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FastPG Installation Error #1

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georgersmith99 opened this issue Mar 26, 2024 · 16 comments
Closed

FastPG Installation Error #1

georgersmith99 opened this issue Mar 26, 2024 · 16 comments

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@georgersmith99
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Hey there!

I am attempting installation of the PICAflow software and am getting a recurring error despite performing the troubleshooting/manual installation in your website.

The error occurs at the end of the installation and is:
`In file included from buildNextPhase.cpp:42:
./defs.h:52:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
make: *** [buildNextPhase.o] Error 1
ERROR: compilation failed for package ‘FastPG’

That ultimately leads to error:

`ERROR: dependency ‘FastPG’ is not available for package ‘PICAFlow’

  • removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/PICAFlow’
    Warning messages:
    1: In i.p(...) :
    installation of package ‘/var/folders/b1/pcvwjjh51f3gv8pp4jf8ktqh0000gn/T//RtmpCIdgQS/file86ef5954f840/FastPG_0.0.8.tar.gz’ had non-zero exit status
    2: In i.p(...) :
    installation of package ‘/var/folders/b1/pcvwjjh51f3gv8pp4jf8ktqh0000gn/T//RtmpCIdgQS/file86ef67dd0c74/PICAFlow_1.0.tar.gz’ had non-zero exit status`

Any help would be greatly appreciated!
Cheers,
George
@PaulRegnier
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Hello @georgersmith99,

I am sorry that you are facing installation issues.

Indeed the error is related to the failing installation of the FastPG package.

Here are some potential ways to resolve this:

  1. Did you already have the FastPG package installed before PICAFlow installation? If yes, locate where the FastPG package is installed on your computer and manually delete it from your library then proceed to the step 2.

  2. I realized that the command provided in the troubleshooting section of the tutorial was not exactly the right one, as it tried to install FastPG from the Bioconductor repository, whereas PICAFlow actually prefers the GitHub version for installation. Thus, please try the following command to install FastPG: devtools::install_github("sararselitsky/FastPG", force = TRUE)

  3. What version of R do you use? I tried a fresh install right before writing this message and it worked like a charm (I am using the very last version of R, version 4.3.3 on Windows 11 OS)

  4. What version of the Bioconductor package/repository do you use? I recently had several problems with the latest version (3.18), because a lot of packages needed to be updated. So try to update the Bioconductor package, as well as all of your R packages (after checking the step 3).

If you do not manage to make it work after all this, feel free to write another message and we will see what we can do to solve it.

Thank you for your interest in PICAFlow :)

Have a nice day!

@georgersmith99
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Thank you very much for your reply!

Unfortunately I still get the same error after going through these troubleshooting methods. I am using MacOS however, so maybe it is different for that. I updated both RStudio and bioconductor and ran again but got the same result..

I appreciate all your help!
Cheers
George

@PaulRegnier
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Alright George, we will try to resolve this then.

Does the following command return an error? devtools::install_github("sararselitsky/FastPG", force = TRUE)

@georgersmith99
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georgersmith99 commented Mar 26, 2024 via email

@PaulRegnier
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I just found that the FastPG GitHub page has a special installation procedure for MacOS:

If you are on Mac OS X, you will need the x-code command line tools and probably need to install the OpenMP library, which Apple no longer distributes as part of x-code. One way to do that is to install the data.table package as described here: https://firas.io/post/data.table_openmp/. Afterwards, FastPG and any other programs that use OpenMP should work.

@PaulRegnier
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In your error log, the line ./defs.h:52:10: fatal error: 'omp.h' file not found directly refers to the OpenMP API, which seems not to be installed on your computer. Try to follow the procedure from FastPG GitHub page and let me know if it works.

@georgersmith99
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georgersmith99 commented Mar 26, 2024 via email

@PaulRegnier
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From what I found on Internet, people nowadays follow the procedure here to install OpenMP on recent Mac computers : https://stackoverflow.com/questions/76374014/use-openmp-on-m2-mac-with-r-and-data-table.

Maybe you can take a look and see if it works for you? I am not very familiar with MacOS system but I will try my best to help you.

@georgersmith99
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georgersmith99 commented Mar 26, 2024 via email

@PaulRegnier
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Can you tell me which version of MacOS you are using, and if your Mac has a M1/M2 processor?

@georgersmith99
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georgersmith99 commented Mar 26, 2024 via email

@PaulRegnier
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Thanks a lot.

Apparently the Stack Overflow user TheSkyeLord managed to install OpenMP on a M1 Mac: https://stackoverflow.com/questions/71061894/how-to-install-openmp-on-mac-m1, and another user confirmed that it also worked on a M2 Mac.

Apparently this problem is something recurrent on Macs because Apple uses a compiler (Xcode) which does not come anymore with OpenMP... https://discussions.apple.com/thread/254465066?sortBy=best

But the installation of another compiler (such as gcc) allows to correctly install OpenMP according to this Apple website page.

@PaulRegnier
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To allow you to install the package, I decided to move the FastPG dependency from Imports to Suggests in the DESCRIPTION file of PICAFlow. You should now be able to correctly install it as FastPG is now facultative. But if you don't install it, please note that you won't be able to perform the FastPG clustering method during the cell clustering step. Let me know if this resolved the problem on your side!

@georgersmith99
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georgersmith99 commented Mar 27, 2024 via email

@PaulRegnier
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I'm glad it works now :) May I close this issue as fixed?

@georgersmith99
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georgersmith99 commented Mar 27, 2024 via email

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@PaulRegnier @georgersmith99