Error

[ChetanGaonkar]

Autogenerated report:

{
  "name": "Error",
  "message": "Error trying to execute raxml binary '/tmp/.mount_raxmlGw2KeKS/resources/static/bin/raxml-ng': spawn /tmp/.mount_raxmlGw2KeKS/resources/static/bin/raxml-ng EACCES",
  "stack": "Error: Error trying to execute raxml binary '/tmp/.mount_raxmlGw2KeKS/resources/static/bin/raxml-ng': spawn /tmp/.mount_raxmlGw2KeKS/resources/static/bin/raxml-ng EACCES\n    at IpcMainImpl.<anonymous> (/tmp/.mount_raxmlGw2KeKS/resources/app.asar/build/electron.js:1:21843)"
}

Active state:

{
  "command": "raxml-ng --all --msa /home/campbelllab/synology/transcriptome_data/metabarcoding/HAB_paper/hab_v4_dec21.txt --model GTR+I --prefix /home/campbelllab/synology/transcriptome_data/metabarcoding/HAB_paper/hab_v4_dec21 --seed 128646 --bs-metric tbe --tree rand{10} --bs-trees 1000",
  "stdout": ""
}

---

Process: renderer raxmlGUI 2.0.6 Electron 13.5.1 linux 5.8.0-50-generic Locale: en-US

[danieledler]

Hi @ChetanGaonkar and thanks for reporting the issue.

The spawn /tmp/.mount_raxmlGw2KeKS/resources/static/bin/raxml-ng EACCES part means that raxmlGUI doesn't have access to the directory. From what I have found it seems to be a sandboxing issue with Debian:

AppImages based on Electron require the kernel to be configured in a certain way to allow for its sandboxing to work as intended (specifically, the kernel needs to be allowed to provide “unprivileged namespaces”). Many distributions come with this configured out of the box (like Ubuntu for instance), but some do not (for example Debian).

It also seems that this was solved in later versions:

If you run the Debian 10 (Buster) stable kernel 4.19 you will still be affected by this issue. If you upgrade to Bullseye (which will become the new stable release in a few months) you will not be affected. If you install the 5.10 kernel from Buster-backports you will not be affected.

As you have kernel 5.8, this seems to be a likely cause of the problem. Are you able to upgrade the kernel or Debian?

[ChetanGaonkar]

Dear Daniel,

I got a popup saying new version is available so I upgraded. The older version dont have any issue as I have two PC one with older and other with upgraded version. I ran the phylogenies on the older one and they work well. Thank you, Chetan

On Wed, Dec 8, 2021 at 1:41 AM Daniel Edler @.***> wrote:

Hi @ChetanGaonkar https://github.com/ChetanGaonkar and thanks for reporting the issue.

The spawn /tmp/.mount_raxmlGw2KeKS/resources/static/bin/raxml-ng EACCES part means that raxmlGUI doesn't have access to the directory. From what I have found it seems to be a sandboxing issue https://docs.appimage.org/user-guide/troubleshooting/electron-sandboxing.html with Debian:

AppImages based on Electron require the kernel to be configured in a certain way to allow for its sandboxing to work as intended (specifically, the kernel needs to be allowed to provide “unprivileged namespaces”). Many distributions come with this configured out of the box (like Ubuntu for instance), but some do not (for example Debian).

It also seems that this was solved in later versions https://github.com/laurent22/joplin/issues/2246#issuecomment-808570233:

If you run the Debian 10 (Buster) stable kernel 4.19 you will still be affected by this issue. If you upgrade to Bullseye (which will become the new stable release in a few months) you will not be affected. If you install the 5.10 kernel from Buster-backports you will not be affected.

As you have kernel 5.8, this seems to be a likely cause of the problem. Are you able to upgrade the kernel or Debian?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/AntonelliLab/raxmlGUI/issues/226#issuecomment-988572235, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJT3FMJNNC5W5UEGJHIY5NTUP4D35ANCNFSM5JSHUZ3Q . 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.

[danieledler]

Ok, in raxmlGUI 2.0.6 there was a new version of raxml-ng added, maybe @jtklein knows something about this?

[danieledler]

In the meantime @ChetanGaonkar, if you can upgrade the kernel pleasy try that. That will help us if more get the same problem.

[ChetanGaonkar]

I am not 100% sure how to upgrade the kernel. Will look into it and try again Chetan

On Wed, Dec 8, 2021 at 11:43 AM Daniel Edler @.***> wrote:

In the meantime @ChetanGaonkar https://github.com/ChetanGaonkar, if you can upgrade the kernel pleasy try that. That will help us if more get the same problem.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/AntonelliLab/raxmlGUI/issues/226#issuecomment-989031571, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJT3FMMNIA3KLQ3ILZEHKFDUP6KKRANCNFSM5JSHUZ3Q . 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.

[thauffe]

I'm having the same issue. My kernel version is 5.10-98. I checked that unprivileged namespaces are enabled by my distribution and they are.

Keep up the good work! Torsten

[danieledler]

Hi @thauffe, thanks for your information!

To help us check if the problem is the new raxml-ng binary since 2.0.6, can you or @ChetanGaonkar try running the 2.0.5 version and tell us how it goes?

[thauffe]

Hi, Version 2.0.5 works.

I run a sudo ./raxmlGUI-2.0.5.AppImage --no-sandbox with version 2.0.5 and 2.0.6 and attach the output as text file. There are some more detailed messages than in the standard error report.

Beginning in line 85 of v205.txt:

ALIGNMENT_SELECTED {
  canceled: false,
  filePaths: [ '/home/.../Pota_cytb.fas' ]
}
Parse alignment /home/.../Pota_cytb.fas
error Error: Command failed: /tmp/.mount_raxmlGTZ1NCf/resources/static/bin/readal -in /home/.../Pota_cytb.fas -type -format
/bin/sh: line 1: /tmp/.mount_raxmlGTZ1NCf/resources/static/bin/readal: Permission denied

    at ChildProcess.exithandler (child_process.js:317:12)
    at ChildProcess.emit (events.js:315:20)
    at maybeClose (internal/child_process.js:1048:16)
    at Socket.<anonymous> (internal/child_process.js:439:11)
    at Socket.emit (events.js:315:20)
    at Pipe.<anonymous> (net.js:673:12) {
  killed: false,
  code: 126,
  signal: null,
  cmd: '/tmp/.mount_raxmlGTZ1NCf/resources/static/bin/readal -in /home/.../Pota_cytb.fas -type -format',
  stdout: '',
  stderr: '/bin/sh: line 1: /tmp/.mount_raxmlGTZ1NCf/resources/static/bin/readal: Permission denied\n'
}

v205.txt v206.txt

.

[danieledler]

Thanks @thauffe, that is very helpful!

From this we should investigate the readal binary too.

@jtklein, do you know if the raxml-ng in 2.0.6 was compiled or signed in another way than the version in 2.0.5? Are you able to test the latest in a linux environment? We can take the opportunity to replace raxml-ng 1.0.3 with the latest 1.1.0 also.

[ChetanGaonkar]

Hi I had to go back to the older version and ran my phylogenies. I can send you the version and the log tomorrow if that is ok? Regards Chetan

Sent from my iPhone

On Feb 18, 2022, at 5:55 AM, Daniel Edler @.***> wrote:

 Hi @thauffe, thanks for your information!

To help us check if the problem is the new raxml-ng binary since 2.0.6, can you or @ChetanGaonkar try running the 2.0.5 version and tell us how it goes?

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you were mentioned.

[danieledler]

@ChetanGaonkar, we are testing a new version today, hopefully that will solve the issue. Will let you know.

[danieledler]

Hi all, we just released v2.0.7 that should fix this Linux issue. You should get it on the automatic update check when raxmlGUI starts. Please try and write if it solves the issue for you!

[thauffe]

Great, works in my case. Thank you!

[ChetanGaonkar]

Great thanks. Will check it out too in next few days and keep you updated. Chetan

On Tue, Feb 22, 2022 at 1:01 PM Torsten Hauffe @.***> wrote:

Great, works in my case. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/AntonelliLab/raxmlGUI/issues/226#issuecomment-1048116155, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJT3FMPJRSPWNFNB4XLK6TTU4PMQZANCNFSM5JSHUZ3Q . 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.

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