Installation of SCT v6.2 failed

eva · April 21, 2024, 10:07pm

I downloaded install_sct-6.2_macos.sh and ran bash install_sct-6.2_macos.sh which failed with the errors shown in the screenshot. The error states that I should post the contents of a file named “install_sct_log.txt”, however this file does not appear on my system.

Output of sct_check_dependencies:

SCT info:

version: 5.3.0
path: /Users/evaalonsoortiz/sct_5.3.0
OS: osx (Darwin-23.0.0-x86_64-i386-64bit)
CPU cores: Available: 8, Used by ITK functions: 8
RAM: Total: 16384MB, Used: 1536MB, Available: 984MB
Check Python executable…[OK]
Using bundled python 3.6.10 |Anaconda, Inc.| (default, Mar 25 2020, 18:53:43)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] at /Users/evaalonsoortiz/sct_5.3.0/python/envs/venv_sct/bin/python
Check if data are installed…[OK]
Check if colored is installed…[OK] (1.4.2)
Check if dipy is installed…[OK] (1.4.0)
Check if futures is installed…[OK]
Check if h5py is installed…[OK] (2.10.0)
Check if Keras (2.1.5) is installed…[OK] (2.1.5)
Check if ivadomed is installed…[OK] (2.7.4)
Check if matplotlib is installed…[OK] (3.3.4)
Check if nibabel is installed…[OK] (3.2.1)
Check if numpy is installed…[OK] (1.19.5)
Check if onnxruntime (1.4.0) is installed…[OK] (1.4.0)
Check if pandas is installed…[OK] (1.1.5)
Check if psutil is installed…[OK] (5.8.0)
Check if pyqt5 (5.11.3) is installed…[OK] (5.11.3)
Check if pytest is installed…[OK] (6.2.3)
Check if pytest-cov is installed…[OK] (version = ‘2.11.1’)
Check if raven is installed…[OK]
Check if requests is installed…[OK] (2.25.1)
Check if requirements-parser is installed…[OK] (0.2.0)
Check if scipy is installed…[OK] (1.5.4)
Check if scikit-image is installed…[OK] (0.17.2)
Check if scikit-learn is installed…[OK] (0.24.1)
Check if tensorflow (1.5.0) is installed…[OK] (1.5.0)
Check if torch (1.5.0) is installed…[OK] (1.5.0)
Check if torchvision (0.6.0) is installed…[OK] (0.6.0)
Check if xlwt is installed…[OK] (1.3.0)
Check if tqdm is installed…[OK] (4.60.0)
Check if transforms3d is installed…[OK] (0.3.1)
Check if urllib3 is installed…[OK] (1.26.4)
Check if pytest_console_scripts is installed…[OK]
Check if wquantiles is installed…[OK] (0.4)
Check if spinalcordtoolbox is installed…[OK]
Check ANTs compatibility with OS …[OK]
Check PropSeg compatibility with OS …[OK]
Check if DISPLAY variable is set…[OK]
Check if figure can be opened with PyQt…[OK]

joshuacwnewton · April 22, 2024, 2:20pm

Hi @eva,

Thank you for reporting this!

Unfortunately, without the full context, it is trickier to diagnose the issue. If possible, could you re-run the installer, then copy and paste the full output (rather than taking a screenshot)?

Kind regards,
Joshua

eva · April 23, 2024, 5:59pm

Here you go:

*******************************
* Welcome to SCT installation *
*******************************



Checking OS type and version...

Darwin iMac.local 23.0.0 Darwin Kernel Version 23.0.0: Fri Sep 15 14:41:34 PDT 2023; root:xnu-10002.1.13~1/RELEASE_ARM64_T8103 x86_64
ProductVersion:		14.0

Checking requirements...


OK!

Source files not present. Downloading source files (@ 6.2) to /var/folders/xf/n1v2pg_j2ysf0rj39ysrcm9r0000gn/T/tmp.M0ixZmiNnj/spinalcordtoolbox.
Cloning into '/var/folders/xf/n1v2pg_j2ysf0rj39ysrcm9r0000gn/T/tmp.M0ixZmiNnj/spinalcordtoolbox'...
Note: switching to '9ee15da2735ae91d7d57664e2f9cbf1232a322ae'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false


SCT version ......... 6.2
Installation type ... package
Operating system .... osx (	14.0)
Shell config ........ /Users/evaalonsoortiz/.zshrc

SCT will be installed here: [/Users/evaalonsoortiz/sct_6.2]



Do you agree? [y]es/[n]o: y

Copying source files from /var/folders/xf/n1v2pg_j2ysf0rj39ysrcm9r0000gn/T/tmp.M0ixZmiNnj/spinalcordtoolbox to /Users/evaalonsoortiz/sct_6.2

................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y

Downloading Miniconda...


wget -nv -O /var/folders/xf/n1v2pg_j2ysf0rj39ysrcm9r0000gn/T/tmp.M0ixZmiNnj/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

2024-04-23 13:56:54 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh [107987235/107987235] -> "/var/folders/xf/n1v2pg_j2ysf0rj39ysrcm9r0000gn/T/tmp.M0ixZmiNnj/miniconda.sh" [1]

Installing Miniconda...


bash /var/folders/xf/n1v2pg_j2ysf0rj39ysrcm9r0000gn/T/tmp.M0ixZmiNnj/miniconda.sh -p /Users/evaalonsoortiz/sct_6.2/python -b -f

PREFIX=/Users/evaalonsoortiz/sct_6.2/python
Unpacking payload ...

Installing base environment...

Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.

Creating conda environment...

Retrieving notices: ...working... done
Channels:
 - bioconda
 - defaults
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package python-3.9.15-h218abb5_2 requires libffi >=3.4,<3.5, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
└─ python 3.9**  is not installable because there are no viable options
   ├─ python [3.9.0|3.9.1|...|3.9.7] would require
   │  └─ libffi >=3.3,<3.4.0a0 , which conflicts with any installable versions previously reported;
   ├─ python [3.9.15|3.9.16|3.9.17|3.9.18|3.9.19] would require
   │  └─ libffi >=3.4,<3.5 , which conflicts with any installable versions previously reported;
   └─ python [3.9.0|3.9.1|...|3.9.9] conflicts with any installable versions previously reported.


Installation failed!

Please find the file "/Users/evaalonsoortiz/sct_6.2/install_sct_log.txt",
then upload it as a .txt attachment in a new topic on SCT's forum:
--> http://forum.spinalcordmri.org/c/sct

joshuacwnewton · April 24, 2024, 6:50pm

My apologies for the late reply – I’ve been working on the latest SCT release in preparation for ISMRM.

This is the part that immediately stands out to me, since SCT doesn’t specify bioconda as a channel when creating its own Miniconda environment. This suggests to me that you may have an existing .condarc configuration setup on your workstation that is interfering with SCT’s conda installation.

We have experienced similar things in the past:

`.condarc` `envs_dirs:` breaks `install_sct` · Issue #3982 · spinalcordtoolbox/spinalcordtoolbox · GitHub

Could you please try the following troubleshooting commands?

# check the contents of .condarc
cat ~/.condarc
# check to see if the $CONDARC environment variable is set
echo $CONDARC
# this command will only work if you have `conda` on the path
conda config --get

Depending on the contents, we may be able to identify which setting possibly broke the installation, and then work around it somehow.

Kind regards,
Joshua

eva · April 26, 2024, 2:24pm

Here are the outputs:

/Users/evaalonsoortiz/Downloads$ cat ~/.condarc
channels:
  - bioconda
  - defaults
  - conda-forge
auto_activate_base: false
ssl_verify: true
channel_priority: strict

/Users/evaalonsoortiz/Downloads$ echo $CONDARC

/Users/evaalonsoortiz/Downloads$ conda config --get
--set auto_activate_base False
--set channel_priority strict
--add channels 'conda-forge'   # lowest priority
--add channels 'defaults'
--add channels 'bioconda'   # highest priority
--set ssl_verify True

joshuacwnewton · April 26, 2024, 8:51pm

I’m having a bit of trouble reproducing the issue on my personal computer (Ubuntu 22.04).

I started with a replica of your .condarc file, but noticed that it does not mention the libmamba solver, which is mentioned in the warnings.
If I manually set the solver to be libmamba in the .condarc file, there is still no error.
Even when I explicitly specify --strict-channel-priority + --solver libmamba during the conda create command (where the installer fails), I cannot reproduce the warnings.

I’m unsure if this is due to macOS, or if it’s due to some other environment quirk on your system. But, I think a good starting point for your environment might be to switch back to the default channel_priority: flexible and solver: classic. You can do this by calling:

conda config --set solver classic
conda config --set channel_priority flexible

If this fixes the issue, then I can try to dig deeper into understanding why these settings are being enabled in your environment, but not in mine.

Thank you for your patience as I work to troubleshoot this issue.

Kind regards,
Joshua

eva · April 26, 2024, 9:46pm

Success! Thanks