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SciToS - the Scientific Tool Set
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Scitos wont open #35

Closed sammycarey closed 2 years ago

sammycarey commented 3 years ago

Hi there, I have a Mac computer and have downloaded the latest version of Scitos, and when I click on the app to open it, it will not work. It comes up momentarily in my dock before disappearing again.

Is there something I can do to fix this?

Thanks, Sam

CarstenWickner commented 2 years ago

Hi Sam,

TL;DR; it sounds like you're describing what I explain under "Issue 2" below. I'm just listing the other items for completeness' sake.

It's true macOS dislikes anything that is not properly validated and downloaded through the App Store. That's why most things downloaded from the internet are deemed not trustworthy, including SciToS (since I'm unwilling to pay for the Apple Developer License one would need in order to be accepted into the App Store, let alone all the other hoops one would have to jump through. It's a free tool and it should stay that way, but I digress...).

Issue 1: “SciToS” is damaged and can’t be opened. You should move it to the Bin.

In some cases, macOS will show this rather misleading message, which is just a harsh way of letting you know, that the application was put into "quarantine".
However, if you do trust the application you can lift that "quarantine" via the following steps:

  1. Open a Terminal (or another console). By default, this may open in your user's home folder.
  2. Navigate to the directory where the unpacked SciToS.app is – via the cd command, e.g. cd Downloads/target if you simply unpacked it directly in your Downloads directory.
  3. Then lift the quarantine with the following command: 
    sudo xattr -r -d com.apple.quarantine SciToS.app
  4. Enter your password to confirm the elevated access of the "super-user-do"/sudo command.
  5. Now you can start close the Terminal and start using the SciToS.app.

Issue 2: the SciToS.app closes immediately after start (insufficient permissions)

There may be insufficient permissions for the application to access all its parts.
Let's fix 'em then:

  1. Open a Terminal
  2. Navigate to the directory where the unpacked SciToS.app is – via the cd command, e.g. cd Downloads/target if you simply unpacked it directly in your Downloads directory.
  3. Then (recursively) allow all parts in the app bundle (which is really just a special directory) to be executed: 
    chmod -R +x SciToS.app

If that still doesn't help:

  1. Open a Terminal
  2. Navigate to the directory where the unpacked SciToS.app is – via the cd command.
  3. Then do what the double-click does: 
    open SciToS.app
  4. Let me know what the output is after the application crash

If you don't want to do the above or there is still no meaningful error output, you can give up the convenience of the special macOS .app and just use the portable Java application directly, by downloading the .zip file from the Releases page and double-click the unpacked scitos.jar in the base folder. If you do that though, you may encounter the next challenge.

Issue 3: “scitos.jar” cannot be opened because it is from an unidentified developer.

Again, the downloaded file has been put into "quarantine", but the fix supposedly does not involve any Terminal commands:

  1. Open your "System Preferences"
  2. Select "Security & Privacy"
  3. Go to the "General" tab
  4. At the bottom it should say:

    "scitos.jar" was blocked from use because it is not from an identified developer.

  5. Click on the "Open Anyway" button on the right, resulting in another warning being shown:

    macOS cannot verify the developer of "scitos.jar". Are you sure you want to open it?
    By opening this app, you will be overriding system security which can expose your computer and personal information to malware that may harm your Mac or compromise your privacy.

  6. If you still trust me, click "Open". 😉

Once that is done, you may still encounter the next challenge:

Issue 4: the scitos.jar closes immediately after double-clicking

I know, you've been here before, but we have one more way to get this running:

  1. Open a Terminal
  2. Navigate to the directory where the unpacked scitor.jar is – via the cd command
  3. Start the Java application directly: 
    java -jar scitos.jar
  4. If that is still not working, perhaps you have no suitable Java installation after all. Check for the currently installed version and let me know what it says: 
    java --version

    Or go directly to https://adoptopenjdk.net/ and download the installer for JDK11 or newer.

I hope something of the above helped you. Looking forward to your feedback.

Cheers, Carsten

sammycarey commented 2 years ago

Hi Carsten,

I have just managed to get it working through the java command! Thank you very much for your quick and detailed response! It is greatly appreciated and I look forward to using it!

All the best, Sam

On 18/09/2021, at 8:23 AM, Carsten Wickner @.***> wrote:

Hi Sam,

TL;DR; it sounds like you're describing what I explain under "Issue 2" below. I'm just listing the other items for completeness' sake.

It's true macOS dislikes anything that is not properly validated and downloaded through the App Store. That's why most things downloaded from the internet are deemed not trustworthy, including SciToS (since I'm unwilling to pay for the Apple Developer License one would need in order to be accepted into the App Store, let alone all the other hoops one would have to jump through. It's a free tool and it should stay that way, but I digress...).

Issue 1: “SciToS” is damaged and can’t be opened. You should move it to the Bin.

In some cases, macOS will show this rather misleading message, which is just a harsh way of letting you know, that the application was put into "quarantine". However, if you do trust the application you can lift that "quarantine" via the following steps:

Open a Terminal (or another console). By default, this may open in your user's home folder. Navigate to the directory where the unpacked SciToS.app is – via the cd command, e.g. cd Downloads/target if you simply unpacked it directly in your Downloads directory. Then lift the quarantine with the following command: sudo xattr -r -d com.apple.quarantine SciToS.app Enter your password to confirm the elevated access of the "super-user-do"/sudo command. Now you can start close the Terminal and start using the SciToS.app. Issue 2: the SciToS.app closes immediately after start (insufficient permissions)

There may be insufficient permissions for the application to access all its parts. Let's fix 'em then:

Open a Terminal Navigate to the directory where the unpacked SciToS.app is – via the cd command, e.g. cd Downloads/target if you simply unpacked it directly in your Downloads directory. Then (recursively) allow all parts in the app bundle (which is really just a special directory) to be executed: chmod -R +x SciToS.app If that still doesn't help:

Open a Terminal Navigate to the directory where the unpacked SciToS.app is – via the cd command. Then do what the double-click does: open SciToS.app Let me know what the output is after the application crash If you don't want to do the above or there is still no meaningful error output, you can give up the convenience of the special macOS .app and just use the portable Java application directly, by downloading the .zip file from the Releases https://github.com/scientific-tool-set/scitos/releases page and double-click the unpacked scitos.jar in the base folder. If you do that though, you may encounter the next challenge.

Issue 3: “scitos.jar” cannot be opened because it is from an unidentified developer.

Again, the downloaded file has been put into "quarantine", but the fix supposedly does not involve any Terminal commands:

Open your "System Preferences" Select "Security & Privacy" Go to the "General" tab At the bottom it should say: "scitos.jar" was blocked from use because it is not from an identified developer. Click on the "Open Anyway" button on the right, resulting in another warning being shown: macOS cannot verify the developer of "scitos.jar". Are you sure you want to open it? By opening this app, you will be overriding system security which can expose your computer and personal information to malware that may harm your Mac or compromise your privacy. If you still trust me, click "Open". 😉 Once that is done, you may still encounter the next challenge:

Issue 4: the scitos.jar closes immediately after double-clicking

I know, you've been here before, but we have one more way to get this running:

Open a Terminal Navigate to the directory where the unpacked scitor.jar is – via the cd command Start the Java application directly: java -jar scitos.jar If that is still not working, perhaps you have no suitable Java installation after all. Check for the currently installed version and let me know what it says: java --version Or go directly to https://adoptopenjdk.net/ https://adoptopenjdk.net/ and download the installer for JDK11 or newer.

I hope something of the above helped you. Looking forward to your feedback.

Cheers, Carsten

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/scientific-tool-set/scitos/issues/35#issuecomment-922060181, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVVNFYQEZA4HYEYTLERCWWLUCOPVHANCNFSM5EGFCVHA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

sammycarey commented 2 years ago

Aleea also mentioned that the same command enables her to open Scitos on her windows computer.

All the best, Sam

On 18/09/2021, at 8:23 AM, Carsten Wickner @.***> wrote:

Hi Sam,

TL;DR; it sounds like you're describing what I explain under "Issue 2" below. I'm just listing the other items for completeness' sake.

It's true macOS dislikes anything that is not properly validated and downloaded through the App Store. That's why most things downloaded from the internet are deemed not trustworthy, including SciToS (since I'm unwilling to pay for the Apple Developer License one would need in order to be accepted into the App Store, let alone all the other hoops one would have to jump through. It's a free tool and it should stay that way, but I digress...).

Issue 1: “SciToS” is damaged and can’t be opened. You should move it to the Bin.

In some cases, macOS will show this rather misleading message, which is just a harsh way of letting you know, that the application was put into "quarantine". However, if you do trust the application you can lift that "quarantine" via the following steps:

Open a Terminal (or another console). By default, this may open in your user's home folder. Navigate to the directory where the unpacked SciToS.app is – via the cd command, e.g. cd Downloads/target if you simply unpacked it directly in your Downloads directory. Then lift the quarantine with the following command: sudo xattr -r -d com.apple.quarantine SciToS.app Enter your password to confirm the elevated access of the "super-user-do"/sudo command. Now you can start close the Terminal and start using the SciToS.app. Issue 2: the SciToS.app closes immediately after start (insufficient permissions)

There may be insufficient permissions for the application to access all its parts. Let's fix 'em then:

Open a Terminal Navigate to the directory where the unpacked SciToS.app is – via the cd command, e.g. cd Downloads/target if you simply unpacked it directly in your Downloads directory. Then (recursively) allow all parts in the app bundle (which is really just a special directory) to be executed: chmod -R +x SciToS.app If that still doesn't help:

Open a Terminal Navigate to the directory where the unpacked SciToS.app is – via the cd command. Then do what the double-click does: open SciToS.app Let me know what the output is after the application crash If you don't want to do the above or there is still no meaningful error output, you can give up the convenience of the special macOS .app and just use the portable Java application directly, by downloading the .zip file from the Releases https://github.com/scientific-tool-set/scitos/releases page and double-click the unpacked scitos.jar in the base folder. If you do that though, you may encounter the next challenge.

Issue 3: “scitos.jar” cannot be opened because it is from an unidentified developer.

Again, the downloaded file has been put into "quarantine", but the fix supposedly does not involve any Terminal commands:

Open your "System Preferences" Select "Security & Privacy" Go to the "General" tab At the bottom it should say: "scitos.jar" was blocked from use because it is not from an identified developer. Click on the "Open Anyway" button on the right, resulting in another warning being shown: macOS cannot verify the developer of "scitos.jar". Are you sure you want to open it? By opening this app, you will be overriding system security which can expose your computer and personal information to malware that may harm your Mac or compromise your privacy. If you still trust me, click "Open". 😉 Once that is done, you may still encounter the next challenge:

Issue 4: the scitos.jar closes immediately after double-clicking

I know, you've been here before, but we have one more way to get this running:

Open a Terminal Navigate to the directory where the unpacked scitor.jar is – via the cd command Start the Java application directly: java -jar scitos.jar If that is still not working, perhaps you have no suitable Java installation after all. Check for the currently installed version and let me know what it says: java --version Or go directly to https://adoptopenjdk.net/ https://adoptopenjdk.net/ and download the installer for JDK11 or newer.

I hope something of the above helped you. Looking forward to your feedback.

Cheers, Carsten

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/scientific-tool-set/scitos/issues/35#issuecomment-922060181, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVVNFYQEZA4HYEYTLERCWWLUCOPVHANCNFSM5EGFCVHA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.