I meanwhile rebooted our server. Now autoQC starts up, but when I execute a instrument config it tells me there is no valid skyline installation:

[7/23/2020 4:28:23 PM]    Getting the acquisition date on the newest file imported into the Skyline document.
[7/23/2020 4:28:23 PM]    Running SkylineRunner.exe with args: 
[7/23/2020 4:28:23 PM]     --in="Z:\QEXACTIVEHF_2\autoQC01_HF2_from20190821.sky" --report-conflict-resolution=overwrite --report-add="C:\Users\autoQC_user\AppData\Local\Apps\2.0\6M6QL0GJ.33L\YR0BD0OQ.30N\auto..tion_e4141a2a22107248_0001.0001_6f67fb96aa7015e7\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="Z:\QEXACTIVEHF_2\AcquisitionTimes.csv"
[7/23/2020 4:28:28 PM]    ERROR: Error: Could not connect to Skyline.
[7/23/2020 4:28:28 PM]    Make sure you have a valid Skyline installation.
[7/23/2020 4:28:28 PM]    ERROR: SkylineRunner.exe exited with code 0. Error reported.
[7/23/2020 4:28:28 PM]    ERROR: Error getting the last acquired file date from the Skyline document.
[7/23/2020 4:28:28 PM]    ERROR: An error occurred. Stopping configuration.
[7/23/2020 4:31:13 PM]    Logging initialized...
Version: AutoQC Loader 1.1.0.19128
Name: QEXACTIVEHF_2
Enabled: True
Panorama User: tobias.kockmann@fgcz.ethz.ch
Created: 8/21/201910:02 AM
Modified: 8/23/20199:38 AM

Main Settings
Skyline file: Z:\QEXACTIVEHF_2\autoQC01_HF2_from20190821.sky
Folder to watch: Z:\QEXACTIVEHF_2
Include subfolders: False
Filter Type: Contains; Pattern: autoQC01
Instrument: Thermo
Results window: 31 days
Acquisition time: 1 minutes

Panorama Settings
Panorama server URL: https://panoramaweb.org/
Panorama user email: tobias.kockmann@fgcz.ethz.ch
Panorama folder: /Functional Genomics Center Zurich - Proteomics & Protein Analysis Group/Qcloud/20190823_QEXACTIVEHF_2


[7/23/2020 4:31:16 PM]    Getting the acquisition date on the newest file imported into the Skyline document.
[7/23/2020 4:31:16 PM]    Running SkylineRunner.exe with args: 
[7/23/2020 4:31:16 PM]     --in="Z:\QEXACTIVEHF_2\autoQC01_HF2_from20190821.sky" --report-conflict-resolution=overwrite --report-add="C:\Users\autoQC_user\AppData\Local\Apps\2.0\6M6QL0GJ.33L\YR0BD0OQ.30N\auto..tion_e4141a2a22107248_0001.0001_6f67fb96aa7015e7\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="Z:\QEXACTIVEHF_2\AcquisitionTimes.csv"
[7/23/2020 4:31:22 PM]    ERROR: Error: Could not connect to Skyline.
[7/23/2020 4:31:22 PM]    Make sure you have a valid Skyline installation.
[7/23/2020 4:31:22 PM]    ERROR: SkylineRunner.exe exited with code 0. Error reported.
[7/23/2020 4:31:22 PM]    ERROR: Error getting the last acquired file date from the Skyline document.
[7/23/2020 4:31:22 PM]    ERROR: An error occurred. Stopping configuration.

But there is skyline installed. I can start it manually. It is installed in C:\Program Files\Skyline. How does autoQC start SkylineRunner? Can I point to a specific installation?

Best,
Tobi

Hi Tobi,

Good to hear that the original problem is resolved by restarting the computer. The error you are seeing now is most likely due to SkylineRunner taking longer than the allowed time to start an instance of Skyline. I will update SkylineRunner and post a new installer soon. Sorry for the disruption in your QC tracking workflow.

Thanks,
Vagisha

Hi Vagisha,

could it be that autoQC tries to install a separate instance of skyline into \\Users\....\AppData\... instead of using the installation in C:\Program FIles\Skyline?

Best,
Tobi

see attached screenshot

Hi Tobi,

Sorry I jumped the gun a bit and didn't notice that you have Skyline installed in C:\Program Files\Skyline. Brendan pointed out that you have Skyline installed with the administrative installer. SkylineRunner expects to find Skyline in the usual location, typically C:\Users<User>\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Skyline\Skyline.appref-ms. It is not going to look for it in C:\Program Files\Skyline.

Brendan thinks that we should update AutoQC Loader to be able to point to a folder that has SkylineCmd.exe and use that instead of SkylineRunner. This is also what you were wondering at the end of your post. Sorry I missed that part!

I can probably post a new AutoQC Loader installer next week. In the mean time are you able to install Skyline the usual way, as a ClickOnce installer? I don't know if the two can coexist.

Thanks,
Vagisha

ok. Now it makes sense. So I would need to deinstall the Skyline admin and reinstall the "normal" one. The fix you suggested would be a good think, because we experience problems with the "normal" skyline on our Windows Server 2012. Therefore going back is not really what I want.

Now it gets crazy:

I deinstalled skyline admin and tried to reinstall skyline:

PLATFORM VERSION INFO
	Windows 			: 6.3.9600.0 (Win32NT)
	Common Language Runtime 	: 4.0.30319.42000
	System.Deployment.dll 		: 4.7.3062.0 built by: NET472REL1
	clr.dll 			: 4.7.3468.0 built by: NET472REL1LAST_C
	dfdll.dll 			: 4.7.3062.0 built by: NET472REL1
	dfshim.dll 			: 6.3.9600.16384 (winblue_rtm.130821-1623)

SOURCES
	Deployment url			: file:///C:/Users/autoQC_user/AppData/Roaming/Microsoft/Windows/Start%20Menu/Programs/Skyline/Skyline.appref-ms%7C
	Deployment Provider url		: https://skyline.gs.washington.edu/software/Skyline-release-64_20_1/Skyline.application
	Application url			: https://skyline.gs.washington.edu/software/Skyline-release-64_20_1/Application%20Files/Skyline_20_1_0_155/Skyline.exe.manifest

IDENTITIES
	Application Identity		: Skyline.exe, Version=20.1.0.155, Culture=neutral, PublicKeyToken=e4141a2a22107248, processorArchitecture=msil, type=win32

ERROR SUMMARY
	Below is a summary of the errors, details of these errors are listed later in the log.
	* An exception occurred while determining trust. Following failure messages were detected:
		+ Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)
	* Activation of C:\Users\autoQC_user\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Skyline\Skyline.appref-ms| resulted in exception. Following failure messages were detected:
		+ Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)

COMPONENT STORE TRANSACTION FAILURE SUMMARY
	No transaction error was detected.

WARNINGS
	There were no warnings during this operation.

OPERATION PROGRESS STATUS
	* [7/24/2020 9:14:06 AM] : Activation of C:\Users\autoQC_user\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Skyline\Skyline.appref-ms| has started.
	* [7/24/2020 9:14:07 AM] : Installation of the application has started.
	* [7/24/2020 9:14:09 AM] : Processing of application manifest has successfully completed.
	* [7/24/2020 9:14:11 AM] : Found compatible runtime version 4.0.30319.

ERROR DETAILS
	Following errors were detected during this operation.
	* [7/24/2020 9:14:11 AM] System.Runtime.InteropServices.COMException
		- Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)
		- Source: mscorlib
		- Stack trace:
			at System.Deployment.Internal.Isolation.IStore.Transact(IntPtr cOperation, StoreTransactionOperation[] rgOperations, UInt32[] rgDispositions, Int32[] rgResults)
			at System.Deployment.Internal.Isolation.Store.Transact(StoreTransactionOperation[] operations)
			at System.Security.Policy.ApplicationTrustCollection.CommitApplicationTrust(ApplicationIdentity applicationIdentity, String trustXml)
			at System.Security.Policy.ApplicationTrustCollection.Add(ApplicationTrust trust)
			at System.Security.Policy.ApplicationSecurityManager.DetermineApplicationTrustInternal(ActivationContext activationContext, TrustManagerContext context)
			at System.Security.Policy.ApplicationSecurityManager.DetermineApplicationTrust(ActivationContext activationContext, TrustManagerContext context)
			at System.Deployment.Application.ApplicationTrust.RequestTrust(SubscriptionState subState, Boolean isShellVisible, Boolean isUpdate, ActivationContext actCtx, TrustManagerContext tmc)
			at System.Deployment.Application.ApplicationTrust.RequestTrust(SubscriptionState subState, Boolean isShellVisible, Boolean isUpdate, ActivationContext actCtx)
			at System.Deployment.Application.ApplicationActivator.DownloadApplication(SubscriptionState subState, ActivationDescription actDesc, Int64 transactionId, TempDirectory& downloadTemp)
			at System.Deployment.Application.ApplicationActivator.InstallApplication(SubscriptionState& subState, ActivationDescription actDesc)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivation(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl, Uri& deploymentUri)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
--- End of stack trace from previous location where exception was thrown ---
			at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
			at System.Deployment.Application.ApplicationActivator.ActivateDeploymentWorker(Object state)
	* [7/24/2020 9:14:11 AM] System.Runtime.InteropServices.COMException
		- Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)
		- Source: mscorlib
		- Stack trace:
			at System.Deployment.Internal.Isolation.IStore.Transact(IntPtr cOperation, StoreTransactionOperation[] rgOperations, UInt32[] rgDispositions, Int32[] rgResults)
			at System.Deployment.Internal.Isolation.Store.Transact(StoreTransactionOperation[] operations)
			at System.Security.Policy.ApplicationTrustCollection.CommitApplicationTrust(ApplicationIdentity applicationIdentity, String trustXml)
			at System.Security.Policy.ApplicationTrustCollection.Add(ApplicationTrust trust)
			at System.Security.Policy.ApplicationSecurityManager.DetermineApplicationTrustInternal(ActivationContext activationContext, TrustManagerContext context)
			at System.Security.Policy.ApplicationSecurityManager.DetermineApplicationTrust(ActivationContext activationContext, TrustManagerContext context)
			at System.Deployment.Application.ApplicationTrust.RequestTrust(SubscriptionState subState, Boolean isShellVisible, Boolean isUpdate, ActivationContext actCtx, TrustManagerContext tmc)
			at System.Deployment.Application.ApplicationTrust.RequestTrust(SubscriptionState subState, Boolean isShellVisible, Boolean isUpdate, ActivationContext actCtx)
			at System.Deployment.Application.ApplicationActivator.DownloadApplication(SubscriptionState subState, ActivationDescription actDesc, Int64 transactionId, TempDirectory& downloadTemp)
			at System.Deployment.Application.ApplicationActivator.InstallApplication(SubscriptionState& subState, ActivationDescription actDesc)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivation(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl, Uri& deploymentUri)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
--- End of stack trace from previous location where exception was thrown ---
			at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
			at System.Deployment.Application.ApplicationActivator.ActivateDeploymentWorker(Object state)

COMPONENT STORE TRANSACTION DETAILS
	No transaction information is available.

another reboot of the server, still the same problem. I can not install skyline anymore:

PLATFORM VERSION INFO
	Windows 			: 6.3.9600.0 (Win32NT)
	Common Language Runtime 	: 4.0.30319.42000
	System.Deployment.dll 		: 4.7.3062.0 built by: NET472REL1
	clr.dll 			: 4.7.3468.0 built by: NET472REL1LAST_C
	dfdll.dll 			: 4.7.3062.0 built by: NET472REL1
	dfshim.dll 			: 6.3.9600.16384 (winblue_rtm.130821-1623)

SOURCES
	Deployment url			: https://skyline.gs.washington.edu/software/Skyline-release-64_20_1/Skyline.application
	Deployment Provider url		: https://skyline.gs.washington.edu/software/Skyline-release-64_20_1/Skyline.application
	Application url			: https://skyline.gs.washington.edu/software/Skyline-release-64_20_1/Application%20Files/Skyline_20_1_0_155/Skyline.exe.manifest

IDENTITIES
	Deployment Identity		: Skyline.application, Version=20.1.0.155, Culture=neutral, PublicKeyToken=e4141a2a22107248, processorArchitecture=msil
	Application Identity		: Skyline.exe, Version=20.1.0.155, Culture=neutral, PublicKeyToken=e4141a2a22107248, processorArchitecture=msil, type=win32

APPLICATION SUMMARY
	* Installable application.

ERROR SUMMARY
	Below is a summary of the errors, details of these errors are listed later in the log.
	* An exception occurred while determining trust. Following failure messages were detected:
		+ Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)
	* Activation of https://skyline.gs.washington.edu/software/Skyline-release-64_20_1/Skyline.application resulted in exception. Following failure messages were detected:
		+ Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)

COMPONENT STORE TRANSACTION FAILURE SUMMARY
	No transaction error was detected.

WARNINGS
	There were no warnings during this operation.

OPERATION PROGRESS STATUS
	* [7/24/2020 9:39:09 AM] : Activation of https://skyline.gs.washington.edu/software/Skyline-release-64_20_1/Skyline.application has started.
	* [7/24/2020 9:39:10 AM] : Processing of deployment manifest has successfully completed.
	* [7/24/2020 9:39:10 AM] : Installation of the application has started.
	* [7/24/2020 9:39:11 AM] : Processing of application manifest has successfully completed.
	* [7/24/2020 9:39:15 AM] : Found compatible runtime version 4.0.30319.

ERROR DETAILS
	Following errors were detected during this operation.
	* [7/24/2020 9:39:15 AM] System.Runtime.InteropServices.COMException
		- Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)
		- Source: mscorlib
		- Stack trace:
			at System.Deployment.Internal.Isolation.IStore.Transact(IntPtr cOperation, StoreTransactionOperation[] rgOperations, UInt32[] rgDispositions, Int32[] rgResults)
			at System.Deployment.Internal.Isolation.Store.Transact(StoreTransactionOperation[] operations)
			at System.Security.Policy.ApplicationTrustCollection.CommitApplicationTrust(ApplicationIdentity applicationIdentity, String trustXml)
			at System.Security.Policy.ApplicationTrustCollection.Add(ApplicationTrust trust)
			at System.Security.Policy.ApplicationSecurityManager.DetermineApplicationTrustInternal(ActivationContext activationContext, TrustManagerContext context)
			at System.Security.Policy.ApplicationSecurityManager.DetermineApplicationTrust(ActivationContext activationContext, TrustManagerContext context)
			at System.Deployment.Application.ApplicationTrust.RequestTrust(SubscriptionState subState, Boolean isShellVisible, Boolean isUpdate, ActivationContext actCtx, TrustManagerContext tmc)
			at System.Deployment.Application.ApplicationTrust.RequestTrust(SubscriptionState subState, Boolean isShellVisible, Boolean isUpdate, ActivationContext actCtx)
			at System.Deployment.Application.ApplicationActivator.DownloadApplication(SubscriptionState subState, ActivationDescription actDesc, Int64 transactionId, TempDirectory& downloadTemp)
			at System.Deployment.Application.ApplicationActivator.InstallApplication(SubscriptionState& subState, ActivationDescription actDesc)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivation(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl, Uri& deploymentUri)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
--- End of stack trace from previous location where exception was thrown ---
			at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
			at System.Deployment.Application.ApplicationActivator.ActivateDeploymentWorker(Object state)
	* [7/24/2020 9:39:15 AM] System.Runtime.InteropServices.COMException
		- Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)
		- Source: mscorlib
		- Stack trace:
			at System.Deployment.Internal.Isolation.IStore.Transact(IntPtr cOperation, StoreTransactionOperation[] rgOperations, UInt32[] rgDispositions, Int32[] rgResults)
			at System.Deployment.Internal.Isolation.Store.Transact(StoreTransactionOperation[] operations)
			at System.Security.Policy.ApplicationTrustCollection.CommitApplicationTrust(ApplicationIdentity applicationIdentity, String trustXml)
			at System.Security.Policy.ApplicationTrustCollection.Add(ApplicationTrust trust)
			at System.Security.Policy.ApplicationSecurityManager.DetermineApplicationTrustInternal(ActivationContext activationContext, TrustManagerContext context)
			at System.Security.Policy.ApplicationSecurityManager.DetermineApplicationTrust(ActivationContext activationContext, TrustManagerContext context)
			at System.Deployment.Application.ApplicationTrust.RequestTrust(SubscriptionState subState, Boolean isShellVisible, Boolean isUpdate, ActivationContext actCtx, TrustManagerContext tmc)
			at System.Deployment.Application.ApplicationTrust.RequestTrust(SubscriptionState subState, Boolean isShellVisible, Boolean isUpdate, ActivationContext actCtx)
			at System.Deployment.Application.ApplicationActivator.DownloadApplication(SubscriptionState subState, ActivationDescription actDesc, Int64 transactionId, TempDirectory& downloadTemp)
			at System.Deployment.Application.ApplicationActivator.InstallApplication(SubscriptionState& subState, ActivationDescription actDesc)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivation(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl, Uri& deploymentUri)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
--- End of stack trace from previous location where exception was thrown ---
			at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
			at System.Deployment.Application.ApplicationActivator.ActivateDeploymentWorker(Object state)

COMPONENT STORE TRANSACTION DETAILS
	No transaction information is available.

Hi Tobi,

I am so sorry it got all messed up! Have there been any recent changes / upgrades on the computer? Some things to check, which you have probably already done:

1. Is enough disk space on the computer?
2. Run TaskManager and look at memory usage.
3. If there is anti-virus software running on the computer try disabling it.

When I searched for the error code (HRESULT: 0x800705AA) I found this link: https://answers.microsoft.com/en-us/windows/forum/all/error-code-0x800705aa-and-insufficient-system/06fdc4fd-a2fe-4c11-b1ae-d60acef18caa. It suggests running System File Checker and Hardware and Device Troubleshooter.

I will ask Brendan to jump in at this point.

-Vagisha

Hi Tobi,
Have you ever had AutoQC working in your lab? If so, how might you get it back to that state? Knowing that our intended long-term fix what Vagisha has described and I expect it to be ready within a week or two.

Did you used to be able to install the normal Skyline on this computer? Or were you using a different computer? Or have you never had AutoQC working?

I'd rather not have my team sink a bunch of time into understanding what is wrong with this computer that prevents it from installing with the Skyline web installers, if the intended solution is to return to the administrative installers as soon as the fix is available.

Thinks short-term. Think about what you have working and have had working. I am sure you can get something working for the next 2 weeks. If you absolutely feel you have gotten yourself totally stuck and now can't perform AutoQC operations that were working until very recently, we will try to get you back out of that situation, but if you can figure out a way to handle it yourself. We will get you what you have requested as the ultimate solution quicker.

--Brendan

Hi Vagisha,

I checked resources like memory, disk. All good. No anti virus software running.

Best,
Tobi

Hi Brendan,

we are using autoQC for several years now. Every LC-MS system of our lab uploads through this server to our PanoramaPublic project. I haven't touched the system for several month. So no changes that I am aware of. But it is a Windows server...so maybe the environment was modified by somebody (admin?) somehow. I can't tell.

Unfortunately, it is not the first time that the normal skyline install behaves strange on our computers that are centrally managed and use roaming profiles. We had a lot fo customer complains and at some point started installing on our pool computers using the admin version.

I check if making changes to users rights helps.

Best,
Tobi

The user that executes autoQC (and the skyline installer) is now part of the admin group. No changes.

When I switch to my personal domain user (same machine) the installer works without a problem. So it must be something user specific.

Nice progress. Using the admin installer is definitely the right solution for centrally managed computers like what you described. And we will make this work with AutoQC Loader. Though, it never has before. Any computer that has been running AutoQC Loader successfully in the past must have been doing it with a web or ZIP installer, and not the admin installer.

Sounds like you are onto something with user privileges. We will keep working on improving AutoQC Loader to work with the admin installer and assume that you will find a workaround to allow you to continue using AutoQC Loader until this is ready.

Thanks for the sleuthing and keeping us posted on your progress.

--Brendan

I guess autoQC loader used the regular skyline that was installed. But I deinstalled that one after having placed the admin version on the same system. Unfortunate!

Hi Brendan,

any news regarding the autoQC loader updates?

Best,
Tobi

Hi Tobi,

I will release an update in a couple of days that will be able to work with the Administrator install of Skyline.

Thanks,
Vagisha