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sararselitsky / FastPG_accuracy_performance_scripts

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Installation error #1

Open georgersmith99 opened 6 months ago

georgersmith99 commented 6 months ago

Hi there!

I am trying to use PICAflow which required FastPG and upon installation with: BiocManager::install("sararselitsky/FastPG") get a recurring error:

`In file included from buildNextPhase.cpp:42: ./defs.h:52:10: fatal error: 'omp.h' file not found

include 

     ^~~~~~~

1 error generated. make: *** [buildNextPhase.o] Error 1 ERROR: compilation failed for package ‘FastPG’

Would love some help!

All the best, George

georgersmith99 commented 6 months ago

I have attempted installing libomp and have specificed the path in R in multiple different ways but still get the same error

sararselitsky commented 6 months ago

Does it work if you install using this command?

On Tue, Mar 26, 2024 at 7:23 AM georgersmith99 @.***> wrote:

I have attempted installing libomp and have specificed the path in R in multiple different ways but still get the same error

— Reply to this email directly, view it on GitHub https://github.com/sararselitsky/FastPG_accuracy_performance_scripts/issues/1#issuecomment-2020165047, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQD6T37GD2HQ225PCPURWTY2FEANAVCNFSM6AAAAABFIUXNQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRQGE3DKMBUG4 . You are receiving this because you are subscribed to this thread.Message ID: <sararselitsky/FastPG_accuracy_performance_scripts/issues/1/2020165047 @github.com>

sararselitsky commented 6 months ago

Sorry, didn't mean to send the above email as is.

Does it work if you install using this command? @.***")

+Stuart Jefferys @.***>, have you seen that error before? Thanks!

On Tue, Mar 26, 2024 at 8:09 AM Sara Selitsky @.***> wrote:

Does it work if you install using this command?

On Tue, Mar 26, 2024 at 7:23 AM georgersmith99 @.***> wrote:

I have attempted installing libomp and have specificed the path in R in multiple different ways but still get the same error

— Reply to this email directly, view it on GitHub https://github.com/sararselitsky/FastPG_accuracy_performance_scripts/issues/1#issuecomment-2020165047, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQD6T37GD2HQ225PCPURWTY2FEANAVCNFSM6AAAAABFIUXNQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRQGE3DKMBUG4 . You are receiving this because you are subscribed to this thread.Message ID: <sararselitsky/FastPG_accuracy_performance_scripts/issues/1/2020165047@ github.com>

georgersmith99 commented 6 months ago

@sararselitsky sorry, im not too sure what this

"Does it work if you install using this command? @.***") " means.

Sorry for being a pain! George

sararselitsky commented 6 months ago

No worries, I'd like to help. Did it not copy over correctly? I've had success when installing from the dev https://github.com/sararselitsky/FastPG/tree/dev branch. Does that work for you?

On Tue, Mar 26, 2024 at 8:13 AM georgersmith99 @.***> wrote:

@sararselitsky https://github.com/sararselitsky sorry, im not too sure what this

"Does it work if you install using this command? @.***") " means.

Sorry for being a pain! George

— Reply to this email directly, view it on GitHub https://github.com/sararselitsky/FastPG_accuracy_performance_scripts/issues/1#issuecomment-2020267253, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQD6T2P2ZX4ENCWYYETGSDY2FJ5BAVCNFSM6AAAAABFIUXNQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRQGI3DOMRVGM . You are receiving this because you were mentioned.Message ID: <sararselitsky/FastPG_accuracy_performance_scripts/issues/1/2020267253@ github.com>

georgersmith99 commented 6 months ago

Sara,

Thank you very much for your reply!

Unfortunately it does not I get the same error about not being able to access omp.h…

George

From: Sara Selitsky @.> Date: Tuesday, 26 March 2024 at 12:25 To: sararselitsky/FastPG_accuracy_performance_scripts @.> Cc: georgersmith99 @.>, State change @.> Subject: Re: [sararselitsky/FastPG_accuracy_performance_scripts] Installation error (Issue #1) No worries, I'd like to help. Did it not copy over correctly? I've had success when installing from the dev https://github.com/sararselitsky/FastPG/tree/dev branch. Does that work for you?

On Tue, Mar 26, 2024 at 8:13 AM georgersmith99 @.***> wrote:

@sararselitsky https://github.com/sararselitsky sorry, im not too sure what this

"Does it work if you install using this command? @.***") " means.

Sorry for being a pain! George

— Reply to this email directly, view it on GitHub https://github.com/sararselitsky/FastPG_accuracy_performance_scripts/issues/1#issuecomment-2020267253, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQD6T2P2ZX4ENCWYYETGSDY2FJ5BAVCNFSM6AAAAABFIUXNQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRQGI3DOMRVGM . You are receiving this because you were mentioned.Message ID: <sararselitsky/FastPG_accuracy_performance_scripts/issues/1/2020267253@ github.com>

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sararselitsky commented 6 months ago

I'm pretty sure that's a C compiler issue. Is that right, Mahantesh?

On Tue, Mar 26, 2024 at 9:24 AM georgersmith99 @.***> wrote:

Sara,

Thank you very much for your reply!

Unfortunately it does not I get the same error about not being able to access omp.h…

George

From: Sara Selitsky @.> Date: Tuesday, 26 March 2024 at 12:25 To: sararselitsky/FastPG_accuracy_performance_scripts @.> Cc: georgersmith99 @.>, State change @.> Subject: Re: [sararselitsky/FastPG_accuracy_performance_scripts] Installation error (Issue #1) No worries, I'd like to help. Did it not copy over correctly? I've had success when installing from the dev https://github.com/sararselitsky/FastPG/tree/dev branch. Does that work for you?

On Tue, Mar 26, 2024 at 8:13 AM georgersmith99 @.***> wrote:

@sararselitsky https://github.com/sararselitsky sorry, im not too sure what this

"Does it work if you install using this command? @.***") " means.

Sorry for being a pain! George

— Reply to this email directly, view it on GitHub < https://github.com/sararselitsky/FastPG_accuracy_performance_scripts/issues/1#issuecomment-2020267253>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ACQD6T2P2ZX4ENCWYYETGSDY2FJ5BAVCNFSM6AAAAABFIUXNQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRQGI3DOMRVGM>

. You are receiving this because you were mentioned.Message ID: <sararselitsky/FastPG_accuracy_performance_scripts/issues/1/2020267253@ github.com>

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sararselitsky commented 6 months ago

“omp.h” is OpenMP header file needed for parallel computing.

GCC on Mac: http://www.mathcancer.org/blog/setting-up-gcc-openmp-on-osx-homebrew-edition/ GCC on Windows/Linux: https://www.geeksforgeeks.org/openmp-introduction-with-installation-guide/

Regards, Mahantesh (he/him)

From: Sara Selitsky @.> Date: Tuesday, 26 March 2024 at 6:40 AM To: sararselitsky/FastPG_accuracy_performance_scripts @.> Cc: sararselitsky/FastPG_accuracy_performance_scripts @.>, Mention @.>, Halappanavar, Mahantesh M @.***> Subject: Re: [sararselitsky/FastPG_accuracy_performance_scripts] Installation error (Issue #1) Check twice before you click! This email originated from outside PNNL.

I'm pretty sure that's a C compiler issue. Is that right, Mahantesh?

On Tue, Mar 26, 2024 at 9:24 AM georgersmith99 @.**@.>> wrote: Sara,

Thank you very much for your reply!

Unfortunately it does not I get the same error about not being able to access omp.h…

George

From: Sara Selitsky @.> Date: Tuesday, 26 March 2024 at 12:25 To: sararselitsky/FastPG_accuracy_performance_scripts @.> Cc: georgersmith99 @.>, State change @.> Subject: Re: [sararselitsky/FastPG_accuracy_performance_scripts] Installation error (Issue #1) No worries, I'd like to help. Did it not copy over correctly? I've had success when installing from the dev https://github.com/sararselitsky/FastPG/tree/dev branch. Does that work for you?

On Tue, Mar 26, 2024 at 8:13 AM georgersmith99 @.***> wrote:

@sararselitsky https://github.com/sararselitsky sorry, im not too sure what this

"Does it work if you install using this command? @.***") " means.

Sorry for being a pain! George

— Reply to this email directly, view it on GitHub https://github.com/sararselitsky/FastPG_accuracy_performance_scripts/issues/1#issuecomment-2020267253, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQD6T2P2ZX4ENCWYYETGSDY2FJ5BAVCNFSM6AAAAABFIUXNQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRQGI3DOMRVGM . You are receiving this because you were mentioned.Message ID: <sararselitsky/FastPG_accuracy_performance_scripts/issues/1/2020267253@ github.comhttp://github.com/>

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