Service wont start on boot

Dear ec2-macos-init contributors,
I've now tried multiple times (directly through launchd and through ec2-macos-init) to run a simple binary on system boot. This aims to join the machine to an Active Directory, etc... What I managed with this config so far was, that the script got executed correctly - but only a few seconds after a (random) user logged in to the machine - not on boot.
The config looks like this:
 [[Module]]
  Name = "SetupStartup"
  PriorityGroup = 4
  [Module.Command]
    Cmd = ["/usr/local/bin/startup.sh.x"]
    # I've tried this both with root and ec2-user
    RunAsUser = "ec2-user"

chmod on the binary is a+x

Hey @rescaux, I'm sorry to hear that you're having issues with ec2-macos-init.
Would you be able to include any error message that was logged by ec2-macos-init? The log file's location is /var/log/amazon/ec2/ec2-macos-init.log.
Also, that's strange that the script was only executed after a user logged in... I've tried reproducing the problem with the config you posted and my own test script. However, I wasn't able to see the exact behavior that you're describing.
There was an error with the module you included -- it's missing a run type configuration (RunOnce, RunPerBoot, or RunPerInstance). Once I added that, ec2-macos-init was able to run my test script just fine. I'll include my test environment below.
My config looked like this:
[[Module]]
    Name = "SetupStartup"
    PriorityGroup = 4
    RunPerBoot = true
    [Module.Command]
        Cmd = ["/usr/local/bin/startup.sh.x"]
        RunAsUser = "ec2-user"

The contents of /usr/local/bin/startup.sh.x:
#!/bin/bash

echo "Hello World!"

The permissions I have on the script:
-rwxr-xr-x  1 ec2-user  admin  33 Apr 20 19:00 /usr/local/bin/startup.sh.x

The logs from priority level 4 after restarting the instance:
2022/04/20 19:15:26.399460 Processing priority level 4 (2 modules)...
2022/04/20 19:15:26.399472 Running module [SetupStartup] (type: command, group: 4)
2022/04/20 19:15:26.399489 Skipping module [ExecuteUserData] (type: userdata, group: 4) due to Run type setting
2022/04/20 19:15:26.451198 Successfully completed module [SetupStartup] (type: command, group: 4) with message: successfully ran command [[/usr/local/bin/startup.sh.x]] with stdout [Hello World!] and stderr []
2022/04/20 19:15:26.451252 Successfully completed processing of priority level 4

Could you try adding the run type configuration to your module and let me know what happens. Any error logs from that run would also be useful.

Okay, I've now tried everything so far and it's still behaving weird. As one can see in this video, the script runs only when macos-ec2-init is invoked manually. It is invoked on boot as well, but won't do anything.

Hi @rescaux, thanks for sharing the logs~

What I managed with this config so far was, that the script got executed correctly - but only a few seconds after a (random) user logged in to the machine - not on boot.

@mattcataws and I are wondering where in the script that this hangs. For example, does the script hang on the Domain Join, or when setting up the VPN connection?
From the description provided and logs in your video seems, it like the script might be invoking a command that requires an active user login to complete (maybe a prompt, or initialization of some state by the OS).

Have you identified any particular command in this script that causes the script to hang?
The logs that @mattcataws shared above have corresponding start/stop lines that the impacted instances' logs (briefly shown in your video) does not contain. These lines look like:
2022/04/20 19:15:26.399472 Running module [SetupStartup] (type: command, group: 4)
        ... other Modules' messages ...
2022/04/20 19:15:26.451198 Successfully completed module [SetupStartup] (type: command, group: 4) with message: successfully ran command [[/usr/local/bin/startup.sh.x]] with stdout [Hello World!] and stderr []

If the script was able to complete its run, even if non-zero, we should see some corresponding log messages in ec2-macos-init's logs.

When you say the script runs "a few seconds after a (random) user logged in to the machine", what do you mean? Are these users SSH-ing into the host or are they VNC/NX-ing in?
The act of (and method of) logging in might unblock the script, so this might help inform us of where to look next.

Hi @jahkeup, I also have a similar issue. I am using mac2.metal and ec2-macos-init version 1.5.3 [2022-06-09 16:07:51 -0700] and in my ec2-macos-init I have the following:
### Group 6
## Custom services

[[Module]]
  Name = "StartGitlabRunner"
  PriorityGroup = 6
  RunPerBoot = true
  [Module.Command]
    Cmd = ["/Users/ec2-user/.gitlab-runner/run.sh"]
    RunAsUser = "ec2-user"

with my script as follows:
#!/bin/bash

if pgrep -x gitlab-runner >/dev/null
then
  echo "Skipping starting gitlab-runner as process is already running"
else
  echo "Starting gitlab-runner process..."
  /opt/homebrew/bin/gitlab-runner run &> /Users/ec2-user/.gitlab-runner/runner.log &
  echo "Started gitlab-runner process"
fi

echo "process id: $(pgrep -x gitlab-runner)"

The logs from the system restart are:
2022/07/15 13:41:37.774763 Fetching instance ID from IMDS...
2022/07/15 13:41:37.811484 Unable to get instance ID - IMDS may not be available yet...retrying every 1s [0/600]
2022/07/15 13:41:41.822631 Running on instance i-03b4cf7416cbc2031
2022/07/15 13:41:41.822802 Reading init config...
2022/07/15 13:41:41.829855 Successfully read init config
2022/07/15 13:41:41.829921 Validating config...
2022/07/15 13:41:41.830192 Successfully validated config
2022/07/15 13:41:41.830222 Prioritizing modules...
2022/07/15 13:41:41.830257 Successfully prioritized modules
2022/07/15 13:41:41.830281 Creating instance history directories for current instance...
2022/07/15 13:41:41.830420 Successfully created directories
2022/07/15 13:41:41.830449 Getting instance history...
2022/07/15 13:41:41.838421 Successfully gathered instance history
2022/07/15 13:41:41.838481 Processing priority level 1 (2 modules)...
2022/07/15 13:41:41.839368 Running module [UnmountLocalSSD] (type: command, group: 1)
2022/07/15 13:41:41.844034 Running module [DisableEthernet] (type: command, group: 1)
2022/07/15 13:41:43.131293 Successfully completed module [UnmountLocalSSD] (type: command, group: 1) with message: successfully ran command [[/bin/zsh -c diskutil list internal physical | egrep -o '^/dev/disk\d+' | xargs diskutil eject || true]] with stdout [] and stderr [Volume failed to eject]
2022/07/15 13:41:53.761170 Successfully completed module [DisableEthernet] (type: command, group: 1) with message: successfully ran command [[/usr/sbin/networksetup -setnetworkserviceenabled Ethernet off]] with stdout [] and stderr []
2022/07/15 13:41:53.761301 Successfully completed processing of priority level 1
2022/07/15 13:41:53.761326 Processing priority level 2 (1 modules)...
2022/07/15 13:41:53.761374 Running module [CheckNetworkIsUp] (type: networkcheck, group: 2)
2022/07/15 13:41:53.772429 Successfully completed module [CheckNetworkIsUp] (type: networkcheck, group: 2) with message: successfully pinged default gateway with a RTT of 368µs
2022/07/15 13:41:53.772520 Successfully completed processing of priority level 2
2022/07/15 13:41:53.772545 Processing priority level 3 (11 modules)...
2022/07/15 13:41:53.772609 Running module [DisableWiFi] (type: command, group: 3)
2022/07/15 13:41:53.772628 Running module [EC2SuggestedDefaultConfigPerformance] (type: systemconfig, group: 3)
2022/07/15 13:41:53.772680 Skipping module [ManageEC2User] (type: usermanagement, group: 3) due to Run type setting
2022/07/15 13:41:53.772720 Running module [EC2SuggestedDefaultConfigSecurity] (type: systemconfig, group: 3)
2022/07/15 13:41:53.772810 Skipping module [SetDefaultTimezone] (type: command, group: 3) due to Run type setting
2022/07/15 13:41:53.773784 Skipping module [DisableSleep] (type: command, group: 3) due to Run type setting
2022/07/15 13:41:53.773854 Skipping module [NeverSleep] (type: command, group: 3) due to Run type setting
2022/07/15 13:41:53.773885 Skipping module [NeverSleepDisplay] (type: command, group: 3) due to Run type setting
2022/07/15 13:41:53.774044 Running module [UpdateMOTD] (type: motd, group: 3)
2022/07/15 13:41:53.774129 Skipping module [RemoveSSHGroup] (type: command, group: 3) due to Run type setting
2022/07/15 13:41:53.772618 Skipping module [SetAmazonTimeSync] (type: command, group: 3) due to Run type setting
2022/07/15 13:41:53.774703 Did not modify SSHD configuration
2022/07/15 13:41:53.787156 Successfully completed module [EC2SuggestedDefaultConfigSecurity] (type: systemconfig, group: 3) with message: system configuration completed with [0 changed / 1 unchanged / 0 error(s)] out of 1 requested changes
2022/07/15 13:41:53.800800 Modified sysctl property [net.inet.tcp.autosndbufmax=33554432]
2022/07/15 13:41:53.802630 Modified sysctl property [net.inet.tcp.sendspace=1048576]
2022/07/15 13:41:53.802706 Modified sysctl property [net.link.generic.system.rcvq_maxlen=1024]
2022/07/15 13:41:53.803838 Modified sysctl property [kern.aiothreads=64]
2022/07/15 13:41:53.803945 Modified sysctl property [net.inet.tcp.win_scale_factor=8]
2022/07/15 13:41:53.804990 Did not modify default [AutomaticCheckEnabled]
2022/07/15 13:41:53.805009 Did not modify default [AutomaticDownload]
2022/07/15 13:41:53.805111 Did not modify default [AutomaticallyInstallMacOSUpdates]
2022/07/15 13:41:53.805242 Modified sysctl property [net.inet.tcp.autorcvbufmax=33554432]
2022/07/15 13:41:53.805271 Modified sysctl property [kern.aiomax=900]
2022/07/15 13:41:53.805493 Did not modify default [CriticalUpdateInstall]
2022/07/15 13:41:53.805659 Did not modify default [ConfigDataInstall]
2022/07/15 13:41:53.806199 Modified sysctl property [net.inet.tcp.recvspace=1048576]
2022/07/15 13:41:53.814463 Successfully completed module [UpdateMOTD] (type: motd, group: 3) with message: successfully updated motd file [/etc/motd] with version string [macOS Monterey 12.4]
2022/07/15 13:41:53.837840 Error while running module [DisableWiFi] (type: command, group: 3) with message:  and err: ec2macosinit: error executing command [[/bin/zsh -c wifidevice="$(networksetup -listallhardwareports | grep -A 1 "Wi-Fi" | tail -n 1 | cut -d " " -f2)"; if [[ ! -z $wifidevice ]]; then networksetup -setairportpower $wifidevice off; fi]] with stdout [Wireless is not available.
** Error: Wireless is not currently available on this machine.] and stderr []: exit status 9
2022/07/15 13:41:53.905767 Modified sysctl property [kern.aioprocmax=256]
2022/07/15 13:41:53.905875 Successfully completed module [EC2SuggestedDefaultConfigPerformance] (type: systemconfig, group: 3) with message: system configuration completed with [9 changed / 5 unchanged / 0 error(s)] out of 14 requested changes
2022/07/15 13:41:53.905917 Successfully completed processing of priority level 3
2022/07/15 13:41:53.905935 Processing priority level 4 (1 modules)...
2022/07/15 13:41:53.905968 Skipping module [GetSSHKeys] (type: sshkeys, group: 4) due to Run type setting
2022/07/15 13:41:53.905986 Successfully completed processing of priority level 4
2022/07/15 13:41:53.906000 Processing priority level 5 (1 modules)...
2022/07/15 13:41:53.906021 Skipping module [ExecuteUserData] (type: userdata, group: 5) due to Run type setting
2022/07/15 13:41:53.906036 Successfully completed processing of priority level 5
2022/07/15 13:41:53.906046 Processing priority level 6 (1 modules)...
2022/07/15 13:41:53.906067 Running module [StartGitlabRunner] (type: command, group: 6)
2022/07/15 13:41:53.963004 Successfully completed module [StartGitlabRunner] (type: command, group: 6) with message: successfully ran command [[/Users/ec2-user/.gitlab-runner/run.sh]] with stdout [Starting gitlab-runner process...
Started gitlab-runner process
process id: 433] and stderr []
2022/07/15 13:41:53.963070 Successfully completed processing of priority level 6
2022/07/15 13:41:53.963082 Writing instance history for instance i-03b4cf7416cbc2031...
2022/07/15 13:41:53.969077 Successfully wrote instance history
2022/07/15 13:41:53.969110 EC2 macOS Init completed in 12.151719875s

Which suggests that the server is actually starting, but then exits.
I've tried adding a sleep 600 to the end of the run.sh file and when SSHing onto the instance I can see the process running:
ec2-user@ip-10-211-190-39 ~ % ps -ef | grep gitlab
  501   428   109   0  1:55pm ??         0:00.00 /bin/bash /Users/ec2-user/.gitlab-runner/run.sh
  501   431   428   0  1:55pm ??         0:00.31 /opt/homebrew/bin/gitlab-runner run
  501   503   487   0  1:56pm ttys000    0:00.00 grep gitlab

Waiting for the sleep 600 to finish and the the process is killed:
ec2-user@ip-10-211-190-39 ~ % ps -ef | grep gitlab
  501   656   487   0  2:06pm ttys000    0:00.00 grep gitlab

logs:
2022/07/15 13:55:41.302136 Running module [StartGitlabRunner] (type: command, group: 6)
2022/07/15 14:05:41.601508 Successfully completed module [StartGitlabRunner] (type: command, group: 6) with message: successfully ran command [[/Users/ec2-user/.gitlab-runner/run.sh]] with stdout [Starting gitlab-runner process...
Started gitlab-runner process
process id: 431] and stderr []
2022/07/15 14:05:41.601820 Successfully completed processing of priority level 6
2022/07/15 14:05:41.601866 Writing instance history for instance i-03b4cf7416cbc2031...
2022/07/15 14:05:41.608182 Successfully wrote instance history
2022/07/15 14:05:41.608241 EC2 macOS Init completed in 10m14.065216375s

Thanks for reporting in and posting logs @rj93!
We suspect you're up against a separate (but related) issue that comes into play when processes spawn in the context of a Launchd Daemon (and/or Agents). Processes created by Launchd Daemons (directly or indirectly) must not make system calls that would spawn a whole other conceptual "daemon process" according to the "Required Behaviors" section of Launchd documentation. It is likely you'll need a separate Launchd Daemon instance that launches and owns the GitLab CI runner process (set up with your flags and environment as needed).
As written, the shared script creates a "background" process (from the gitlab-runner run ... & command), that belongs to the same session as ec2-macos-init and terminates/exits along with the primary Launchd process - ie: ec2-macos-init.
@okudajun and I tried alternatives to spawn from executed scripts and still found that they failed to stick around or failed to run at all (the usual trustworthy nohup had its syscalls fail as inappropriate IOCTLs). My knee-jerk suggestion would have been to try with nohup... but.. doesn't appear to work (as expected based on docs).
Our team will need to look at how ec2-macos-init itself spawns and what it executes from new angles to determine if ec2-macos-init can transparently support or have helpers to support managing ad-hoc daemon processes. As written today, however, and based on the Launchd - Required Behavior documentation, ec2-macos-init cannot spawn daemon processes.

@rescaux - is there a process spawned in startup.sh that might want to daemonize? If so, you might need to spawn a Launchd Daemon (or multiple, dependent on your use case) in order to work around this Launchd limitation.

Hi @jahkeup, it may be worth me pointing out that this run.sh script is also called from userdata at instance launch and it keeps the process running once the ec2-macos-init process has completed.
Heres a snippet from my userdata:

# install gitlab-runner, etc
# ...

echo "Starting gitlab-runner..."
su - ec2-user -c '/Users/ec2-user/.gitlab-runner/run.sh'
echo "Started gitlab-runner"

# Won't run run as part of this ec2-macos-init process, but if the instance reboots will start the gitlab-runner
EC2_MACOS_INIT_FILE=/usr/local/aws/ec2-macos-init/init.toml
if ! grep -q "StartGitlabRunner" $EC2_MACOS_INIT_FILE
then
  echo "Adding group ec2-macos-init..."
  cat >> $EC2_MACOS_INIT_FILE <<-EOF

	### Group 6
	## Custom services

	[[Module]]
	  Name = "StartGitlabRunner"
	  PriorityGroup = 6
	  RunPerBoot = true
	  [Module.Command]
	    Cmd = ["/Users/ec2-user/.gitlab-runner/run.sh"]
	    RunAsUser = "ec2-user"
	EOF
  echo "Added group ec2-macos-init"
else
  echo "Skipping adding group to ec2-macos-init"
fi

echo "Finished userdata script"

I was hoping to get away without having to use launchd, but thanks for the feedback I will go down that route instead.

Hi @rj93 - what did you end up doing?  I'm trying to do the same thing (setup gitlab-runner to run at boot on a m2.metal instance) and ran into a different set of issues (trying to use gitlab-runner install which creates a launchd user agent which fails to start because there is no user session).

It is likely you'll need a separate Launchd Daemon instance that launches and owns the GitLab CI runner process (set up with your flags and environment as needed).

I'm confused about what is being recommended.  I created a launch daemon in /Library/LaunchDaemons that was basically the same contents of what gitlab-runner install created, plus UserName ec2-user.  This seems to work.  I'm assuming that the only issue with daemonization is running gitlab-runner via ec2-macos-init.  That running it as a regular launchd daemon is fine (lack of Gitlab support notwithstanding).  Does that sound right?
Thanks!

I created a launch daemon in /Library/LaunchDaemons that was basically the same contents of what gitlab-runner install created, plus UserName ec2-user.

Ah, sorry! You're right, yes, we are recommending to create a job - using user data - and then loading it to run under launchd. And yeah, that lack of support seems to me because of the particulars of creating and managing the LaunchDaemon and/or LaunchAgent. (to @sourcedelica , skip to the bottom of this reply then come back here!)
For general needs, it could be simple enough to run a LaunchDaemon in the system domain but then your gitlab-runner could be missing out on some services.. Also see recent PR to configure the LaunchAgent for Actions Runner tuning exactly this - these are cases of dealing with launchd sessions and the services available to them, if I'm reading things right.
This means that a launchd job, say gitlab-runner, may not work for your CI because a subset of services are available to that CI run when running outside of a gui/$uid session (eg: the Dock, appropriate in a GUI session; some security framework services). However, there are use cases that don't need the full graphical session. In other words, it depends 😅 - it depends on what you (and your invoked tools) need.
And, yeah, that means we're going to have to work with launchd jobs.
Some relevant links (n.b. in archive docs):

sessions, domains and how they impact services:
https://developer.apple.com/library/archive/technotes/tn2083/_index.html#//apple_ref/doc/uid/DTS10003794-CH1-SUBSECTION10

general LaunchDaemon, LaunchAgent:
https://developer.apple.com/library/archive/documentation/MacOSX/Conceptual/BPSystemStartup/Chapters/CreatingLaunchdJobs.html

guidelines for LaunchDaemon vs. LaunchAgent:
https://developer.apple.com/library/archive/documentation/MacOSX/Conceptual/BPSystemStartup/Chapters/DesigningDaemons.html#//apple_ref/doc/uid/10000172i-SW4-SW9

(maybe this works for you @sourcedelica ?)
There are some convenience service helpers in Homebrew for formulas to use. This works for formulas that define a service - and this is set gitlab-runner formula!
Per https://docs.brew.sh/Manpage#services-subcommand something like this should do the trick:
#!/usr/bin/env sh
logger -s -t userdata "installing gitlab-runner"
brew install gitlab-runner
logger -s -t userdata "enabling, starting gitlab-runner service"
# re: "sudo" - see https://docs.brew.sh/Manpage#services-subcommand
sudo brew services start gitlab-runner

I ended up getting the Gitlab runner-installed LaunchAgent working through some hackery.  Basically this was:

Set ec2-user as the auto-login user
Set the user password and the auto-login password to the same value
Reboot
When the machine reboots (and every boot thereafter) the ec2-user is auto-logged in and now the LaunchAgent associated with ec2-user works.  Here are the last few commands in the user-data script:

plutil -replace autoLoginUser -string ${user} /Library/Preferences/com.apple.loginwindow.plist
sudo dscl . -passwd /Users/ec2-user "${pw}"
python3 set_kcpassword.py "${pw}"
reboot


Help with "ModuleNotFoundError: No module named 'src'"

Hello,
I am trying to run the example_notebook.ipynb notebook but I get this error: ModuleNotFoundError: No module named 'src', could you help me please?

Thank you in advance!

Hello,
Try  putting the notebook in the root directory of the repo, it may answer your issue
Good luck,
Hakim

Hi,
Nothing too complicated nor related to Jupyter notebook, just move the file example_notebook.ipynb out of the directory notebook. This should do the trick.
Also you don't need to download anything additional for the notebook to run smoothly
Good luck
Hakim

Hello,
sorry again. When I run:
model.explain(lt_samples, omics_df, clinical_df, 'gene_exp', 1, 'cluster.id', device, show=True)
I'm getting this error:
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[17], line 1
----> 1 model.explain(lt_samples, omics_df, clinical_df, 'gene_exp', 1, 'cluster.id', device, show=True)

File ~/Documents/GitHub/CustOmics/src/network/customics.py:469, in CustOMICS.explain(self, sample_id, omics_df, clinical_df, source, subtype, label, device, show)
    465 male_expr_tensor = addToTensor(expr_selection=tumour_expr, device=device)
    468 e = shap.DeepExplainer(ModelWrapper(self, source=source), background)
--> 469 shap_values_female = e.shap_values(male_expr_tensor, ranked_outputs=None)
    471 shap.summary_plot(shap_values_female[0],features=tumour_expr,feature_names=list(tumour_expr.columns), show=False, plot_type="violin", max_display=10, plot_size=[4,6])
    472 plt.savefig('shap_{}_{}.png'.format(source, subtype), bbox_inches='tight')

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/shap/explainers/_deep/__init__.py:125, in DeepExplainer.shap_values(self, X, ranked_outputs, output_rank_order, check_additivity)
     91 def shap_values(self, X, ranked_outputs=None, output_rank_order='max', check_additivity=True):
     92     """ Return approximate SHAP values for the model applied to the data given by X.
     93
     94     Parameters
   (...)
    123         were chosen as "top".
    124     """
--> 125     return self.explainer.shap_values(X, ranked_outputs, output_rank_order, check_additivity=check_additivity)

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/shap/explainers/_deep/deep_pytorch.py:191, in PyTorchDeep.shap_values(self, X, ranked_outputs, output_rank_order, check_additivity)
    189 # run attribution computation graph
    190 feature_ind = model_output_ranks[j, i]
--> 191 sample_phis = self.gradient(feature_ind, joint_x)
    192 # assign the attributions to the right part of the output arrays
    193 if self.interim:

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/shap/explainers/_deep/deep_pytorch.py:107, in PyTorchDeep.gradient(self, idx, inputs)
    105 self.model.zero_grad()
    106 X = [x.requires_grad_() for x in inputs]
--> 107 outputs = self.model(*X)
    108 selected = [val for val in outputs[:, idx]]
    109 grads = []

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
   1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
   1510 else:
-> 1511     return self._call_impl(*args, **kwargs)

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1520, in Module._call_impl(self, *args, **kwargs)
   1515 # If we don't have any hooks, we want to skip the rest of the logic in
   1516 # this function, and just call forward.
   1517 if not (self._backward_hooks or self._backward_pre_hooks or self._forward_hooks or self._forward_pre_hooks
   1518         or _global_backward_pre_hooks or _global_backward_hooks
   1519         or _global_forward_hooks or _global_forward_pre_hooks):
-> 1520     return forward_call(*args, **kwargs)
   1522 try:
   1523     result = None

File ~/Documents/GitHub/CustOmics/src/ex_vae/shap_vae.py:76, in ModelWrapper.forward(self, input)
     75 def forward(self, input):
---> 76     return self.vae_model.source_predict(input, self.source)

File ~/Documents/GitHub/CustOmics/src/network/customics.py:314, in CustOMICS.source_predict(self, expr_df, source)
    312 elif source == 'methyl':
    313     z = self.lt_encoders[2](tensor_expr)
--> 314 y_pred_proba = self.classifier(z)
    315 return y_pred_proba

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
   1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
   1510 else:
-> 1511     return self._call_impl(*args, **kwargs)

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1520, in Module._call_impl(self, *args, **kwargs)
   1515 # If we don't have any hooks, we want to skip the rest of the logic in
   1516 # this function, and just call forward.
   1517 if not (self._backward_hooks or self._backward_pre_hooks or self._forward_hooks or self._forward_pre_hooks
   1518         or _global_backward_pre_hooks or _global_backward_hooks
   1519         or _global_forward_hooks or _global_forward_pre_hooks):
-> 1520     return forward_call(*args, **kwargs)
   1522 try:
   1523     result = None

File ~/Documents/GitHub/CustOmics/src/tasks/classification.py:60, in MultiClassifier.forward(self, x)
     59 def forward(self, x):
---> 60     y = self.net(x)
     61     return y

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
   1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
   1510 else:
-> 1511     return self._call_impl(*args, **kwargs)

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1520, in Module._call_impl(self, *args, **kwargs)
   1515 # If we don't have any hooks, we want to skip the rest of the logic in
   1516 # this function, and just call forward.
   1517 if not (self._backward_hooks or self._backward_pre_hooks or self._forward_hooks or self._forward_pre_hooks
   1518         or _global_backward_pre_hooks or _global_backward_hooks
   1519         or _global_forward_hooks or _global_forward_pre_hooks):
-> 1520     return forward_call(*args, **kwargs)
   1522 try:
   1523     result = None

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/container.py:217, in Sequential.forward(self, input)
    215 def forward(self, input):
    216     for module in self:
--> 217         input = module(input)
    218     return input

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
   1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
   1510 else:
-> 1511     return self._call_impl(*args, **kwargs)

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1520, in Module._call_impl(self, *args, **kwargs)
   1515 # If we don't have any hooks, we want to skip the rest of the logic in
   1516 # this function, and just call forward.
   1517 if not (self._backward_hooks or self._backward_pre_hooks or self._forward_hooks or self._forward_pre_hooks
   1518         or _global_backward_pre_hooks or _global_backward_hooks
   1519         or _global_forward_hooks or _global_forward_pre_hooks):
-> 1520     return forward_call(*args, **kwargs)
   1522 try:
   1523     result = None

File ~/Documents/GitHub/CustOmics/src/tools/net_utils.py:64, in FullyConnectedLayer.forward(self, x)
     63 def forward(self, x):
---> 64     y = self.fc_block(x)
     65     return y

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
   1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
   1510 else:
-> 1511     return self._call_impl(*args, **kwargs)

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1520, in Module._call_impl(self, *args, **kwargs)
   1515 # If we don't have any hooks, we want to skip the rest of the logic in
   1516 # this function, and just call forward.
   1517 if not (self._backward_hooks or self._backward_pre_hooks or self._forward_hooks or self._forward_pre_hooks
   1518         or _global_backward_pre_hooks or _global_backward_hooks
   1519         or _global_forward_hooks or _global_forward_pre_hooks):
-> 1520     return forward_call(*args, **kwargs)
   1522 try:
   1523     result = None

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/container.py:217, in Sequential.forward(self, input)
    215 def forward(self, input):
    216     for module in self:
--> 217         input = module(input)
    218     return input

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
   1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
   1510 else:
-> 1511     return self._call_impl(*args, **kwargs)

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/module.py:1561, in Module._call_impl(self, *args, **kwargs)
   1558     bw_hook = hooks.BackwardHook(self, full_backward_hooks, backward_pre_hooks)
   1559     args = bw_hook.setup_input_hook(args)
-> 1561 result = forward_call(*args, **kwargs)
   1562 if _global_forward_hooks or self._forward_hooks:
   1563     for hook_id, hook in (
   1564         *_global_forward_hooks.items(),
   1565         *self._forward_hooks.items(),
   1566     ):
   1567         # mark that always called hook is run

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/modules/activation.py:774, in LeakyReLU.forward(self, input)
    773 def forward(self, input: Tensor) -> Tensor:
--> 774     return F.leaky_relu(input, self.negative_slope, self.inplace)

File /Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/torch/nn/functional.py:1646, in leaky_relu(input, negative_slope, inplace)
   1644     return handle_torch_function(leaky_relu, (input,), input, negative_slope=negative_slope, inplace=inplace)
   1645 if inplace:
-> 1646     result = torch._C._nn.leaky_relu_(input, negative_slope)
   1647 else:
   1648     result = torch._C._nn.leaky_relu(input, negative_slope)

RuntimeError: Output 0 of BackwardHookFunctionBackward is a view and is being modified inplace. This view was created
 inside a custom Function (or because an input was returned as-is) and the autograd logic to handle view+inplace would
override the custom backward associated with the custom Function, leading to incorrect gradients. This behavior is forbidden.
 You can fix this by cloning the output of the custom Function.

any idea about this?
Thank you in advance!

Hi,
Try downgrading your version of the shop library to 0.42.1. It may solve your issue.
Good luck,
Hakim

It worked, thank you so much!
However, when I run this code:
model.explain(lt_samples, omics_df, clinical_df, 'gene_exp', 1, 'cluster.id', device, show=True)
I still get this message with the plots (attached pic):
Using a non-full backward hook when the forward contains multiple autograd Nodes is deprecated and will be removed in future versions. This hook will be missing some grad_input. Please use register_full_backward_hook to get the documented behavior.
No data for colormapping provided via 'c'. Parameters 'vmin', 'vmax' will be ignored

Do I need to do anything else or is this ok?
Best regards,
Silvia

Hi,
Don't worry about it, I will try to address this warning in future versions.
Best,
Hakim


The FPS goes to inf/s and crash

First time I've heard of this happening, would probably be a good idea to limit your framerate a little bit to something lower than 999.

I am having a very similar issue where the framerate slows to about 2/s (and shift+f5 shows inf/s), if the flag is present at all (even at the default, 60, and with 0 it just crashes on launch). The normal roblox player works fine, and Bloxstrap has no way to stop it adding the fint in the client settings file.

the issue in a nutshell:
https://github.com/pizzaboxer/bloxstrap/assets/41478239/b1b6a374-75f3-443f-9a9d-cfaabddf5551

Issue has been awaiting clarification for over a month, closing as stale. If you have anything further to add, just respond and I'll reopen.


Fix Integration tests

Fixes integration tests for NGINX... not yet sure why this passes

@joshuatcasey once https://github.com/paketo-buildpacks/php-nginx/pull/28 is merged and released the tests will pass. It is related to the Nginx buildpack changes introduced in the latest release.

Thanks for the context @sophiewigmore , I was looking at recent NGINX changes and blindly tried a revert to an older version but was not sure why that actually worked.

I'll leave this open in the meantime


images centered using center tag

Images in Readme file centered using center

Images centered in README.md file. I new to development sorry for so many commits


mitra: Init at 3.9.0

Federated micro-blogging platform and content subscription service
https://codeberg.org/silverpill/mitra
Things done

Built on platform(s)

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

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[ ] Tested, as applicable:

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

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
25.05 Release Notes (or backporting 24.11 and 25.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Add a :+1: reaction to pull requests you find important.

Error memo:

Steps to reproduce

Run nix-build with below default.nix

{
  pkgs ?
    import
      (builtins.fetchTarball "https://github.com/haruki7049/nixpkgs/archive/9b8f5ee278a58a5ae505e9697e66b30daa1c0414.tar.gz")
      { },
}:

pkgs.mitra

nix-shell -p nix-info --run "nix-info -m"
 - system: `"aarch64-darwin"`
 - host os: `Darwin 24.1.0, macOS 15.1`
 - multi-user?: `yes`
 - sandbox: `no`
 - version: `nix-env (Nix) 2.18.2`
 - channels(root): `"nixpkgs"`
 - nixpkgs: `/nix/store/63lvc59rjz075kb1f11xww2x2xqpw1pn-source`

Error log: https://gist.github.com/haruki7049/6330d7b6867c2d847561c3f22da9fb34

https://github.com/NixOS/nixpkgs/pull/356298#issuecomment-2480103930
This error is resolved by 52381424f8b0f7dc1bc881dd56f485b4e1b387f2

How to merge master branch into my mitra branch without mentioning...?

You can try pull --rebase origin master, where origin is the NixOS/nixpkgs repo. (You may need to add it as another remote if you cloned your fork)

You can try pull --rebase origin master, where origin is the NixOS/nixpkgs repo. (You may need to add it as another remote if you cloned your fork)

How to merge master branch into my mitra branch without mentioning...?

DONE


Update port in deployment.md

The port is different in the description than on the shell script.

The description is correct, serve will listen at port 5000 by default, the statement say that we can change to listen at port 4000 via -l` option.


https://issues.apache.org/jira/browse/ARTEMIS-964

Moving XML conversion logic to a common XmlDataExporterUtil class so it
can be used elsewhere.

@cshannon it looks good...
just one minor thing.. I have been trying to keep the commit message understandable at the first line...
something like:
ARTEMIS-964 Moving XML Conversion to blablabla

https://issues.apache.org/jira/browse/ARTEMIS-964
more blablablablablal...

We have that on the hacking guide...
you are a committer, you could of course bypass the "rule" if you have a strong feeling for this format.. .but it's just that this is helpful when doing bisects and git logs... I have had to bisect before and reading stuff on the first line would be helpful.

@clebertsuconic, I had a similar thought as you.

I changed the commit message.

Nice one!

@cshannon  👍


[Empire in Ruins] Missing spells and weapon/gear effects

The spells on Grey Seer Skrittar are missing. Also missing is the special weapon effect for Maliss' Warpblade Halberd and the effect of his Warpsmoke Generator.From: tomwithadonfoundry: 11.308wfrp4e: 7.0.3wfrp4e-altdorf: 4.0.1wfrp4e-archives1: 4.0.2wfrp4e-archives2: 4.0.2wfrp4e-core: 4.0.2wfrp4e-dotr: 4.0.2wfrp4e-eis: 4.0.1wfrp4e-empire-ruins: 4.0.2wfrp4e-horned-rat: 4.0.2wfrp4e-middenheim: 4.0.1wfrp4e-owb1: 4.0.1wfrp4e-pbtt: 4.0.2wfrp4e-rnhd: 4.0.1wfrp4e-starter-set: 4.0.0wfrp4e-ua1: 4.0.1wfrp4e-ua2: 4.0.2wfrp4e-up-in-arms: 4.0.1wfrp4e-wom: 4.0.1wfrp4e-zoo: 4.0.1Active Modules: arms-reach, ATL, compendium-folders, dice-so-nice, drag-all-to-hotbar, drag-ruler, forien-armoury, foundryvtt-simple-calendar, item-piles, lib-wrapper, socketlib, stairways, times-up, vtta-tokenizer, wfrp4-wfrp4e-npc-generator, wfrp4e-dotr-maps, wfrp4e-eis-maps, wfrp4e-gm-toolkit, wfrp4e-pbth-maps, wfrp4e-ubersreik-maps

Sorry I put this under the wrong module. This should be under The Horned Rat


Add evented colormap

Description
This is a super preliminary attempt at adding our own named colormap object that is pure python (no shader code) and vispy independent. Will close #862, can up in context of https://github.com/napari/napari/pull/1475#issuecomment-665295798.
I've got a bunch of stuff still to do, so not ready for review yet, but just putting out there in case @tlambert03 wants to see. Note this includes #1475, but definitely didn't need to and all sorts of stuff isn't hooked up yet!!
Type of change

[x] Refactor (non-breaking change which fixes an issue)

References

How has this been tested?

[ ] example: the test suite for my feature covers cases x, y, and z
[ ] example: all tests pass with my change

Final checklist:

[ ] My PR is the minimum possible work for the desired functionality
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[ ] I have added tests that prove my fix is effective or that my feature works

I can’t seem to find the main color map object... is this missing /utils/colormaps/colormap.py?

I can’t seem to find the main color map object... is this missing /utils/colormaps/colormap.py?

I forgot to do git add .... done now

Thanks for the review @tlambert03 glad you're ok with the general direction.
I think I'll make a new PR with a pure class based approach and your additional suggestions, we can then think about the dataclass one later

Superceeded by #1523


prepopulate the email address for password reset

Is there way to prepopulate email address or sign-In name for password reset just like in the sign-in flow below.
https://docs.microsoft.com/en-us/azure/active-directory-b2c/direct-signin
I have tried to download the user flow and adding the claimprovider mentioned in the above link. It didnt work as I can't inherit base policy. are there any other ways of achieving this?

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 01f308c4-9c2a-06c6-d460-5b4b9ed3877f
Version Independent ID: 9ffaa9db-650b-a250-0e16-b450d69cc3f3
Content: Set up direct sign-in using Azure Active Directory B2C
Content Source: articles/active-directory-b2c/direct-signin.md
Service: active-directory
Sub-service: b2c
GitHub Login: @mmacy
Microsoft Alias: marsma

@jayanthurs-au Thank you for your query . We will investigate and update the thread further.

@jayanthurs-au I am afraid this will not work in password reset policy. This is supported only in combined signup or signin policy

Is there any other way of achieving this?
Get Outlook for iOShttps://aka.ms/o0ukef

From: K N Manoj Reddy<EMAIL_ADDRESS>Sent: Wednesday, August 21, 2019 8:58:10 PM
To: MicrosoftDocs/azure-docs<EMAIL_ADDRESS>Cc: jayanthurs-au<EMAIL_ADDRESS>Mention<EMAIL_ADDRESS>Subject: Re: [MicrosoftDocs/azure-docs] prepopulate the email address for password reset (#37487)
@jayanthurs-auhttps://github.com/jayanthurs-au I am afraid this will not work in password reset policy. This is supported only in combined signup or signin policy
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com/MicrosoftDocs/azure-docs/issues/37487?email_source=notifications&email_token=AHMPH2JJU5HG4ULNCCYU5ULQFUNUFA5CNFSM4IN62PAKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4ZI4TY#issuecomment-523406927, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHMPH2OC3ESCMJP5RSPMJU3QFUNUFANCNFSM4IN62PAA.

@jayanthurs-au AFAIK, there is no direct way to pre-populate the email address in this flow.

@jayanthurs-au I am closing this issue for now. Let me know if you have any further questions.


[v1.1] Delete broker only (#1811)

Cherry-pick of https://github.com/knative-sandbox/eventing-kafka-broker/pull/1811

/test pull-knative-sandbox-eventing-kafka-broker-channel-integration-tests-ssl

/cc @matzew @aliok @devguyio

Done in https://github.com/knative-sandbox/eventing-kafka-broker/pull/1848


Office Hours - 2024-10-17

Date
Thursday, 17th Oct 2024 - 15:30 BST
Untracked attendees

Name
Firm
Comment

Meeting notices

FINOS Project leads are responsible for observing the FINOS guidelines for running project meetings. Project maintainers can find additional resources in the FINOS Maintainers Cheatsheet.

All participants in FINOS project meetings are subject to the LF Antitrust Policy, the FINOS Community Code of Conduct and all other FINOS policies.

FINOS meetings involve participation by industry competitors, and it is the intention of FINOS and the Linux Foundation to conduct all of its activities in accordance with applicable antitrust and competition laws. It is therefore extremely important that attendees adhere to meeting agendas, and be aware of, and not participate in, any activities that are prohibited under applicable US state, federal or foreign antitrust and competition laws. Please contact<EMAIL_ADDRESS>with any questions.

FINOS project meetings may be recorded for use solely by the FINOS team for administration purposes. In very limited instances, and with explicit approval, recordings may be made more widely available.

Agenda

[ ] Convene, roll call, welcome new people
[ ] Approve previous meeting minutes
[ ] Add Items Here
[ ] AOB, Q&A & Adjourn (5mins)

Decisions Made

[ ] Decision 1
[ ] Decision 2
[ ] ...

Action Items

[ ] Action 1
[ ] Action 2
[ ] ...

Zoom info
Join Zoom Meeting

https://zoom.us/j/94904595244
Meeting ID: 949 0459 5244
Passcode: 545224
Find your local number: https://zoom.us/u/aesEqmNODb

Github Repo: https://github.com/finos/architecture-as-code/
Project Board: https://github.com/orgs/finos/projects/98
Mailing List: Email<EMAIL_ADDRESS>to subscribe to our mailing list

Matthew Bain / Morgan Stanley

Ross Maden / Morgan Stanley

Aidan McPhelim / Morgan Stanley

Karl Moll / FINOS

Srinivas Lakhanigam / Morgan Stanley

Denis Coffaro / Morgan Stanley

Minutes

Round of introductions

@jpgough-ms  Gave detail of the purpose of the new Office Hours meeting: intended for maintainers and active contributors to touch base once a week, set priorities.

Priorities
Artefact Store
[ ] Issue pending @rocketstack-matt

Top priority @jpgough-ms  for building an artefact store that firms will be able to publish patterns / instantiations / control-requirements, etc.
@karlmoll asked are these things we wouldn't host in the main repo?
@jpgough-ms explained that this is for hosting the documents pertinent to each user of CALM
@rocketstack-matt gave additional colour that it would be required for some of our tools to function, such as a visualiser being able to navigate between nodes and the detailed-architecture elements, for being able to reference reusable artefacts like control-requirements, etc.
@dc-ms added that this is related to what some vendors are asking for about what needs to be contributed
@karlmoll mentioned that RedHat have contributed a public / private vault - perhaps something we could reuse? Karl to add link to the comments.

Bundling

https://github.com/finos/architecture-as-code/issues/449
@jpgough-ms also raised the ability to "bundle" artefacts together
@Thels thinks there are a few angles to this, keen to pick up this issue once done with vs code plugin he's working on

Identifying CALM documents

https://github.com/finos/architecture-as-code/discussions/482
@Thels raised this discussion on whether we should introduce a naming convention to be able to enable the plugin to recognise file types without interning and looking at the schema tag, e.g. *.pattern.json
@rocketstack-matt has concerns that we have to look at the schema anyway as we support multiple disparate schemas that combined make up CALM
@willosborne  / @Thels  / @jpgough-ms think having a convention makes things easier
All the files are JSON, what we're talking about is adding a 'helper' to the tools to point them in the right direction.
@Thels to raise an issue showing where he sees the value
@rocketstack-matt highlighted that we're still going to have to do the error checks to confirm the files really are what the file names claim they are, but fine for this to go ahead if folks think it makes life easier.
[ ] @Thels to raise an issue showing the value here and we will go ahead and implement.

CLI Small Tasks

@willosborne highlighted there are a number of small issues in the CLI that make the development experience jarring and wants to get some of these fixed.
@rocketstack-matt asked @willosborne to post the items in the comments to this issue and to add the "Good first issue" tag.

Top Priorities

@rocketstack-matt : enhance visualiser / artefact store foundation / documentation generator from flows
@jpgough-ms : need to get the existing tooling up to date with the schema (we're currently still working against 2024-04 for most tooling)
@rocketstack-matt : agreed we need to focus on getting tooling to up date with schema; would like to jump all the way to 2024-10 even if we have priority order of which features we enable through the tools (e.g. do control-requirement then flows)
@rocketstack-matt also raised that we need to enhance the documentation

[ ] Add a "definition of done" into the DEVELOPER.md
[ ] Build project board to show the items we want to get done to agree a v1 release @jpgough-ms / @rocketstack-matt / @Thels

https://github.com/os-climate/OS-Climate-Community-Hub/blob/main/FAQ.md#what-data-is-in-the-data-commons

Konadu Appiah/ Turntabl

Raised an issue as promised - https://github.com/finos/architecture-as-code/issues/490 - input would be massively apperciated.

Elisha Amenuveve | Turntabl


Remove bower depoendencies

https://github.com/daigofuji/jekyll-foundation-6-starter/issues/3#issuecomment-320500266

SInce https://github.com/zurb/foundation-sites-template uses bower, I am sticking with it for the moment.


ERROR ~ No such variable: GRCh37

I'm getting this problem with both last versions of the workflow and nextflow
ERROR ~ No such variable: GRCh37
N E X T F L O W  ~  version 0.30.2
Launching `./chipseq/main.nf` [kickass_ptolemy] - revision: b11db350eb
ERROR ~ No such variable: GRCh37

nextflow run  ./chipseq/ \
     -profile docker \
     --max_memory '31.GB' \
     --macsconfig 'macssetup.config' \
     --genome GRCh37 \
     --reads 'data/*{1,2}.fastq.gz' \
     -resume \
     --email<EMAIL_ADDRESS>\
     --outdir 'results_hg19/'

Same problem is profile set to -profile standard,docker.

Also just to check. I'm not getting this output from macs, does the tests produce this file?
.bdg bedGraph format files which can be imported to UCSC genome browser or be converted into even smaller bigWig files.

Hi @ewels Yes. I got this with the last version of the master.

Line 104 is: params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
This is the log file.

If I print params.genome and params.genomes before line 104 I got.
genome = GRCh37, genomes = false

So comparing the rna-seq github.
It is missing to add this line in the chipseq config:
https://github.com/nf-core/rnaseq/blob/master/nextflow.config#L44

This will solve the problem, but the profile will still have to be  -profile standard,docker

Not yet resolved...

So I think I figured this out. If your HPC has igenomes available on your system, update the igenomes.config file to reflect that base directory, and include it in your profile. I also tried adding my own bwa index and gtf file, but for whatever reason, that doesn't work. Should I submit that as another issue, or add it here?

Add another issue then - that shouldn't be the case. Include some sample call so we can try to reproduce the issue :-)


amplify configure was failed.

Page: /start/q/integration/angular
Feedback:
I tried new amplify project "tutorial".
I read this page, and execute amplify configure, but it was failed.
Error on my console.
Cannot read property 'v4' of undefined
TypeError: Cannot read property 'v4' of undefined
    at new UsageDataConfig (/home/user/tutorial/node_modules/@aws-amplify/cli/lib/app-config/config.js:52:48)
    at new Config (/home/user/tutorial/node_modules/@aws-amplify/cli/lib/app-config/config.js:38:32)
    at Function.get Instance [as Instance] (/home/user/tutorial/node_modules/@aws-amplify/cli/lib/app-config/config.js:42:29)
    at Object.init (/home/user/tutorial/node_modules/@aws-amplify/cli/lib/app-config/config.js:23:27)
    at Object.attachUsageData (/home/user/tutorial/node_modules/@aws-amplify/cli/lib/context-manager.js:16:33)
    at Object.run (/home/user/tutorial/node_modules/@aws-amplify/cli/lib/index.js:68:33)

My environment.
$ node -v
v12.18.2
$ npm -v
6.14.5

@saintsouth do you still see the Cannot read property 'v4' of undefined error when using the latest CLI (4.24.3)

Thank you for reply. I found something.
Start on clean npm environment with npm init for each.

npn install @aws-amplify/cli first, and execute amplify configure, is successful.
But, npm install @angular/cli first, then npm install @aws-amplify/cli, appear this problem.
npm install @aws-amplify/cli first, then npm install @angular/cli, is successful.

Each amplify configure show me following message.
Scanning for plugins...
The following official plugins are missing or inactive:
    awscloudformation: provider |<EMAIL_ADDRESS>    analytics: category |<EMAIL_ADDRESS>    api: category |<EMAIL_ADDRESS>    auth: category |<EMAIL_ADDRESS>    function: category |<EMAIL_ADDRESS>    hosting: category | amplify-category-hosting@undefined
    hosting: category | amplify-console-hosting@undefined
    interactions: category |<EMAIL_ADDRESS>    notifications: category |<EMAIL_ADDRESS>    predictions: category |<EMAIL_ADDRESS>    storage: category |<EMAIL_ADDRESS>    xr: category |<EMAIL_ADDRESS>    codegen: util |<EMAIL_ADDRESS>    android: frontend |<EMAIL_ADDRESS>    ios: frontend |<EMAIL_ADDRESS>    javascript: frontend |<EMAIL_ADDRESS>    mock: util |<EMAIL_ADDRESS>Plugin scan successful

Memo: I don't like installing npm packages in the global environment, so I've added ./node_modules/.bin to my PATH so I can run it locally.

@saintsouth We don't support local installation of the CLI at this time, the package must be installed globally to avoid this issue. Please comment if you have further questions.


[QUESTION] def-package-hook! which-key Doesn't fire

I'm trying to put which-key-idle-delay in a hook, because just setqing it in .doom.d/init.el or .doom.d/config.el as suggested here didn't work.  Replacing which-key with doom-themes as in example works. Why? def-package is called right there.
Would replacing this with a duplicate def-package! in my config.el be a "good" solution? Because it works, and seem to preserve all the settings from core-keybinds.el. My guess is that it reloads the package, but the variables remain intact, so it reads my configuration overriding which-key-idle-delay. I may be completely wrong though.

I guess it's because
The overall load order of Doom is as follows:
  ~/.emacs.d/init.el
  ~/.emacs.d/core/core.el
  ~/.doom.d/init.el
  Module init.el files
  `doom-before-init-modules-hook'
  Module config.el files
  ~/.doom.d/config.el
  `doom-init-modules-hook'
  `after-init-hook'
  `emacs-startup-hook'
  `doom-init-ui-hook'
  `window-setup-hook'

And def-package! which-key is in the core =\
Any workaround?

Great research on the topic. I can agree with putting another def-package! block in your config - it should just reload the package, and which-key is not that expensive to load. It's really annoying that you can't just change the delay after which-key has loaded, but oh well.

Using this atm:
(add-hook 'window-setup-hook
  (setq which-key-idle-delay 0.01)
  (which-key-mode +1))

I think this should be a bit faster than reloading the whole package and should preserve all of core-keybinds.el configurations. there is a cleaner solution, right? ;(

Yes, this should work well enough. Maybe @hlissner would have some Emacs Lisp magic to help you.

Your assessment is correct. This is a load order issue. You can't reconfigure a core package with def-package-hook!, because it has to run before a package's def-package! block.
(add-hook 'window-setup-hook
  (progn
    (setq which-key-idle-delay 0.01)
    (which-key-mode +1)))

This won't work the way you're expecting. The progn block evaluates immediately and returns t, which is what gets added to window-setup-hook, and does nothing (if it doesn't throw an error).
This is probably what you want:
(after! which-key
  (setq which-key-idle-delay 0.01)
  (which-key-mode +1))

However, what I don't understand is why this doesn't work:
(setq which-key-idle-delay 0.01)

I can reproduce this issue, but for whatever reason which-key ignores it on first invokation. This would appear to be a which-key bug. I'll look into it.


csv, excel, pdf, print not working

Hi
those, button functions not working for me. Can anyone help me? Its just print json value.
{"draw":1,"recordsTotal":11,"recordsFiltered":11,"data":[{"full_name":"Mr. Nithan Raj","id":2,"gender":"Mane","email":"","telephone_no":"","mobile_no":"","date_of_birth":"0000-00-00","city":"","action":"<a href="../member/2/stream/pdf" target="_blank" class="btn btn-xs btn-primary">

Did you include the datatables.buttons.js?
On 2015-12-07 9:50 AM, "Shankar"<EMAIL_ADDRESS>wrote:

Hi
those, button functions not working for me. Can anyone help me? Its just
print json value.
{"draw":1,"recordsTotal":11,"recordsFiltered":11,"data":[{"full_name":"Mr.
Nithan
Raj","id":2,"gender":"Mane","email":"","telephone_no":"","mobile_no":"","date_of_birth":"0000-00-00","city":"","action":"
—
Reply to this email directly or view it on GitHub
https://github.com/yajra/laravel-datatables/issues/293.

Also are you running datatables as service?

yes I included js file. here is my script
@section('script-table')

    <script>
        var oTable = $('#users-table').DataTable({
             processing: true,
             serverSide: true,
             ajax: {
                 url: '{{URL::to('admin/reports/members/json')}}',
                 data: function (d) {
                     d.gender = $('#gender').val();
                     d.email = $('input[name=email]').val();
                 }
                     },
             dom: 'Bfrtip',
             buttons: ['csv', 'excel', 'pdf', 'print', 'reset', 'reload'],
             columns: [
                 {data: 'id', name: 'id'},
                 {data: 'full_name', name: 'full_name'},
                 {data: 'gender', name: 'gender'},
                 {data: 'date_of_birth', name: 'date_of_birth'},
                 {data: 'email', name: 'email'},
                 {data: 'telephone_no', name: 'telephone_no'},
                 {data: 'mobile_no', name: 'mobile_no'},
                 {data: 'city', name: 'city'},
                 {data: 'action', name: 'action', orderable: false, searchable: false}
             ]
         });

     $('#search-form').on('submit', function(e) {
             oTable.draw();
             e.preventDefault();
         });
    </script>

@endsection

controller file
where('gender', $gender);
        }

        if (Input::get('email')) {
            $email = Input::get('email');
            $members = $members->where('email', 'like', "%$email%");
        }

        return Datatables::of($members)
            ->addColumn('action', function ($members) {
                return ' View';
            })
        ->make(true);
    }
}

use yajra\Datatables\Facades\Datatables;? Are you sure you're using dev-develop/6.0 branch? New namespace will be Yajra\Datatables (capital Y). Also please use, Yajra\Datatables\Datatables;. Facade seems not working properly.

@yajra  im using yajra/laravel-datatables-oracle": "~5.0

yes. I use 'use yajra\Datatables\Facades\Datatables;'

@shanka12, csv, excel, pdf, print will only work on 6.0 version and it's not yet released. You need to use  yajra/laravel-datatables-oracle": "6.*" or dev-develop branch. Please see 6.0 branch for details.

@yajra It will work with laravel 5.0 ?

when I upgrade to yajra/laravel-datatables-oracle:6.*   , I receive following error
FatalErrorException in DatatablesServiceProvider.php line 57: syntax error, unexpected 'class' (T_CLASS), expecting identifier (T_STRING) or variable (T_VARIABLE) or '{' or '$'

@shanka12, package will work on Laravel 5.0 but would need at least PHP 5.5.9 for it to work. https://github.com/yajra/laravel-datatables/commit/e7687fc102b397435aca38071f352570503ce90a
The error you received means that you are using PHP 5.4 or below.

@yajra Its working now with latest PHP version. but, still exce,pdf,print buttons not working. received like this
{"draw":1,"recordsTotal":6,"recordsFiltered":6,"data":[{"first_name":"Nithan","id":2,"gender":"Male","email":"user@user.com","telephone_no

Please follow this tuts http://datatables.yajrabox.com/service to make it work.

Using 6.0 branch and following the tuts should fix this. Thanks!


How to define a foreign key in Realm (objective-C)

Is there way to define a foreign key with Realm model inside objective-C.

Realm has a native concepts of link, so that you don't need foreign keys to describe relationships. Please see the relevant chapter in our docs for more information and let me know if you have any questions in addition.


Can RedBPF programs be loaded without cargo?

Hey, I've followed and compiled the example in the cargo-bpf docs (to block port 80)
I'm running an OpenWRT instance and I've tried to load the .elf file using
ip link set dev eth0 xdp obj block_http.elf
And I'm getting Error fetching program/map!
Maybe the compiled program isn't compiled for the right architecture? what can cause that? maybe I'm loading it wrong

Having the same issue. Running on a vagrant VM with fedora 33, kernel version 5.8.15-301.fc33.x86_64, with cargo version 1.47.0, cargo-bpf 1.2.0, redbpf-macros 1.2.0 and redbpf-probes 1.2.0. I'm running
ip link set dev eth0 xdp obj <path to elf file> sec xdp/xdp_program
I'm also still getting Error fetching program/map!
man ip link has some helpful info on loading XDP programs, under the ip link set section, especially the xdp option.
From what I can tell from that doc, we need to give a sec option because the elf file redbpf generates names the program section elf/<whatever you named the function with the #[xdp] macro>. You can check the section names in your elf file with readelf -S .

I think the issue is that we're not compatible with libbpf, and therefore ip and tc will not work without some hacks. Try post-processing your probe as a workaround, like @aquarhead did it here. This is something we will need to address at some point in cargo-bpf, though.

If you're loading XDP you can also bundle the BPF program into a single binary, and you will only need to deploy/run this single binary to load it (and don't even need to post-process the BPF ELF program).
I explored this idea in this project, so the final deployable includes the raw BPF ELF bytes here and use RedBPF functions to attach it the outer loop is a rather naive method to discover all network interfaces. The whole process is also captured in a cargo-make file the strip is only there as an attempt to reduce deployable size (I don't think it changed much, for whatever reason) and it's not necessary iirc.

@rsdy the workaround from @aquarhead works. I made a minimal repro for anyone else running into this that wants to use the ip cli: https://github.com/neallred/redbpf-postprocessing

@aquarhead I like it! I'm going to have to poke around with my project to see if I can do something similar.

@neallred neat repo :) BTW my XDP attach code are mostly extracted from cargo-bpf, it mainly shows an idea to do single binary deployment :)

Hey! I wanted to tell you that it is working indeed! The only issue which is unrelated seems to be OpenWRT's luck of support in XDP BPF programs, but I've loaded a program successfully on Ubuntu!

Do you guys know whether the compiled ELF program can be loaded on different Distros?
I've compiled the block_http on an Ubuntu 18.04 and I'm not trying to load it on an Ubuntu Server 18.04 the same way I've loaded on the non server one, and for some reason I get an error says Cannot initialize ELF context!, Maybe it has something to do with the kernel headers?


Custom meshes

There is no possibility yet to make a custom meshes, only default voxels?

I'm not sure as to what you're refering to by custom meshes, did you meant voxel objects which aren't aligned to the world grid ? This is something that I plan to add.

Exactly, thanks.


refactor(test:helpers): clean up pack compiler

Coverage remained the same at 87.179% when pulling c79c79691e86929dca2eeff17b75b39c560d6975 on JaKXz:correct-pack-helper into 53a19b54e5e1f109e904411aff61695bd5170126 on vieron:master.


Fix rendering in non-Turbolink apps and improve Turbolink docs

React components were not being rendered because of a double
nesting of event handlers when React on Rails did not detect
that Turbolinks was installed. This has been fixed.
Add debug_turbolinks helper file so that the user can simply
require their file in their application.js file to debug turbolinks.
Documentation has been improved to show how to do this.
Add section to turbolinks troubleshooting documentation recommending
that users use the node package versions of jQuery and jQuery-ujs.

Review status: 0 of 12 files reviewed at latest revision, 1 unresolved discussion.

CHANGELOG.md, line 12 [r1] (raw file):
all tests

Comments from the review on Reviewable.io

Review status: 0 of 12 files reviewed at latest revision, 1 unresolved discussion.

CHANGELOG.md, line 12 [r1] (raw file):
Done.

Comments from the review on Reviewable.io

Reviewed 12 of 12 files at r1.
Review status: 11 of 12 files reviewed at latest revision, 3 unresolved discussions.

docs/additional_reading/turbolinks.md, line 26 [r1] (raw file):
The generated apps do this as well.
Maybe see the sample gen repo.

rakelib/run_rspec.rake, line 21 [r1] (raw file):
this should be poltergeist -- can we try taking out the DRIVER part

spec/dummy/app/assets/javascripts/application_with_turbolinks.js, line 5 [r1] (raw file):
:+1:

Comments from the review on Reviewable.io

Reviewed 1 of 1 files at r2, 2 of 2 files at r3.
Review status: all files reviewed at latest revision, 3 unresolved discussions.

Comments from the review on Reviewable.io


Fix: Search function gone with 'What's Happening' and 'Who To Follow' boxes #197

Hi, the new "hide 'what's happening' and 'Who to follow' option will take the search away with them. This PR should fix the issue.
Please let me know if there is any problem. Thank you!

Bump. If possible would be great to get this merged as I've seen other feedback on Chrome store as well. I looked before filing an issue and realized this should fix it.

Sorry, closing as this extension is now deprecated: https://github.com/sindresorhus/refined-twitter/commit/8dd9df749d3a4e82c95b2bd6628c8d65f0f72e6c


Cannot build previous of Flutter Android App that I download from github project

Steps to Reproduce
I download my source from

Open project
Click 'Run 'main.dart'
console show me an this error with this warning

Your Flutter application is created using an older version of the Android
embedding. It's being deprecated in favor of Android embedding v2. Follow the
steps at

https://flutter.dev/go/android-project-migration

to migrate your project.

Launching lib\main.dart on sdk gphone x86 arm in debug mode...
Running Gradle task 'assembleDebug'...

FAILURE: Build failed with an exception.

* Where:
Build file 'C:\Users\person\Documents\GitHub\RemoteFiles\android\app\build.gradle' line: 54

* What went wrong:
A problem occurred evaluating project ':app'.
> path may not be null or empty string. path='null'

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

Expected results:
I tried various methods in Google and Stackoverflow but I cannot find how to build this source code.
It seems that the errors are from flutter SDK and gradle version something. The warning show me to migrate the app but, another people said that it is more easy to use FVM and downgrade flutter SDK an use previous version of flutter because this project is developed long time ago and it might very hard to migrate to flutter 2.0.5 SDK.
So I decide to use previous version of Flutter SDK. But even I use previous version SDK it's still not wokring.
I thought it's really easy to run and build it with clicked the Run button or build button but it really hard to find the solution. Now I find one week to find this solution but, still cannot build.
Actual results:
Still got an lots of error and cannot build it.
flutter doctor -v
[√] Flutter (Channel stable, 2.0.5, on Microsoft Windows [Version 10.0.19042.928], locale ko-KR)
    • Flutter version 2.0.5 at C:\Users\person\Downloads\important\flutter2.0.5
    • Framework revision adc687823a (9 days ago), 2021-04-16 09:40:20 -0700
    • Engine revision b09f014e96
    • Dart version 2.12.3

[√] Android toolchain - develop for Android devices (Android SDK version 30.0.3)
    • Android SDK at C:\Users\person\AppData\Local\Android\sdk
    • Platform android-30, build-tools 30.0.3
    • Java binary at: C:\Program Files\Android\Android Studio\jre\bin\java
    • Java version OpenJDK Runtime Environment (build 1.8.0_242-release-1644-b01)
    • All Android licenses accepted.

[√] Chrome - develop for the web
    • Chrome at C:\Program Files\Google\Chrome\Application\chrome.exe

[√] Android Studio (version 4.1.0)
    • Android Studio at C:\Program Files\Android\Android Studio
    • Flutter plugin can be installed from:
       https://plugins.jetbrains.com/plugin/9212-flutter
    • Dart plugin can be installed from:
       https://plugins.jetbrains.com/plugin/6351-dart
    • Java version OpenJDK Runtime Environment (build 1.8.0_242-release-1644-b01)

[√] VS Code (version 1.55.2)
    • VS Code at C:\Users\person\AppData\Local\Programs\Microsoft VS Code
    • Flutter extension can be installed from:
       https://marketplace.visualstudio.com/items?itemName=Dart-Code.flutter

[√] Connected device (3 available)
    • sdk gphone x86 arm (mobile) • emulator-5554 • android-x86    • Android 11 (API 30) (emulator)
    • Chrome (web)                • chrome        • web-javascript • Google Chrome 90.0.4430.85
    • Edge (web)                  • edge          • web-javascript • Microsoft Edge 89.0.774.48

• No issues found!

Hi  @writingdeveloper  did you try the guild here
https://flutter.dev/go/android-project-migration

you can create a new dummy flutter app then you compare the AndroidManifest.xml files, the build.gradle files and the MainActivity.kt or MainActivity.java file. Hopefully something stands out

@writingdeveloper If you go to the link specified and migrate your project, your issue will be solved.

@writingdeveloper
Looking at the error you are getting:
path may not be null or empty string. path='null',  check this SO link and see if it helps to resolve your issue.

@writingdeveloper
Looking at the error you are getting:
path may not be null or empty string. path='null', check this SO link and see if it helps to resolve your issue.

Problem Solved. with migration method.
But still previous SDK also works either.


buttons missing on license dialog

I'm on Ubuntu Bionic using Melodic and when I try to run the viewer the accept button is missing for the license agreement:

I get these warnings when I try to run it:
(smacc_viewer_node.py:8675): Gtk-WARNING **: 14:37:35.676: Negative content height -11 (allocation 1, extents 6x6) while allocating gadget (node button, owner GtkButton)

(smacc_viewer_node.py:8675): Gtk-WARNING **: 14:37:35.676: Negative content height -11 (allocation 1, extents 6x6) while allocating gadget (node button, owner GtkButton)

Got around it by doing this:
mkdir -p touch ~/.reelrobotix/smacc_viewer
touch ~/.reelrobotix/smacc_viewer/SMACC_VIEWER_LICENSE.txt

lmk if I can help you debug this.  I followed instruction on website for installing.


File "ddos-detect.py", line 44, in scrape_data     decoder = arff.ArffDecoder() AttributeError: module 'arff' has no attribute 'ArffDecoder'

Hi, thanks for sharing this project, i faced this error, may you help please with it .
File "ddos-detect.py", line 85, in
scrape_data()
File "ddos-detect.py", line 44, in scrape_data
decoder = arff.ArffDecoder()
AttributeError: module 'arff' has no attribute 'ArffDecoder'

Ensure you have the proper arff decoder package installed. The proper
package should be this one
https://github.com/renatopp/liac-arff
On Sat, Jul 11, 2020 at 8:40 AM Malhabib<EMAIL_ADDRESS>wrote:

Hi, thanks for sharing this project, i faced this error, may you help
please with it .
File "ddos-detect.py", line 85, in
scrape_data()
File "ddos-detect.py", line 44, in scrape_data
decoder = arff.ArffDecoder()
AttributeError: module 'arff' has no attribute 'ArffDecoder'
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.

thanks for your reply , i solved this but when i tried to run it in
anaconda i faced many errors :tensorflow has no attribute 'combat'.
regards
في الأحد، 12 يوليو 2020 في 6:05 ص تمت كتابة ما يلي بواسطة Jacob van
Steyn <notifications@github.com>:

Ensure you have the proper arff decoder package installed. The proper
package should be this one
https://github.com/renatopp/liac-arff
On Sat, Jul 11, 2020 at 8:40 AM Malhabib<EMAIL_ADDRESS>wrote:

Hi, thanks for sharing this project, i faced this error, may you help
please with it .
File "ddos-detect.py", line 85, in
scrape_data()
File "ddos-detect.py", line 44, in scrape_data
decoder = arff.ArffDecoder()
AttributeError: module 'arff' has no attribute 'ArffDecoder'
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<
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may you please advise which TensorFlow and Kresa versions this work is compatible with.
I'm trying to reproduce the results but couldn't run it on Anaconda with TensorFlow 2.1

Hi,
I apologize for the late response. When I wrote this project 3 years ago I believe I was using Keras 2.2.4.
You should be able to run ddos-detect.py to train & test the model. If you encounter further errors, please attach the traceback & the full error.

Hi,
May you please advise about the dataset description?
Thanks


My Learning Route (user analytics)

Show users information from all the data that we’ve collected on them over the past 1 to 4 weeks. “You have completed 5 activities.” “You got feedback 14 times on your way to completing activities.” “You used 13 python skills” “You used 9 html skills” “You created 5 new activities” “15 people attempted your activities last week”.Etc.
This feature should give students more feedback and insight into what they have been practicing.

Additionally log the user clicks in My Learnings to be used for analytics later.


Checksum mismatch for pytorch::torchvision-0.10.0-py39_cu111

Conda throws a ChecksumMismatchError when trying to install pytorch::torchvision-0.10.0-py39_cu111. This issue persists even with the workaround command mentioned in #4071.
Considering that there have been no downloads of the package since it was updated 4 days ago, I'm guessing I'm not alone in this issue.

Yes, I'm getting the same error  (Ubuntu 18, CUDA 11.2).
To reproduce the error -
conda create --name my-env python=3
conda activate my-env
conda install pytorch torchvision cudatoolkit=10.2 -c pytorch

Following's the error-
ChecksumMismatchError: Conda detected a mismatch between the expected content and downloaded content
for url 'https://conda.anaconda.org/pytorch/linux-64/torchvision-0.10.0-py39_cu102.tar.bz2'.
  download saved to: /home/akshaj/miniconda3/pkgs/torchvision-0.10.0-py39_cu102.tar.bz2
  expected md5: 52fb22d2035ac4d8209af52741987076
  actual md5: 9c90cbee72e70083ff912b574c01759f

What's weird is that I can't actually reproduce with a fresh machine, is it possible for you to clear your cache using conda clean -a and see if that resolves your issue?

I've gone ahead and deleted the old packages and the hash mismatch appears to have been resolved, feel free to re-open the issue if still persists, see https://github.com/pytorch/pytorch/issues/63006#issuecomment-896174963


Nvidia Jetson Xavier - fails to load image Python extension and Couldn't load custom C++ ops when drawing bounding boxes

🐛 Describe the bug
Note: This was posted to the PyTorch repo as issue # 80576
Errors when running approved combinations of:
A) Pytorch 11.0 and Torchvision 0.12.0
and
B) Pytorch 12.0 and Torchvision 0.13.0
Case A environment and run results:

davo@ubuntu:~$ python3 collect_env.py
Collecting environment information...
PyTorch version: 1.11.0
Is debug build: False
CUDA used to build PyTorch: 11.4
ROCM used to build PyTorch: N/A
OS: Ubuntu 20.04.4 LTS (aarch64)
GCC version: (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Clang version: Could not collect
CMake version: version 3.16.3
Libc version: glibc-2.31
Python version: 3.8.10 (default, Mar 15 2022, 12:22:08) [GCC 9.4.0] (64-bit runtime)
Python platform: Linux-5.10.65-tegra-aarch64-with-glibc2.29
Is CUDA available: True
CUDA runtime version: 11.4.239
GPU models and configuration: Could not collect
Nvidia driver version: Could not collect
cuDNN version: Probably one of the following:
/usr/lib/aarch64-linux-gnu/libcudnn.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_train.so.8.3.2
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: True
Versions of relevant libraries:
[pip3] numpy==1.22.4
[pip3] torch==1.11.0
[pip3] torchvision==0.12.0
[conda] Could not collect
davo@ubuntu:~/yolov5$ python3 detect.py --source 0
'''/home/davo/.local/lib/python3.8/site-packages/torchvision/io/image.py:13: UserWarning: Failed to load image Python extension:
warn(f"Failed to load image Python extension: {e}")'''
detect: weights=yolov5s.pt, source=0, data=data/coco128.yaml, imgsz=[640, 640], conf_thres=0.25, iou_thres=0.45, max_det=1000, device=, view_img=False, save_txt=False, save_conf=False, save_crop=False, nosave=False, classes=None, agnostic_nms=False, augment=False, visualize=False, update=False, project=runs/detect, name=exp, exist_ok=False, line_thickness=3, hide_labels=False, hide_conf=False, half=False, dnn=False
YOLOv5 rocket v6.1-258-g1156a32 Python-3.8.10 torch-1.11.0 CUDA:0 (Xavier, 31011MiB)
Fusing layers...
YOLOv5s summary: 213 layers, 7225885 parameters, 0 gradients
1/1: 0... Success (inf frames 640x480 at 30.00 FPS)
0: 480x640 Done. (4.190s)
0: 480x640 Done. (0.041s)
0: 480x640 Done. (0.041s)
0: 480x640 Done. (0.045s)
'''Traceback (most recent call last):
File "detect.py", line 252, in
main(opt)
File "detect.py", line 247, in main
run(**vars(opt))
File "/home/davo/.local/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
return func(*args, **kwargs)
File "detect.py", line 127, in run
pred = non_max_suppression(pred, conf_thres, iou_thres, classes, agnostic_nms, max_det=max_det)
File "/home/davo/yolov5/utils/general.py", line 859, in non_max_suppression
i = torchvision.ops.nms(boxes, scores, iou_thres) # NMS
File "/home/davo/.local/lib/python3.8/site-packages/torchvision/ops/boxes.py", line 39, in nms
_assert_has_ops()
File "/home/davo/.local/lib/python3.8/site-packages/torchvision/extension.py", line 33, in _assert_has_ops
raise RuntimeError(
RuntimeError: Couldn't load custom C++ ops. This can happen if your PyTorch and torchvision versions are incompatible, or if you had errors while compiling torchvision from source. For further information on the compatible versions, check https://github.com/pytorch/vision#installation for the compatibility matrix. Please check your PyTorch version with torch.version and your torchvision version with torchvision.version and verify if they are compatible, and if not please reinstall torchvision so that it matches your PyTorch install.
terminate called without an active exception
Aborted (core dumped)'''

Case B environment and run results:

davo@ubuntu:~/yolov5$ python3 ../collect_env.py
Collecting environment information...
PyTorch version: 1.12.0a0+2c916ef.nv22.3
Is debug build: False
CUDA used to build PyTorch: 11.4
ROCM used to build PyTorch: N/A
OS: Ubuntu 20.04.4 LTS (aarch64)
GCC version: (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Clang version: Could not collect
CMake version: version 3.16.3
Libc version: glibc-2.31
Python version: 3.8.10 (default, Mar 15 2022, 12:22:08) [GCC 9.4.0] (64-bit runtime)
Python platform: Linux-5.10.65-tegra-aarch64-with-glibc2.29
Is CUDA available: True
CUDA runtime version: 11.4.239
GPU models and configuration: Could not collect
Nvidia driver version: Could not collect
cuDNN version: Probably one of the following:
/usr/lib/aarch64-linux-gnu/libcudnn.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_train.so.8.3.2
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: False
Versions of relevant libraries:
[pip3] numpy==1.22.4
[pip3] torch==1.12.0a0+2c916ef.nv22.3
[pip3] torchvision==0.13.0
[conda] Could not collect
davo@ubuntu:~/yolov5$ python3 detect.py --source 0
'''/home/davo/.local/lib/python3.8/site-packages/torchvision/io/image.py:13: UserWarning: Failed to load image Python extension:
warn(f"Failed to load image Python extension: {e}")'''
detect: weights=yolov5s.pt, source=0, data=data/coco128.yaml, imgsz=[640, 640], conf_thres=0.25, iou_thres=0.45, max_det=1000, device=, view_img=False, save_txt=False, save_conf=False, save_crop=False, nosave=False, classes=None, agnostic_nms=False, augment=False, visualize=False, update=False, project=runs/detect, name=exp, exist_ok=False, line_thickness=3, hide_labels=False, hide_conf=False, half=False, dnn=False
YOLOv5 rocket v6.1-258-g1156a32 Python-3.8.10 torch-1.12.0a0+2c916ef.nv22.3 CUDA:0 (Xavier, 31011MiB)
Fusing layers...
YOLOv5s summary: 213 layers, 7225885 parameters, 0 gradients
1/1: 0... Success (inf frames 640x480 at 30.00 FPS)
0: 480x640 Done. (4.156s)
0: 480x640 Done. (0.043s)
0: 480x640 Done. (0.050s)
0: 480x640 Done. (0.045s)
'''Traceback (most recent call last):
File "detect.py", line 252, in
main(opt)
File "detect.py", linIncluded above - added here as well...
Case A environment
davo@ubuntu:~$ python3 collect_env.py
Collecting environment information...
PyTorch version: 1.11.0
Is debug build: False
CUDA used to build PyTorch: 11.4
ROCM used to build PyTorch: N/A
OS: Ubuntu 20.04.4 LTS (aarch64)
GCC version: (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Clang version: Could not collect
CMake version: version 3.16.3
Libc version: glibc-2.31
Python version: 3.8.10 (default, Mar 15 2022, 12:22:08) [GCC 9.4.0] (64-bit runtime)
Python platform: Linux-5.10.65-tegra-aarch64-with-glibc2.29
Is CUDA available: True
CUDA runtime version: 11.4.239
GPU models and configuration: Could not collect
Nvidia driver version: Could not collect
cuDNN version: Probably one of the following:
/usr/lib/aarch64-linux-gnu/libcudnn.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_train.so.8.3.2
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: True
Versions of relevant libraries:
[pip3] numpy==1.22.4
[pip3] torch==1.11.0
[pip3] torchvision==0.12.0
[conda] Could not collect
Case B environment
davo@ubuntu:~/yolov5$ python3 ../collect_env.py
Collecting environment information...
PyTorch version: 1.12.0a0+2c916ef.nv22.3
Is debug build: False
CUDA used to build PyTorch: 11.4
ROCM used to build PyTorch: N/A
OS: Ubuntu 20.04.4 LTS (aarch64)
GCC version: (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Clang version: Could not collect
CMake version: version 3.16.3
Libc version: glibc-2.31
Python version: 3.8.10 (default, Mar 15 2022, 12:22:08) [GCC 9.4.0] (64-bit runtime)
Python platform: Linux-5.10.65-tegra-aarch64-with-glibc2.29
Is CUDA available: True
CUDA runtime version: 11.4.239
GPU models and configuration: Could not collect
Nvidia driver version: Could not collect
cuDNN version: Probably one of the following:
/usr/lib/aarch64-linux-gnu/libcudnn.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_train.so.8.3.2
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: False
Versions of relevant libraries:
[pip3] numpy==1.22.4
[pip3] torch==1.12.0a0+2c916ef.nv22.3
[pip3] torchvision==0.13.0
[conda] Could not collect
cc @fmassa @vfdev-5 @pmeier
e 247, in main
run(**vars(opt))
File "/home/davo/.local/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
return func(*args, **kwargs)
File "detect.py", line 127, in run
pred = non_max_suppression(pred, conf_thres, iou_thres, classes, agnostic_nms, max_det=max_det)
File "/home/davo/yolov5/utils/general.py", line 859, in non_max_suppression
i = torchvision.ops.nms(boxes, scores, iou_thres) # NMS
File "/home/davo/.local/lib/python3.8/site-packages/torchvision/ops/boxes.py", line 40, in nms
_assert_has_ops()
File "/home/davo/.local/lib/python3.8/site-packages/torchvision/extension.py", line 33, in _assert_has_ops
raise RuntimeError(
RuntimeError: Couldn't load custom C++ ops. This can happen if your PyTorch and torchvision versions are incompatible, or if you had errors while compiling torchvision from source. For further information on the compatible versions, check https://github.com/pytorch/vision#installation for the compatibility matrix. Please check your PyTorch version with torch.version and your torchvision version with torchvision.version and verify if they are compatible, and if not please reinstall torchvision so that it matches your PyTorch install.
terminate called without an active exception
Aborted (core dumped)'''
Versions
Included above - added here as well...
Case A environment
davo@ubuntu:~$ python3 collect_env.py
Collecting environment information...
PyTorch version: 1.11.0
Is debug build: False
CUDA used to build PyTorch: 11.4
ROCM used to build PyTorch: N/A
OS: Ubuntu 20.04.4 LTS (aarch64)
GCC version: (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Clang version: Could not collect
CMake version: version 3.16.3
Libc version: glibc-2.31
Python version: 3.8.10 (default, Mar 15 2022, 12:22:08) [GCC 9.4.0] (64-bit runtime)
Python platform: Linux-5.10.65-tegra-aarch64-with-glibc2.29
Is CUDA available: True
CUDA runtime version: 11.4.239
GPU models and configuration: Could not collect
Nvidia driver version: Could not collect
cuDNN version: Probably one of the following:
/usr/lib/aarch64-linux-gnu/libcudnn.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_train.so.8.3.2
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: True
Versions of relevant libraries:
[pip3] numpy==1.22.4
[pip3] torch==1.11.0
[pip3] torchvision==0.12.0
[conda] Could not collect
Case B environment
davo@ubuntu:~/yolov5$ python3 ../collect_env.py
Collecting environment information...
PyTorch version: 1.12.0a0+2c916ef.nv22.3
Is debug build: False
CUDA used to build PyTorch: 11.4
ROCM used to build PyTorch: N/A
OS: Ubuntu 20.04.4 LTS (aarch64)
GCC version: (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Clang version: Could not collect
CMake version: version 3.16.3
Libc version: glibc-2.31
Python version: 3.8.10 (default, Mar 15 2022, 12:22:08) [GCC 9.4.0] (64-bit runtime)
Python platform: Linux-5.10.65-tegra-aarch64-with-glibc2.29
Is CUDA available: True
CUDA runtime version: 11.4.239
GPU models and configuration: Could not collect
Nvidia driver version: Could not collect
cuDNN version: Probably one of the following:
/usr/lib/aarch64-linux-gnu/libcudnn.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_adv_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_cnn_train.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_infer.so.8.3.2
/usr/lib/aarch64-linux-gnu/libcudnn_ops_train.so.8.3.2
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: False
Versions of relevant libraries:
[pip3] numpy==1.22.4
[pip3] torch==1.12.0a0+2c916ef.nv22.3
[pip3] torchvision==0.13.0
[conda] Could not collect
cc @fmassa @vfdev-5 @pmeier

Are torch and torchvision installed via pip or building from source ? I believe the latter shouldn't give these issues, but it takes quite a lot of time. I've written a small guide about this, hope it helps.

I have had the same problem, recently. Have you solved that problems? Could you help me?


[PAY 16TH MAY][$250] Distance - Amount in confirmation page does not update after changing distance

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Version Number: 1.4.69-0
Reproducible in staging?: Y
Reproducible in production?: N
Logs: https://stackoverflow.com/c/expensify/questions/4856
Issue reported by: Applause-Internal team
Action Performed:

Go to staging.new.expensify.com
Go to workspace chat.
Go to + > Submit expense > Distance.
Enter waypoints A and B.
Proceed to confirmation page.
Note that the amount is X.
Click Distance.
Add a waypoint C and save it.

Expected Result:
The amount in the distance expense confirmation page will update accordingly.
Actual Result:
The amount in the distance expense confirmation page still shows the previous amount X.
Workaround:
Unknown
Platforms:

Which of our officially supported platforms is this issue occurring on?

[x] Android: Native
[x] Android: mWeb Chrome
[x] iOS: Native
[x] iOS: mWeb Safari
[x] MacOS: Chrome / Safari
[x] MacOS: Desktop

Screenshots/Videos
https://github.com/Expensify/App/assets/115492554/c5caf07c-9b34-452c-b6d5-1efba28d48fa

View all open jobs on GitHub
Upwork Automation - Do Not Edit

Upwork Job URL: https://www.upwork.com/jobs/~014927ad327a4ee68d
Upwork Job ID:<PHONE_NUMBER>758776832
Last Price Increase: 2024-05-01
Automatic offers:

jjcoffee | Reviewer | 0

@jliexpensify I haven't added the External label as I wasn't 100% sure about this issue. Please take a look and add the label if you agree it's a bug and can be handled by external contributors.

We think this issue might be related to the #collect project.

Production
https://github.com/Expensify/App/assets/115492554/87f76e3a-29cb-4266-a584-ef23e074db25

This is regression from this PR https://github.com/Expensify/App/pull/40307
Proposal
Please re-state the problem that we are trying to solve in this issue.
The amount field isn't updated when updating waypoint list
What is the root cause of that problem?
We utilize TransactionUtils.getDistance(transaction) to obtain the distance for computing the amount. However, when modifying the waypoint, transaction?.comment?.customUnit?.quantity remains unchanged, resulting in the amount field not being updated.
What changes do you think we should make in order to solve the problem?
When updating the waypoint list, it's also necessary to ensure that transaction?.comment?.customUnit?.quantity is updated accordingly.
What alternative solutions did you explore? (Optional)
Reminder: Please use plain English, be brief and avoid jargon. Feel free to use images, charts or pseudo-code if necessary. Do not post large multi-line diffs or write walls of text. Do not create PRs unless you have been hired for this job.

@cretadn22's proposal makes sense to me!
:ribbon::eyes::ribbon: C+ reviewed

Ah woops, thanks for finding the problem and a good solution @cretadn22. I'll assign you now to get this moving. @grgia please feel free to re-assign to me, or I'm happy for you to manage it if you prefer.

Looks like automation failed here, this hit production May 9, so payment is due May 16. @jliexpensify

Thanks @jjcoffee! Does a checklist need to be completed?
Payment Summary

C+: @jjcoffee $250

Upwork job

@cretadn22 hmm apologies, I didn't see that you were invited to the Upworks job so I assumed you were from one of the agencies.
Are you Nguyen T.?
Can you also add your full name to your GH, so we can easily view and invite you? Thanks!

Offer sent, please add your name to your GH profile - thanks!

The PR that introduced the bug has been identified. Link to the PR: https://github.com/Expensify/App/pull/40307
The offending PR has been commented on, pointing out the bug it caused and why, so the author and reviewers can learn from the mistake. Link to comment: https://github.com/Expensify/App/pull/40307/files#r1601300483
A discussion in #expensify-bugs has been started about whether any other steps should be taken (e.g. updating the PR review checklist) in order to catch this type of bug sooner. Link to discussion: N/A
Determine if we should create a regression test for this bug. Yes
If we decide to create a regression test for the bug, please propose the regression test steps to ensure the same bug will not reach production again.

Regression Test Proposal

Go to any workspace chat
Go to + > Submit expense > Distance.
Enter waypoints A and B.
Proceed to confirmation page.
Note the amount displayed
Click Distance
Add a waypoint C and save it
Confirm that the amount updates correctly on the confirmation screen

Do we agree 👍 or 👎

Thanks for cleaning up after me! 😅

Paid and job closed.


As default theme of jekyll, why minima doesn't have paging style in home page?

As default theme of jekyll, why minima doesn't have paging style in home page?

Similar to #159

@ankitrgadiya Many thanks, this can solve my question!


Max/min mixmatch between numbers and strings

Issue
Lets say you have a field for a username and set the min/max to 3 and 10, entering any A-Z character will work as expected but entering "11" as in the number 11 will say the input is too big for that field, it thinks you're entering a number literal instead of plain text so 11 >= 10 instead of (2 >= 11, the length of the input text). You handle both numbers and strings with the same min/max validation but there isn't an option to specific if you want a number or a string.
Solution?
Add a number type strictly for numbers only and keep the text type as stringifed text. Entering anything other than a number will remove that character and display a tooltip to let the user know only numbers are allowed.

@Solaris9 first of all thank u for ur investigation,
that already implemented on package for react, and currently working on solid version then we will fix for svelte too
so let s challenge the package with different cases to make it more better ;)
https://www.formly-js.com


CAPI v1.5.0-beta.0 has been released and is ready for testing

CAPI v1.5.0-beta.0 has been released and is ready for testing.
Looking forward to your feedback before CAPI 1.5.0 release, the 25th July 2023!
For quick reference

CAPI v1.5.0-beta.0 release notes
Shortcut to CAPI git issues

Following are the planned dates for the upcoming releases

Release
Expected Date

v1.5.0-beta.x
Tuesday 5th July 2023

release-1.5 branch created (Begin [Code Freeze])
Tuesday 11th July 2023

v1.5.0-rc.0 released
Tuesday 11th July 2023

release-1.5 jobs created
Tuesday 11th July 2023

v1.5.0-rc.x released
Tuesday 18th July 2023

v1.5.0 released
Tuesday 25th July 2023

thanks for the update @nawazkh , i am hoping to propose a release for our 1.4 update and then start working on the 1.5 stuff.


Derived languages are not supported

Minetest has support for pt_BR but intllib not. That's a big inconvenience for me. In this situation we have two problems:

The selected language will not be understood correctly
Translators are required to choose only one primary language (eg Portuguese in Portugal or Portuguese in Brazil)
I hope this is resolved soon

Take a look at the ll_CC branch and tell me if that fixes the problem.
You can have both pt_BR.txt and pt.txt (the latter being the default dialect).

I performed the tests. The problem still occurs.
I'm using a test mod that already works with intllib (I changed the pt locale file to pt_BR).
Language Minetest configuration (language) = pt_BR
intlib is not translating.
I want to take the opportunity to ask another feature.
If linguegem ll not exist, intllib should seek any ll_CC language (derived from ll language configured in the game)

I performed the tests. The problem still occurs.
Gah, fixed and force-pushed to ll_CC branch. I can confirm it works now.

If linguegem ll not exist, intllib should seek any ll_CC language (derived from ll language configured in the game)

That would require huge kludges, as you cannot infer the country code from language code. You have things like es_ES and pt_PT, which are just the language code in uppercase. but then there's no such thing as en_EN, for example.
Since many countries may speak the same language (e.g. es_ES, es_UY, es_AR, es_MX, ...), and some countries speak multiple languages (e.g. en_CA, fr_CA), you cannot assume anything.
As an example above, I may select ll_LL, but would break for english (there's no en_EN; the "default" would be en_GB). If we use the first derivative found, you could get en_CA (Canadian english), or de_AU (Austrian german), which may not be what you expect.
It's not worth the effort to support "smart" detection like that, IMHO, but feel free to provide an implementation if you feel like it.

@BrunoMine Can you confirm the issue is fixed?

You can use a very simple algorithm to search for a secondary language.
	local minetest_language = "pt" -- minetest settings
	local intllib_language = "?" -- intllib choice for secondary language
	local locale_list = minetest.get_dir_list(minetest.get_modpath("modname"))
	for n, lang in ipairs(locale_list) do
		if string.find(lang, minetest_language.."_") then
			intllib_language = lang
			break
		end
	end

I understand what you suggest, but I don't think that's the correct way. Can you open a separate issue for that so others can comment?
I'm going to close this one since the original problem is fixed.


fix(2.0.2): change object index using get-pae-source api

Description of Change
fix: Corrected index of invalid object in GetPageSource.
Checklist

[ ] PR description included and stakeholders cc'd
[-] yarn test passes
[-] tests are changed or added
[v] relevant documentation, tutorials, templates and examples are changed or added

Release Notes
Notes:
2.0.2

fix: Corrected index of invalid object in GetPageSource.

I have completed verification. thank you


What's up with the test case and why is this not passing?

Challenge Waypoint: Understand String Immutability has an issue.
User Agent is: Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:42.0) Gecko/20100101 Firefox/42.0.
Please describe how to reproduce this issue, and include links to screenshots if possible.

My code:
// Setup
var myStr = "Jello World";

// Only change code below this line

myStr[0] = "J"; // Fix Me

oops