Open afni-gangc opened 1 year ago
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 GitHubhttps://github.com/ANTsX/ANTsR/issues/387#issuecomment-1554575761, or unsubscribehttps://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
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 GitHubhttps://github.com/ANTsX/ANTsR/issues/387#issuecomment-1554765686, or unsubscribehttps://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).
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 @cookpahttps://github.com/cookpa
— Reply to this email directly, view it on GitHubhttps://github.com/ANTsX/ANTsR/issues/387#issuecomment-1555031078, or unsubscribehttps://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 (https://github.com/python/cpython/pull/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/
Thanks again @cookpa
Confirming _composeDisplacementFields
is an issue as well on MacOS on my end
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):
Additional context See attached text for the full installation log. ANTsR.install.error.txt