moving the indentation rules evaluation time from Enter to Type then indentation gets adjusts immediately when users type keywords which match indent rules. Indentation check while typing is not very useful for TypeScript/JavaScript or similar as we already have special handle of brackets. While for other languages who don't use brackets for blocks, it might benefit a lot. e.g. Ruby users expect the indentation gets adjusted when they type end.
Right now editor.autoIndent is just a boolean but maybe we can make it an object or array which decides whether to use auto indent while Type, Move Lines, Paste separately.
A TypeScript/JavaScript user may expect

Move Line autoIndent: true
Paste autoIndent: true
Type autoIndent: false

While a Ruby user may expect

Move Line autoIndent: true
Paste autoIndent: true
Type autoIndent: true

Or to make things simpler, we don't necessarily make autoIndent turned on by default and users can enable it as wish.

The screenshot is a case when the indentation rules don't know what's the expected indent level by just checking regex.

Reopen as the major ask of this issue is whether we should check indentation rules when type.

I would prefer a keybinding/command to auto-indent the current line/selected lines.

Thank you @rebornix for the explanation and the fast fix.
Would it be possible to reduce the times when indentation rules must be checked to a subset of the typing cases? e.g. check indentation rules only if the line contains a single word.
Or could we reduce the checking to only certain languages (e.g. not C style languages which use {, }) ?
Or finally, could we enhance our brackets supports to extend the pairs beyond ({,}) etc and potentially to (if,end), (for,end), or is that infeasible ?

@alexandrudima Thanks for your suggestions 👍  , they are the right way I should go.
I was thinking about how many times users get benefits from auto indent in Type. I didn't receive a lot bugs (no more than 5, some of them are Move Lines related) after making it turned on by default. It may mean the indentation engine is good, or more likely, most of the time, we don't adjust the indentation for you while you type. The only chance that it gets adjusted is when the content matches decreaseIndentPattern.
Right now my take is not checking indentation always when users are working on C like language. Let's see how the endgame testing goes and decide whether we disable auto indent totally by default, or make it language specific (type auto indent for languages who don't benefit from brackets).

This issue happens now only when the editor.autoIndent is set to full.


punctuation marks are placed on next line.

For some reason punctuation marks are not considered part of the word they come after, but as separate words that can be pushed to the next line.

nvm this is an issue of simple-markdown https://github.com/Khan/simple-markdown/issues/32

I opened a PR that fixes the issue

be nice to see this PR accepted

Please :-)

this repo has been dead for a while, I forked it here:
https://github.com/schumannd/react-native-simple-markdown
to use it in package.json add line:
"react-native-simple-markdown": "git+https://github.com/schumannd/react-native-simple-markdown.git#forkable",

I have done so and great that it is resolved.
Many thanks
G.


API Reference, wrong link

Thanks for open sourcing.
🐛 Bug Report
https://github.com/expo/snack/blob/main/packages/snack-sdk/README.md
API Reference link is dead.

Thanks Gre!


Stuck in command mode

Since 0.4.3 I experience the problem that I get stuck in some kind of hybride mode, where the cursor indicates input mode, but it still reacts as if it was command mode. Pressing Esc doesn't end that mode.
The console shows the following:
TypeError: Cannot read property 'setText' of null
    at VimrcPlugin.logVimModeChange (eval at <anonymous> (app.js:1), <anonymous>:505:27)
    at eval (eval at <anonymous> (app.js:1), <anonymous>:445:43)
    at Function.signal (codemirror.js:568)
    at Object.enterInsertMode (cm-addons.js:2532)
    at Object.newLineAndEnterInsertMode (cm-addons.js:2656)
    at Object.processAction (cm-addons.js:1376)
    at Object.processCommand (cm-addons.js:1289)
    at cm-addons.js:994
    at runInOp (codemirror.js:3942)
    at CodeMirror.operation (codemirror.js:8639)
cm-addons.js:1003 Uncaught TypeError: Cannot read property 'setText' of null
    at VimrcPlugin.logVimModeChange (eval at <anonymous> (app.js:1), <anonymous>:505:27)
    at eval (eval at <anonymous> (app.js:1), <anonymous>:445:43)
    at Function.signal (codemirror.js:568)
    at Object.enterInsertMode (cm-addons.js:2532)
    at Object.newLineAndEnterInsertMode (cm-addons.js:2656)
    at Object.processAction (cm-addons.js:1376)
    at Object.processCommand (cm-addons.js:1289)
    at cm-addons.js:994
    at runInOp (codemirror.js:3942)
    at CodeMirror.operation (codemirror.js:8639)

It is still there for me in 0.4.4.

Just to verify before I dive into the code to understand what went wrong: did you upgrade to 0.4.4, restarted Obsidian and the issue persists?


WebCrawler for associate link

[ ] When the user enters the associate link, the program must capture the link information and fill in the fields

[ ] Amazon

[ ] Aliexpress

Lib HUNTER


Display mission

Hi @sanieni6
I did the following:

Rendered a table with the mission data as per the design of the wireframe.
Styled the mission component.
Used useSelector Redux Hook to select the state slices and render lists of missions in corresponding routes

Thanks for the review


Glue front-end to back-end for Plan your trip page filters

@NickPhura getting a 400 from your fetch activity endpoint but not seeing any errors on the pod, just rolled with activity_type and activity_subtype to prove it out.
If you look at #133 can try use the fetch button to reproduce.
Soon as I'm past that I'll wrap this one up, its 99% there.

ok so as of now you can:
choose activities by type, dates, and a polygon and it will fetch them


Too long data in pinia store cannot use ui button

The current ui button (edit,add,etc) is located to the right of the data in the state.
If the data string is very long, the ui button will be outside the screen and cannot be used.

Hi, can you upload a screenshot here?

Came here for the same issue, here's a screenshot:

Thanks!


Port stretch

Motivation and Context
 Chris, Alex, and I work on porting stretch robot into habitat sim. Either stretch or spot robot will be used in language rearrangement task
 Chris worked on the initial design of stretch robot: https://github.com/cpaxton/hab_stretch/tree/cpaxton/hab-support

How Has This Been Tested
 test_robot_wrapper.py has been added the support of testing stretch robot
Types of changes

New feature (non-breaking change which adds functionality)

Checklist

[x] My code follows the code style of this project.
[ ] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly.
[x] I have read the CONTRIBUTING document.
[x] I have completed my CLA (see CONTRIBUTING)
[x] I have added tests to cover my changes.
[x] All new and existing tests passed.

Video for stretch robot via interactive_play.py
https://user-images.githubusercontent.com/55121504/196302880-14a365f6-df08-4dcc-9e44-fbd9991c01ef.mp4

Awesome!
Minor note -- can we get better material/lighting on that Stretch mesh? It looks so "flat".

[WIP] adding some textual using asset from Noah Maestre
https://user-images.githubusercontent.com/55121504/196820853-4098951f-e77e-4f37-b660-c4c4f748600e.mp4

Nicely getting there!


Why more resty_XXXXXXX file in /tmp ？ How to auto deleted？

Duplicate of #6898, it will be fixed in kong 2.4. To keep discussion centralized, I'm closing this one.

@fffonion  thanks！


Build less frequently

close #255

add a more robust computation of directory change
add a check for "important_files"
ensure that "preview-webhook" is not filtered by diffs (that feels inappropriate)

we ran into a case where a "subdirectory" of a watched directory changing (i.e. my/path, where we watch my/) would not get built. similarly, changing build infrastructure like our "version script" would not trigger new builds either.
A few open questions:

should we remove get-diffs.py from the "important_files"
should we consider excluding unimportant files rather than including important? i.e. should we err on the side of building too much (if a new file / directory is added) or too little (if a new global / CI affecting file is added and not added to "important_files")
is there a better way to think about this problem?
should we remove the "build protection" (build pass required to merge) since some builds may not run, now? Maybe a way to have an "outcome" build that succeeds only if all executed builds in the matrix pass, which we can require?
should there be a way to ensure that "all builds get run"? Not sure what this would look like... a slash command or something?

TODO: ensure that builds will run on main when they land...

@aronatkins that's a great call. That is certainly much cleaner 😅 I was mostly cribbing from a pattern that helm uses, and a bit ignorant of niceties such as the one you mention. A few tricks / challenges that I haven't thought through yet:

a way to reference not origin/main, but the previous parent commit (i.e. when running on main). Probably easy enough with a shell command
where we do the check. Are we altering the matrix so that fewer jobs actually get launched as we do here, or are we checking at runtime (i.e. launch all the jobs and see whether they should exit immediately or not). I like filtering the matrix, which we could potentially do using this mechanism within the python loop
escape hatches for "build everything" (i.e. in the daily cron job for preview, when CI-driving files change, etc.)

I do like how elegant that is though 😄 I will revisit and see if I can simplify

For the record, since this stagnated. The simple solution was to disable "rebase commits." Squash commits are safe b/c the previous commit was on main, and merge commits are safe b/c the previous commit was on main. Still much work to do teasing through these edge cases 😄
I also am hoping to take a look at the community to see if/how other teams have resolved this issue.

Closing this out since the PR is based on an older workflow that did not use docker buildx bake.
We still want to revisit the build frequency of these images, which will likely be addressed by the build tooling refactor we are currently working through.


client_secret is no longer base64 encoded by default

See https://auth0.com/forum/t/client-secret-stored-without-base64-encoding/4338
So do you think it makes sense to have secret_base64_encoded option back?

Yes but didnt have to work on it yet. Do you depend on this? if so I can try to tackle this week

@glena Yea, that would be great!

ok, sorry about this, I will work on that.

which version are you using?
also, this change will require you to upgrade to auth0-php v4

I am using v2

Can you give it a try before releasing? https://github.com/auth0/jwt-auth-bundle/pull/46
The tag to be used with composer is 3.0.0-beta.1.
Remember that you will need to upgrade to auth0-php v4 if you are using this in your project.

3.0.0-beta.1 seems to be broken.

Any updates on this? As @aequasi has mentioned the 3.0.0-beta.1 branch is broken and new customers are unable to use Auth0 due to the December change.

@aequasi thx and sorry. can you check 3.0.0-beta.2?

+1

3.0.0-beta.2 throws
[Symfony\Component\Debug\Exception\ContextErrorException]
  Notice: Uninitialized string offset: 0

@zazoomauro can you provide more info? a callstack would be helpful

Simple latest symfony stable version installed with your bundle on your beta 2 commit

@zazoomauro Can you provide the full error with a call stack please?

I don't know how to do it really...
this just happens when you try to do a simple bin/console or a very small operation.

@zazoomauro Seems that one of the newer releases of symfony cant parse multiline arrays in yml files.
I just pushed 3.0.0-beta3 with the fix.
If it works properly, I will release the final 3.0.0

next error: Attempted to load class \"JWTVerifier\" from namespace \"Auth0\\SDK\".\nDid you forget a \"use\" statement for another namespace?
Check in your Auth0Service class.
use Auth0\SDK\JWTVerifier

does not exists.

sorry cant repro.
Please check that the auth0-php sdk is installed and that it is the correct version required by this package ^4.0.11


Simple example doesn't work on FF (Private mode)

https://googleads.github.io/videojs-ima/examples/simple/
example does not work on FF (Private mode).
Errors in console:
AdsLoader error: AdError 1012: Unable to request ads from server due to network error.videojs.ima.js:323:7
The resource at "https://pagead2.googlesyndication.com/pagead/gen_204?error=1012&lid=7&sdkv=h.&e=420706010&id=ima_html5&c=2682089557129327&domain=googleads.github.io" was blocked because tracking protection is enabled.[Learn More]

It looks like Firefox is blocking our ad server in Private mode. I'm not sure that there's anything we can do about that - the content video plays as expected, we just don't get an ad.
See https://developer.mozilla.org/en-US/Firefox/Privacy/Tracking_Protection

I tried with another VAST document and other adverts urls. Got the same.

That link says Mozilla "will block content loaded from domains that track users across sites" in private mode, so if you're using any major ad server odds are it falls under that categorization.


Updated for Xcode 8 and Swift 2.3

Please fix the tests

Targeting swift 3 now

https://github.com/Haneke/HanekeSwift/pull/350


Update Get-CsUserPolicyAssignment.md

Added some clarification for the practical use of the command for users with less knowledge

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Failed to load file: W:/xa0r-s/teams/teams-ps/teams/Get-CsUserPolicyAssignment.md:19:(192) 'The user identity can be found in Azure AD using t...'
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teams/teams-ps/teams/Get-CsBatchPolicyAssignmentOperation.yml

Line 54, Column 9: [Warning-file-not-found] Invalid file link: 'New-CsBatchPolicyAssignmentOperation.yml'.

teams/teams-ps/teams/Get-CsUserPolicyPackage.yml

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teams/teams-ps/teams/Get-CsUserPolicyPackageRecommendation.yml

Line 12, Column 9: [Warning-file-not-found] Invalid file link: 'Grant-CsUserPolicyPackage.yml'.

teams/teams-ps/teams/Get-Team.yml

Line 14, Column 9: [Warning-file-not-found] Invalid file link: 'new-team.yml'.
Line 16, Column 9: [Warning-file-not-found] Invalid file link: 'set-team.yml'.

teams/teams-ps/teams/index.yml

Line 14, Column 5: [Warning-xref-not-found] Cross reference not found: 'MicrosoftTeamsPowerShell.Get-CsUserPolicyAssignment'.
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Line 20, Column 9: [Warning-file-not-found] Invalid file link: 'Grant-CsTeamsShiftsPolicy.yml'.

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@dariomws I agree. This would be the common pattern that it simply specifies the type of values it accepts. In general, I wouldn't cross modules, e.g. I wouldn't have an example that calls Get-AzureADUser followed by a Teams/SfB cmdlet.

Thanks for looking into my changes. This is the first time I have edited an article so please bare with me.
Just wanted to add some quick context, while I agree with the comments on the modifications so far, my motivation for the edit was the junior members of the team really struggled to understand ObjectID, what it referenced and how to use it. I agree not including Get-AzureADUser is a sensible step but equally, the information included was slightly geared up to those less technically able but keen to learn.
Thanks all, its nice to feel I am finally able to give back to the community after so many years of being the reader!

@Systems-Liam
First of all, thank you so much for your contribution. I hope it's the first of several more.
Although I understand your perspective, I believe that an object's ID or GUID is essential for everyone working in IT.
Again, I'll approve it if you leave a simple sentence under the parameter description to show the possible values.

Hi @dariomws, thanks for the message, sorry for my initial confusion here, I opened my account specifically to modify this article (and hopefully contribute to others) so I didn't realise you needed me to change the changes I had made already.
I have now done this, I hope its more in keeping with the standard Microsoft Docs format but if you need me to modify further then please do let me know.
Thanks!

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Thank you again @Systems-Liam!

@Kateyanne Please merge this PR. Thanks.

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BUG: Cannot fully override key behavior

Did you check docs and existing issues?

[X] I have read all the docs.
[X] I have searched the existing issues.
[X] I have searched the existing discussions.

Neovim Version (nvim -v)
NVIM v0.10.0-dev-948+g0b0d91276
Operating System / Version
Ubuntu 22.04.2 LTS x86_64
Describe the Bug
In my case, I would like to use "o" as shortcut for "open", instead of
After mapping, the shortcut works, but it adds a small delay before open the node. I think it's caused by "nowait" and prefix_key,
Looking into the source code, neotree use vim.tbl_deep_extends, which also copy value under other fields to "o" value.
I also tried to override config setting for o but does not help.
  ["o"] = { "open", nowait = true },
  -- ["o"] = { "open", nowait = true, config = { prefix_key = "" } },
  ["oc"] = { nowait = true },
  ["od"] = { nowait = true },
  ["og"] = { nowait = true },
  ["om"] = { nowait = true },
  ["on"] = { nowait = true },
  ["os"] = { nowait = true },
  ["ot"] = { nowait = true },

Screenshots, Traceback
No response
Steps to Reproduce

change the config
open neotree, press 'o'
There is a small delay

Expected Behavior
No delay when pressing "o"
Your Configuration
-- DO NOT change the paths and don't remove the colorscheme
local root = vim.fn.fnamemodify("./.repro", ":p")

-- set stdpaths to use .repro
for _, name in ipairs({ "config", "data", "state", "cache" }) do
	vim.env[("XDG_%s_HOME"):format(name:upper())] = root .. "/" .. name
end

-- bootstrap lazy
local lazypath = root .. "/plugins/lazy.nvim"
if not vim.loop.fs_stat(lazypath) then
	vim.fn.system({ "git", "clone", "--filter=blob:none", "https://github.com/folke/lazy.nvim.git", lazypath })
end
vim.opt.runtimepath:prepend(lazypath)

-- install plugins
local plugins = {
	"folke/tokyonight.nvim",
	-- add any other plugins here
}

local neotree_config = {
	"nvim-neo-tree/neo-tree.nvim",
	dependencies = { "MunifTanjim/nui.nvim", "nvim-tree/nvim-web-devicons", "nvim-lua/plenary.nvim" },
	cmd = { "Neotree" },
	keys = {
		{ "<Leader>e", "<Cmd>Neotree<CR>" }, -- change or remove this line if relevant.
	},
	opts = {
		window = {
			mappings = {
				["o"] = { "open", nowait = true },
				-- ["o"] = { "open", nowait = true, config = { prefix_key = "" } },
				["oc"] = { nowait = true },
				["od"] = { nowait = true },
				["og"] = { nowait = true },
				["om"] = { nowait = true },
				["on"] = { nowait = true },
				["os"] = { nowait = true },
				["ot"] = { nowait = true },
			},
		},
	},
}

table.insert(plugins, neotree_config)
require("lazy").setup(plugins, {
	root = root .. "/plugins",
})

vim.cmd.colorscheme("tokyonight")
-- add anything else here

If you want to disable the other mapping that start with o, map them to "none" or "noop":
  ["o"] = { "open", nowait = true },
  ["oc"] = "noop",
  ["od"] = "noop",
  ["og"] = "noop",
  ["om"] = "noop",
  ["on"] = "noop",
  ["os"] = "noop",
  ["ot"] = "noop",

See:
:h neo-tree-custom-mappings

Thanks!!!


add more test

Codecov Report

Merging #48 (b8e6c88) into develop (ff38d4b) will increase coverage by 1.98%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop      #48      +/-   ##
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+ Coverage    81.63%   83.62%   +1.98%
===========================================
  Files            1        1
  Lines          403      403
  Branches        19       19
===========================================
+ Hits           329      337       +8
+ Misses          66       60       -6
+ Partials         8        6       -2

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Different ways of computing the fitness of an ORF  from the normalized reads

We can discuss here different approaches on how to get fitness relative values from arbitrary units of normalized reads per ORF

Case # 1: Normalization of the fitness based on the normalized reads per bp in the 80% central region of the gene . Here I use the HO locus to normalize with:

Using this measure of fitness for every ORF , I have for the WT and mutant (dpl1d) from Benoit have:

In particular :

So this means , that using this measure the fitness of bem1 deletion is higher than deleting bem3 (in the growth conditions of Benoit) , which make me suspect that this is not an ideal measure of fitness.

Using this normalization, do you consider the fact of the differences in the number of insertions in each chromosome is not constant? And also that the differences in the number of reads between different SATAY experiments?

Case # 2 :

In this case I get at least that dbem1 fitness is lower than dbem3 , which is what I naively expect .
When I try to predict the most correlated genes to dpl1 , to get the positive and negative interactors I get this:

the gene names that have a "-new" label added to it are the genes I predict that do not match with current annotations in SGD. The ones that do not have the label are matching the current knowledge.
The script can be found here : https://github.com/Gregory94/LaanLab-SATAY-DataAnalysis/blob/dev_Leila/Python_scripts/corrrelation-based-networks/fitness-WT-mutant-from-reads.py

Using this normalization, do you consider the fact of the differences in the number of insertions in each chromosome is not constant? And also that the differences in the number of reads between different SATAY experiments?

I just took the values from your column of 'reads_per_bp_80%' of each gene and divided by the value of HO, as a first trying out .
I opened this issue to discuss on other possible ideas to implement.

Liedewij suggested in the meeting with Werner, to use an exponentially decaying weighted average for the 10kb non-coding regions around a gene. This would give more weight to non-coding regions close to the gene as they are more likely to be affected by similar low-frequency effects than the non-coding regions further away.
Furthermore, it was suggested to only use this averaging, or moving average, over non-coding regions and just add up all the reads/transposons within a gene and divide by the gene length, otherwise, the regions around the genes would have a large impact on the calculated fitness of the gene which we don't expect.

Notes from Werner to calculate the fitness from insertions/reads data
Suppose (to first approximation) every possible transposon insertion (labelled here a, b, c, d, …, n) has the same initial frequency, and is found in N_0 cases in the population. Then each cell with that insertion grows according to its fitness ω_n, commonly defined as inversely proportional to its doubling time τ_n.
After some time T, you stop the experiment and harvest the cells. At this point, the abundance of cells with insertion n , which is N_(n,T), is given by:

You observe N_(n,T), you control T, and you will have to estimate N_0 based on known fitness in the case of non-coding region insertions / HO locus insertions.
Then of course N_0 may not be a single, uniform value for every region in the DNA, probably has Poisson distributed noise, and there is maybe more Poisson noise in converting transposon to reads, and there could be difference in lag times after transforming that may be of influence in your setup (but maybe you know if this is not the case), so you can expand this simple fitness calculation much further, if needed. But as you say, you are still in the testing phase in terms of defining fitness.

I guess the question of the negative binomial has to do with the fact that the "abundance of cells with insertion n at t=T e.g. N(n,T)" is what we want to know , but what we observe is the number of reads of the insertion n,  which  can not be directly coupled with the number of cells with those insertions?

In response to Werner's suggestion; I made a growth model based barely on exponential growth. For me, this was to calculate the optimal growth time before harvesting. I based it on the measured doubling times from biotek experiments on WT and bem1del cells, measured lag times, and the observation that the exponential growth phase lasted to about 0.3OD.

Note that there is a huge variation in both measured doubling times and lag times, so this is just a very rough estimate (two lines show + and - std for variation in measured doubling time). In this model, I assumed that 1 on every 2175 cells is a wildtype and the others are bem1del, this value is calculated from the genome length over the length of genes of which a transposon in these genes would lead to a wildtype phenotype.
As Werner pointed out, in the end it is very difficult to compare the read count due to the difference in lag time (here estimated to be 600min for WT and 1100 for bem1del cells). As this is not known in our SATAY data, it becomes difficult to compare values.
As can be seen from this figure, it might be very difficult to obtain a good resolution between neutral mutations in the bem1del and lethal mutations, as WT cells very quickly sweep the population.

I came across this article that discusses how to get genetic interactions from transposon sequencing data. It uses Bayesian statistics to determine whether a change in read count is significant and can be accounted for a change in fitness rather than stochasticity and/or noise. For this they also take a negative binomial distribution which they estimate using normal distributions. I don't understand the details yet, but maybe it is interesting.
They also have made a python script available in which you can enter data (in the same format that we our data) and it will determine significant changes in read counts. But they have a slightly different experimental setup, so I am not sure if it would be useful for us.

That is great! We should take a look at it, for sure . I knew that someone
would have already the same idea hahaha but I hadnt found it yet, thanks
Greg!
On Thu, Oct 29, 2020, 15:17 Gregory94<EMAIL_ADDRESS>wrote:

I came across this article
https://academic.oup.com/nar/article/45/11/e93/3044354 that discusses
how to get genetic interactions from transposon sequencing data. It uses
Bayesian statistics to determine whether a change in read count is
significant and can be accounted for a change in fitness rather than
stochasticity and/or noise. For this they also take a negative binomial
distribution which they estimate using normal distributions. I don't
understand the details yet, but maybe it is interesting.
They also have made a python script
https://orca1.tamu.edu/essentiality/GI/ available in which you can
enter data (in the same format that we our data) and it will determine
significant changes in read counts. But they have a slightly different
experimental setup, so I am not sure if it would be useful for us.
—
You are receiving this because you were assigned.
Reply to this email directly, view it on GitHub
https://github.com/Gregory94/LaanLab-SATAY-DataAnalysis/issues/25#issuecomment-718782826,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/ACXNYSUGVC22USWDEHYITZ3SNF2P5ANCNFSM4SJ3NCBA
.

I came across this article that discusses how to get genetic interactions from transposon sequencing data. It uses Bayesian statistics to determine whether a change in read count is significant and can be accounted for a change in fitness rather than stochasticity and/or noise. For this they also take a negative binomial distribution which they estimate using normal distributions. I don't understand the details yet, but maybe it is interesting.
They also have made a python script available in which you can enter data (in the same format that we our data) and it will determine significant changes in read counts. But they have a slightly different experimental setup, so I am not sure if it would be useful for us.

Interesting! Their method is indeed a bit different from ours, but it might be an idea to store a sample of the induction culture (just before starting the reseed) @Wteunisse

@EKingma, your comment is consequence of what they describe in Page 2 right?

This is another paper that also takes a sample before reseeding to compare it with the cells after selection. They have a somewhat more similar approach to what we are currently trying to do for determining genetic interactions. The paper from Dejesus et.al. 2017 (the one I previously mentioned) compare their results with this paper and they are not very enthusiastic about it, yet I think it might still be interesting.


Make use of Popup window functionality?

Now that both Vim and Neovim offer the ability to show popup windows, I'd like to know whether it would make sense for airline to support this. So anybody who is interested in here: What are your thoughts? Where would it make sense?
I could imagine it might be useful for displaying the complete warning/error sections. But how long should the popup be visible and when should it vanish again?
Other opinions?

closing, apparently not needed.


Add explicit Dispatch stack in pull request template

📖 Description
Instead of configuring stacks per project in the Dispatch webhook, we want them to be specified per pull request.
This ensures the requested stacks are explicit and not implicit. This also allows to be easily reminded that #dispatch/none is sometimes a good option 😉
🦀 Dispatch

#dispatch/none

🦀 Requesting reviewers for this pull request:

@gcauchon (contributor with 3 commits in the last 90 days and 29 commits overall)


Add constraint support for union types

Description:

$Subject

Blocked on this : https://github.com/ballerina-platform/ballerina-lang/issues/36543


update

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[BUG] Unrecognized nic when installing. 1.2.0-patch1

Describe the bug
When installing, network card not detected correctly. Using the patched iso for USB via pikvm.
To Reproduce
Via pikvm, but i assume via ilo or idrac would work similarly, upload patched iso.
Boot from the iso.
Try to select management network interface

Go to '...'

Expected behavior
nic is up and receives a dhcp ip.
Environment

Harvester ISO version: 1.2.0-patch1
Nic is an Intel I218LM

Additional context
Had ubuntu loaded on it before working and you can see the nic eth0 has an ip.

Then on harvester, it is rename5.

Looks same as https://github.com/harvester/harvester/issues/2084 and the motherboard firmware answer is pretty crap, ubuntu comes up just fine.

Update:
worked around this issue. First, i followed the steps in the other ticket to manually bring up the rename5 (it renamed to rename4 on last run) interface.
Ctrl + Alt + F2
Login as rancher/rancher
ip link set dev rename4 up
Ctrl + Alt + F1

However, on first boot, it got weirder. Rename 4 has now been renamed to eno1, it is up, but did not get DHCP address. Also, the other port on this server has now been renamed as rename3.

Rke2 failed to load along with rest of harvester due to localhost not really being reachable.
Turns out in /oem/90_custom.yaml in the networking session, the interface was not renamed from rename4 to eno1. I updated it to eno1, rebooted, and now harvester is up, and reboots properly. I guess I wont be using rename3 for anything.
Root cause guess:
Looks like harvester is unable to handle more than 1 network port on a card or server in certain cases. Maybe you are checking for the wrong firmware flag based on the other post. Obviously it is a harvester issue due to it working in other operating systems. I personally tested with ubuntu twice just to make sure it was harvester related.

Hi @mkoperator - I was as you mentioned noticing this with [SuperMicro X9DRD-IT][https://www.supermicro.com/products/archive/motherboard/x9drd-it_] as you linked earlier w/ #2084
With the kernel argument if.names=0 - did rename5 ever become eth0?


Combine "Set Session Key" and "Set Commission" into one transaction

https://github.com/darwinia-network/darwinia.js#dispatch-multiple-calls-in-a-single-transaction


Is it really needed to use the patched variable?

According to the readme, it is required to use the patched handlebars variable:
const handlebars = require('handlebars'),
      asyncHelpers = require('handlebars-async-helpers')

const asyncHandlebars = asyncHelpers(handlebars)
const template = asyncHandlebars.compile('123');
const rendered = await template({});

Anyway, to my testings it seems like this is not required, as even the original handlebars is now patched:
const handlebars = require('handlebars'),
      asyncHelpers = require('handlebars-async-helpers')

asyncHelpers(handlebars)

const template = handlebars.compile('123');
const rendered = await template({});

May you confirm? I wonder what method would be the best. By using handlebars at least we have type checking but compile() is not a Promise.

What version did you installed? latest one should not pollute the prototype.


Sort the imports

Hello Joseph,
this pull request sorts the imports.
Best,
Joe

Hello,
relevant issue is #1.
Joe

no it doesn't.

Hello Joseph,
apologies, this is due to old branch. I will remedy this issue.
Best,
Suzy

Hi Suzy,
Thank you for your contribution to the repository.

Joseph,
I have fixed the extra commit issue.
Best wishes,
Joe