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Installation error on Mac OS 12.6.3 with devtools #387

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afni-gangc opened this issue May 19, 2023 · 11 comments
Open

Installation error on Mac OS 12.6.3 with devtools #387

afni-gangc opened this issue May 19, 2023 · 11 comments
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@afni-gangc
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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:

  1. 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

@ntustison
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Can you try installing it in steps?

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

@afni-gangc
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afni-gangc commented May 19, 2023 via email

@ntustison
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Is it still the same error?

@afni-gangc
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afni-gangc commented May 19, 2023 via email

@cookpa cookpa added the bug label May 19, 2023
@cookpa
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cookpa commented May 19, 2023

Same issue as #377 (on Linux).

@ntustison
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Thanks @cookpa

@afni-gangc
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afni-gangc commented May 19, 2023 via email

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

@cookpa
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cookpa commented May 19, 2023

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/

@ntustison
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Thanks again @cookpa

@cookpa cookpa changed the title Installation error on Mac OS 12.6.3 Installation error on Mac OS 12.6.3 with devtools May 22, 2023
@muschellij2
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Confirming _composeDisplacementFields is an issue as well on MacOS on my end

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