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EddyRivasLab / easel

Sequence analysis library used by Eddy/Rivas lab code
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HMMER-make check fail #72

Closed VimaxXAAS closed 10 months ago

VimaxXAAS commented 11 months ago

Running Easel test suite...

make[2]: ./../devkit/sqc: No such file or directory make[2]: [Makefile:34: check] Error 127 make[1]: [Makefile:537: check] Error 2 make: *** [Makefile:116: check] Error 2

HP@DESKTOP-T2RTKVR /home/user/hmmer-3.3.2

How to solve this error

cryptogenomicon commented 11 months ago

Do you have perl, in /usr/bin/perl?

VimaxXAAS commented 11 months ago

No.

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From: Sean Eddy @.> Sent: Wednesday, August 23, 2023 7:44:47 PM To: EddyRivasLab/easel @.> Cc: VimaxXAAS @.>; Author @.> Subject: Re: [EddyRivasLab/easel] HMMER-make check fail (Issue #72)

Do you have perl, in /usr/bin/perl?

— Reply to this email directly, view it on GitHubhttps://github.com/EddyRivasLab/easel/issues/72#issuecomment-1689813357, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7ZKA6SSHIICQI4VA2GXEGLXWXUK7ANCNFSM6AAAAAA33KWKPM. You are receiving this because you authored the thread.Message ID: @.***>

cryptogenomicon commented 11 months ago

The test suite scripts require perl (and python3), but HMMER itself does not. You can safely skip the make check.

VimaxXAAS commented 11 months ago

Problem is "hmmbuild" command not found error

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From: Sean Eddy @.> Sent: Wednesday, August 23, 2023 7:46:58 PM To: EddyRivasLab/easel @.> Cc: VimaxXAAS @.>; Author @.> Subject: Re: [EddyRivasLab/easel] HMMER-make check fail (Issue #72)

The test suite scripts require perl. You can safely skip the make check.

— Reply to this email directly, view it on GitHubhttps://github.com/EddyRivasLab/easel/issues/72#issuecomment-1689816490, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7ZKA6RSCKKXRY6KODZUTRLXWXUTFANCNFSM6AAAAAA33KWKPM. You are receiving this because you authored the thread.Message ID: @.***>

cryptogenomicon commented 11 months ago

I'll need more information. What exactly did you type as your commands, and what exactly was the output, and on what kind of platform/operating system?

VimaxXAAS commented 11 months ago

[cid:66dbe196-9e5e-4dda-b2eb-e43d07340299]

From: Sean Eddy @.> Sent: 23 August 2023 19:52 To: EddyRivasLab/easel @.> Cc: VimaxXAAS @.>; Author @.> Subject: Re: [EddyRivasLab/easel] HMMER-make check fail (Issue #72)

I'll need more information. What exactly did you type as your commands, and what exactly was the output, and on what kind of platform/operating system?

— Reply to this email directly, view it on GitHubhttps://github.com/EddyRivasLab/easel/issues/72#issuecomment-1689823340, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7ZKA6VKITQBHQVARXPBLALXWXVG7ANCNFSM6AAAAAA33KWKPM. You are receiving this because you authored the thread.Message ID: @.***>

VimaxXAAS commented 11 months ago

[cid:f33f2ce7-1c9e-4e09-a85c-800b59b49b3c]

From: Sean Eddy @.> Sent: 23 August 2023 19:52 To: EddyRivasLab/easel @.> Cc: VimaxXAAS @.>; Author @.> Subject: Re: [EddyRivasLab/easel] HMMER-make check fail (Issue #72)

I'll need more information. What exactly did you type as your commands, and what exactly was the output, and on what kind of platform/operating system?

— Reply to this email directly, view it on GitHubhttps://github.com/EddyRivasLab/easel/issues/72#issuecomment-1689823340, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7ZKA6VKITQBHQVARXPBLALXWXVG7ANCNFSM6AAAAAA33KWKPM. You are receiving this because you authored the thread.Message ID: @.***>

cryptogenomicon commented 11 months ago

You seem to be trying to send some sort of link(s), which don't work. I need to see text for your commands, your output, and your platform/OS.

VimaxXAAS commented 11 months ago

I am using a window 11 pro. I am trying to use Hmmer search to screen some genes. I am facing this error. I used Cygwin64 for Hmmer-3.4

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From: Sean Eddy @.> Sent: Wednesday, August 23, 2023 8:00:21 PM To: EddyRivasLab/easel @.> Cc: VimaxXAAS @.>; Author @.> Subject: Re: [EddyRivasLab/easel] HMMER-make check fail (Issue #72)

You seem to be trying to send some sort of link(s), which don't work. I need to see text for your commands, your output, and your platform/OS.

— Reply to this email directly, view it on GitHubhttps://github.com/EddyRivasLab/easel/issues/72#issuecomment-1689833904, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7ZKA6TP4VNHKO7TI6YHFK3XWXWFLANCNFSM6AAAAAA33KWKPM. You are receiving this because you authored the thread.Message ID: @.***>

cryptogenomicon commented 11 months ago

Sorry, you still haven't given me the information I need to understand the error you're seeing. What did you type, and what output did you get? You initially said that make check failed, and you said you don't have perl, so make check is going to fail - and you don't need it, and can skip it. Now you say that you get an hmmbuild not found error, and I'm asking what you did before you got that error, and exactly what it output.

It may be as simple as just understanding how to install and run programs in Windows 11; I can't help you with that, but that'll be something general that you can figure out elsewhere. In Linux and OS/X, if you install a program in a directory (say, hmmbuild in /usr/local/bin) then you either need to have /usr/local/bin in your ${PATH} so you can run it by typing hmmbuild, or you need to specify the path yourself, typing /usr/local/bin/hmmbuild.

VimaxXAAS commented 11 months ago

[cid:f5a6f2de-7e08-4aa9-a25c-d65e4f6ced38] this is more detailed. i am using window 11. can you help me to install "pearl"

From: Sean Eddy @.> Sent: 23 August 2023 20:09 To: EddyRivasLab/easel @.> Cc: VimaxXAAS @.>; Author @.> Subject: Re: [EddyRivasLab/easel] HMMER-make check fail (Issue #72)

Sorry, you still haven't given me the information I need to understand the error you're seeing. What did you type, and what output did you get? You initially said that make check failed, and you said you don't have perl, so make check is going to fail - and you don't need it, and can skip it. Now you say that you get an hmmbuild not found error, and I'm asking what you did before you got that error, and exactly what it output.

It may be as simple as just understanding how to install and run programs in Windows 11; I can't help you with that, but that'll be something general that you can figure out elsewhere. In Linux and OS/X, if you install a program in a directory (say, hmmbuild in /usr/local/bin) then you either need to have /usr/local/bin in your ${PATH} so you can run it by typing hmmbuild, or you need to specify the path yourself, typing /usr/local/bin/hmmbuild.

— Reply to this email directly, view it on GitHubhttps://github.com/EddyRivasLab/easel/issues/72#issuecomment-1689846681, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7ZKA6QSKD6DOICKXWILQADXWXXG5ANCNFSM6AAAAAA33KWKPM. You are receiving this because you authored the thread.Message ID: @.***>