Installation error on Mac OS 12.6.3 with devtools

Describe the bug

Tried to install ANTsR with the command in R (version is 4.3.0) on MacBook Air (OS 12.6.3):

devtools::install_github('ANTsX/ANTsR')

It failed after two hours of compiling with the following error at the end:

Error: package or namespace load failed for ‘ANTsR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-ANTsR/00new/ANTsR/libs/ANTsR.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-ANTsR/00new/ANTsR/libs/ANTsR.so, 0x0006): symbol not found in flat namespace (_composeDisplacementFields)
Error: loading failed

To Reproduce
Steps to reproduce the behavior:

devtools::install_github('ANTsX/ANTsR')

Desktop (please complete the following information):

OS: iOS 12.6.3
R Version: 4.3.0

Additional context
See attached text for the full installation log.
ANTsR.install.error.txt

Can you try installing it in steps?

> devtools::install_github('stnava/ITKR')
> devtools::install_github('ANTsX/ANTsRCore')
> devtools::install_github('ANTsX/ANTsR')

Thanks! After another two hours of installation, the first two commands worked, but the third one devtools::install_github('ANTsX/ANTsR') still failed. Still upload the log? From: Nick Tustison ***@***.***> Date: Friday, May 19, 2023 at 9:26 AM To: ANTsX/ANTsR ***@***.***> Cc: Chen, Gang (NIH/NIMH) [E] ***@***.***>, Author ***@***.***> Subject: [EXTERNAL] Re: [ANTsX/ANTsR] Installation error on Mac OS 12.6.3 (Issue #387) Can you try installing it in steps?

devtools::install_github('stnava/ITKR') devtools::install_github('ANTsX/ANTsRCore') devtools::install_github('ANTsX/ANTsR')

— Reply to this email directly, view it on GitHub<#387 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACPFE6MGLTJ5JMKPXLWS63TXG5YHHANCNFSM6AAAAAAYHGGTPU>. You are receiving this because you authored the thread.Message ID: ***@***.***> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Is it still the same error?

Looks like the same error: ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘ANTsR’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-ANTsR/00new/ANTsR/libs/ANTsR.so': dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-ANTsR/00new/ANTsR/libs/ANTsR.so, 0x0006): symbol not found in flat namespace (_composeDisplacementFields) Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/ANTsR’ Warning message: In i.p(...) : installation of package ‘/var/folders/0z/m_31mkc564bbkx8hh2_wvrfc0000gx/T//RtmpTbtUP6/filefe6c43a65c9e/ANTsR_0.5.7.5.tar.gz’ had non-zero exit status From: Nick Tustison ***@***.***> Date: Friday, May 19, 2023 at 11:37 AM To: ANTsX/ANTsR ***@***.***> Cc: Chen, Gang (NIH/NIMH) [E] ***@***.***>, Author ***@***.***> Subject: [EXTERNAL] Re: [ANTsX/ANTsR] Installation error on Mac OS 12.6.3 (Issue #387) Is it still the same error? — Reply to this email directly, view it on GitHub<#387 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACPFE6JNZS533SATJUCZA3LXG6HTXANCNFSM6AAAAAAYHGGTPU>. You are receiving this because you authored the thread.Message ID: ***@***.***> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Same issue as #377 (on Linux).

@cookpa

Thanks @cookpa

Thanks for the pointer! Method 2 worked. However, when I tried to test the installation per the site https://gist.github.com/ntustison/12a656a5fc2f6f9c4494c88dc09c5621#brain-extraction, the following command t1 <- antsImageRead( getANTsXNetData( 'mprage_hippmapp3r' ) ) led to error: t1 <- antsImageRead( getANTsXNetData( 'mprage_hippmapp3r' ) ) Downloading data from https://ndownloader.figshare.com/files/24984689 Error in py_call_impl(callable, call_args$unnamed, call_args$named) : Exception: URL fetch failure on https://ndownloader.figshare.com/files/24984689: None -- [SSL: UNSAFE_LEGACY_RENEGOTIATION_DISABLED] unsafe legacy renegotiation disabled (_ssl.c:1129) Run `reticulate::py_last_error()` for details. From: Nick Tustison ***@***.***> Date: Friday, May 19, 2023 at 1:53 PM To: ANTsX/ANTsR ***@***.***> Cc: Chen, Gang (NIH/NIMH) [E] ***@***.***>, Author ***@***.***> Subject: [EXTERNAL] Re: [ANTsX/ANTsR] Installation error on Mac OS 12.6.3 (Issue #387) Thanks @cookpa<https://github.com/cookpa> — Reply to this email directly, view it on GitHub<#387 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACPFE6KRPYWQRBC3URDVQ5TXG6XQ3ANCNFSM6AAAAAAYHGGTPU>. You are receiving this because you authored the thread.Message ID: ***@***.***> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Maybe a local access issue. Try directly copying and pasting the url in your browser. Should download a nifti image.

I believe the "UNSAFE_LEGACY_RENEGOTIATION_DISABLED" is a Python issue that will be fixed in a later version of Python (python/cpython#93927).

Most users will probably just want to download manually, but other workarounds have been suggested online, including downgrading Python < 3.11. Reticulate can be made to use a specified conda environment if needed https://rstudio.github.io/reticulate/

@cookpa

Thanks again @cookpa

Confirming _composeDisplacementFields is an issue as well on MacOS on my end

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Installation error on Mac OS 12.6.3 with devtools #387

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Installation error on Mac OS 12.6.3 with devtools #387

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ntustison commented on May 19, 2023

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cookpa commented on May 19, 2023

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